{
  "id": "CofactorMech:pyridoxal-phosphate",
  "name": "pyridoxal 5'-phosphate",
  "chemical_id": "CHEBI:18405",
  "categories": [
    "COENZYME"
  ],
  "description": "pyridoxal 5'-phosphate is represented by the precise ChEBI entity CHEBI:18405. Cofactor roles are chemical-context annotations; ingredient links describe chemical supply and do not establish uptake, bioavailability or a requirement for every organism.",
  "evidence": [
    {
      "reference": "https://www.ebi.ac.uk/chebi/CHEBI:18405",
      "title": "ChEBI CHEBI:18405",
      "claim": "ChEBI assigns a cofactor, coenzyme or prosthetic-group role to CHEBI:18405.",
      "locator": "JSON Pointer /roles_classification",
      "source_license": "CC-BY-4.0"
    }
  ],
  "related_records": [
    {
      "corpus": "mediaingredientmech",
      "identifier": "CHEBI:18405",
      "relation": "SUPPLIED_BY",
      "basis": "The current MIM ontology mapping exactly matches the candidate cofactor chemical identifier. This establishes a compound supply link, not organism-specific uptake or requirement.",
      "source_version": "0529fc6bc065bfa04aba0aed234f6b0cfad6a142",
      "source_path": "data/ingredients/mapped/Pyridoxal_Phosphate.yaml",
      "source_url": "https://github.com/CultureBotAI/MediaIngredientMech/blob/0529fc6bc065bfa04aba0aed234f6b0cfad6a142/data/ingredients/mapped/Pyridoxal_Phosphate.yaml",
      "status": "PROVISIONAL",
      "evidence": [
        {
          "reference": "https://github.com/CultureBotAI/MediaIngredientMech/blob/0529fc6bc065bfa04aba0aed234f6b0cfad6a142/data/ingredients/mapped/Pyridoxal_Phosphate.yaml",
          "title": "MIM ingredient identity",
          "claim": "The cited ingredient is mapped to CHEBI:18405; this is a compound-identity assertion, not a bioavailability measurement.",
          "locator": "JSON Pointer /identifier",
          "source_license": "CC-BY-4.0"
        }
      ]
    },
    {
      "corpus": "proteintraitsmech",
      "identifier": "proteintraitsmech:COFACTOR_REQ_CHEBI_18405",
      "relation": "REQUIRED_BY",
      "basis": "Conceptual requirement coverage: this PTM trait defines the requirement for the same ChEBI chemical. It is not an organism-level or enzyme-level measurement.",
      "source_version": "8d08b33cfbee1e9d1c2fdb2211b82b49dd0c8b1f",
      "source_path": "data/traits/function/cofactor_requirement/chebi/pyridoxal-5-phosphate-chebi18405.yaml",
      "source_url": "https://github.com/CultureBotAI/proteintraitsmech/blob/8d08b33cfbee1e9d1c2fdb2211b82b49dd0c8b1f/data/traits/function/cofactor_requirement/chebi/pyridoxal-5-phosphate-chebi18405.yaml",
      "status": "VERIFIED",
      "evidence": [
        {
          "reference": "https://github.com/CultureBotAI/proteintraitsmech/blob/8d08b33cfbee1e9d1c2fdb2211b82b49dd0c8b1f/data/traits/function/cofactor_requirement/chebi/pyridoxal-5-phosphate-chebi18405.yaml",
          "title": "PTM cofactor-requirement concept",
          "claim": "The target is a CLASS trait with an explicit cross-reference to this chemical, rather than a measured protein observation.",
          "locator": "JSON Pointer /xrefs",
          "source_license": "CC-BY-4.0"
        }
      ]
    },
    {
      "corpus": "pathwaymech",
      "identifier": "MetaCyc:PYRIDOXSYN-PWY",
      "relation": "CONJUGATE_FORM_PRODUCED_BY",
      "basis": "PathwayMech edge edge-035 records RHEA:15150 produces CHEBI:597326. This is a cross-reference to the source-scoped reaction or cofactor annotation, not proof of complete pathway flux. The pathway chemical is CHEBI:597326, a distinct conjugate form of CHEBI:18405; this link does not identify their charge states.",
      "source_version": "9584009d49579267233124f4a1057b9425a007d9",
      "source_path": "data/pathways/pyridoxal-5-phosphate-biosynthesis-i.yaml",
      "source_url": "https://github.com/CultureBotAI/PathwayMech/blob/9584009d49579267233124f4a1057b9425a007d9/data/pathways/pyridoxal-5-phosphate-biosynthesis-i.yaml",
      "status": "VERIFIED",
      "evidence": [
        {
          "reference": "https://github.com/CultureBotAI/PathwayMech/blob/9584009d49579267233124f4a1057b9425a007d9/data/pathways/pyridoxal-5-phosphate-biosynthesis-i.yaml",
          "title": "PathwayMech reaction or cofactor edge",
          "claim": "PathwayMech edge edge-035 records RHEA:15150 produces CHEBI:597326. This is a cross-reference to the source-scoped reaction or cofactor annotation, not proof of complete pathway flux.",
          "locator": "JSON Pointer /mechanistic_edges/34",
          "source_license": "CC-BY-4.0"
        },
        {
          "reference": "https://www.ebi.ac.uk/chebi/CHEBI:18405",
          "title": "ChEBI CHEBI:18405",
          "claim": "ChEBI provides the conjugate-form relationship linking the source chemical family to CHEBI:597326.",
          "locator": "JSON Pointer /ontology_relations",
          "source_license": "CC-BY-4.0"
        }
      ],
      "target_chemical_id": "CHEBI:597326"
    }
  ],
  "research_gaps": [
    {
      "corpus": "proteintraitsmech",
      "reason": "The curated PTM link covers a cofactor-requirement concept only. A separately sourced, named enzyme exemplar requiring this exact chemical has not been curated in this seed record."
    }
  ],
  "curation_history": [
    {
      "timestamp": "2026-11-09T01:42:28Z",
      "curator": "cofactor-stream-c",
      "action": "CREATE",
      "summary": "Curate initial source-backed cofactor and scoped cross-corpus links",
      "history_file": "history/records/pyridoxal-phosphate/2026-11-09T014228Z-cofactor-stream-c-6a26b2.yaml"
    }
  ]
}