Record browser
Faceted, client-side browser over all protein-trait records — search by label, identifier, or definition; filter by axis, category, and source. Each record shows semantically related traits from a local text-embedding model.
Corpus map
A PaCMAP projection of every record's 1024-d text embedding — the whole corpus laid out in 2-D, colored by trait axis. Toggle between the full-record embedding (meaning + source/classification structure) and a definition-only embedding (pure semantics). Hover to identify, click to open a record.
Schema & docs
The LinkML schema (ProteinTraitRecord, causal graphs), a worked P25888 example, and the curation model.
Trait axes
- SEQUENCE — motifs, signal/leader peptides, propeptides, cleavage sites, low-complexity / disordered regions, tandem repeats, compositional biases, conserved regions, epitopes, PTM sites.
- STRUCTURE — folds, structural domains, secondary-structure arrangements, topology classes, quaternary state, subunit interfaces, active / binding / allosteric / metal sites, disulfide bonds, cavities, symmetry, dynamics, structural stability.
- SEQUENCE_STRUCTURE — traits with both a sequence signature and 3D periodicity: coiled coils, and structural tandem repeats with demonstrated periodicity (RepeatsDB →
MIXED_STRUCTURAL_REPEAT). - FUNCTION — enzymatic activity, binding capacity, cofactor requirement, subcellular localisation, environmental response, interaction partner. Grounded by EC / Rhea / ChEBI / GO / UniProt SubCell.
- EVOLUTION — comparative-genomics traits: a protein's conservation across taxa (conserved, clade-specific, variable) and pangenome partition (core, soft-core, shell, cloud, persistent, singleton).
Trait categories
Every record carries a fine-grained trait_category. Counts link into the browser pre-filtered to that subset.
| Category | Axis | Records |
|---|---|---|
STRUCT_DOMAIN | STRUCTURE | 135,044 |
STRUCT_FOLD | STRUCTURE | 55,735 |
FUNC_ENZYMATIC_ACTIVITY | FUNCTION | 26,003 |
STRUCT_HOMOLOGOUS_SUPERFAMILY | STRUCTURE | 20,845 |
FUNC_ORTHOLOG_GROUP | FUNCTION | 9,728 |
FUNC_RESISTANCE | FUNCTION | 7,451 |
STRUCT_TOPOLOGY | STRUCTURE | 5,427 |
SEQ_MOTIF | SEQUENCE | 3,121 |
FUNC_PATHWAY | FUNCTION | 2,883 |
FUNC_TRANSPORT | FUNCTION | 2,285 |
SEQ_REPEAT | SEQUENCE | 2,073 |
UPPER | SEQUENCE | 1,980 |
SEQ_PTM_SITE | SEQUENCE | 1,251 |
STRUCT_ACTIVE_SITE | STRUCTURE | 1,137 |
SEQ_CONSERVATION | SEQUENCE | 775 |
SEQ_MODIFIED_RESIDUE | SEQUENCE | 618 |
SEQ_DISORDER | SEQUENCE | 202 |
FUNC_INTERACTION_PARTNER | FUNCTION | 146 |
MIXED_STRUCTURAL_REPEAT | SEQUENCE_STRUCTURE | 122 |
SEQ_GLYCOSYLATION_SITE | SEQUENCE | 85 |
STRUCT_BINDING_SITE | STRUCTURE | 83 |
SEQ_CROSSLINK_SITE | SEQUENCE | 69 |
STRUCT_ARCHITECTURE | STRUCTURE | 64 |
FUNC_ENVIRONMENTAL_RESPONSE | FUNCTION | 48 |
SEQ_LIPIDATION_SITE | SEQUENCE | 40 |
STRUCT_STABILITY | STRUCTURE | 36 |
SEQ_TARGETING_SIGNAL | SEQUENCE | 28 |
SEQ_LEADER_PEPTIDE | SEQUENCE | 20 |
STRUCT_CLASS | STRUCTURE | 17 |
STRUCT_DYNAMICS | STRUCTURE | 13 |
STRUCT_SURFACE | STRUCTURE | 13 |
SEQ_CLEAVAGE_SITE | SEQUENCE | 11 |
STRUCT_SECONDARY | STRUCTURE | 8 |
EVO_PANGENOME | EVOLUTION | 6 |
STRUCT_CAVITY | STRUCTURE | 5 |
EVO_CONSERVATION | EVOLUTION | 3 |
SEQ_INITIATOR_METHIONINE | SEQUENCE | 1 |
SEQ_MATURE_CHAIN | SEQUENCE | 1 |
SEQ_PROPEPTIDE | SEQUENCE | 1 |
SEQ_SIGNAL_PEPTIDE | SEQUENCE | 1 |
SEQ_TRANSIT_PEPTIDE | SEQUENCE | 1 |
STRUCT_DISULFIDE | STRUCTURE | 1 |
STRUCT_INTERFACE | STRUCTURE | 1 |
STRUCT_METAL_SITE | STRUCTURE | 1 |
Corpus at a glance — sources
Sources listed in order of integration (earliest first). Record counts link into the browser filtered by source. Bucket counts are seeding-time figures; per-bucket rows may slightly exceed the live total after merges.
| Source | Records | Directory |
|---|---|---|
LinkML LocalStructuralFeature valueset | 19 | data/traits/structure/{secondary,active_site,binding_site,cavity,disulfide,metal_site,dynamics,interface}/ |
| PROSITE PATTERN (generic) | 1,279 | data/traits/sequence/pattern/ |
| PROSITE PATTERN routed to PTM subtypes | 32 | data/traits/sequence/{modified_residue,glycosylation,crosslink}/ |
| PROSITE MATRIX (profile) | 1,434 | data/traits/sequence/profile/ |
PROSITE ProRule (DC=Domain) | 1,445 | data/traits/structure/domain/ |
PROSITE ProRule (DC=Site, keyword-routed) | 4 | data/traits/sequence/{modified_residue,glycosylation,prorule}/ |
| TED novel folds (Zenodo v5) | 7,427 | data/traits/structure/fold/novel/ |
| TED highly-symmetric folds | 6,433 | data/traits/structure/fold/high_symmetry/ |
UniProtKB FT/CC/GO demultiplexer (seed_uniprot.py) — demo retired; real entries now attach as canonical_examples on class traits via fetch_uniprot_examples.py | 0 | — |
| PSI-MOD (CC-BY-4.0) | 1,971 | data/traits/sequence/{modified_residue,glycosylation,lipidation,crosslink,ptm_ontology}/ |
| ECOD v295 (A/X/H/T/F hierarchy) | 45,113 | data/traits/structure/{architecture,homologous_superfamily,topology,fold/ecod}/ |
| SCOPe 2.08 — Class/Fold/Superfamily/Family/Domain (Berkeley; instances px/sp excluded) | 22,810 | data/traits/structure/{class,fold,homologous_superfamily,domain}/scope/ |
| M-CSA (CC-BY-4.0) | 1,003 | data/traits/structure/active_site/mcsa/ |
| DisProt — 32 IDPO disorder classes (structural state/transition/function; proteins as examples) (CC-BY-4.0) | 35 | data/traits/sequence/disorder/ |
| PSI-MI interaction types (CC-BY-4.0) | 146 | data/traits/function/interaction_partner/psi_mi/ |
| METPO ecophysiological traits (growth preferences, tolerances, metabolism; CC-BY-4.0) | 118 | data/traits/function/{environmental_response,enzymatic_activity}/metpo/ |
| PATO physicochemical qualities (CC-BY-4.0) | 28 | data/traits/structure/{stability,dynamics,surface}/pato/ |
| Curated stability taxonomy — per-condition (thermal, oxidative, saline, pH, osmotic, pressure, desiccation, chemical, proteolytic, mechanical) × increased/decreased (CC0-1.0) | 33 | data/traits/structure/stability/conditions/ |
| InterPro entries — Domain / Homologous-superfamily / Repeat / Conserved-/Active-/Binding-site / PTM (public domain; GO via interpro2go → mapped_xrefs) | 26,264 | data/traits/{structure,sequence}/…/interpro/ |
| Curated evolutionary / pangenome traits — conserved, clade-specific, variable; pangenome core/soft-core/shell/cloud/persistent/singleton (CC0-1.0) | 9 | data/traits/evolution/{conservation,pangenome}/ |
| Pfam-A families — Domain/Family→domain, Repeat, Coiled-coil, Disordered, Motif (public domain; GO+InterPro via pfam2go/pfam2interpro → mapped_xrefs) | 30,134 | data/traits/{structure/domain,sequence/repeat,mixed/coiled_coil,sequence/disorder,sequence/motif}/pfam/ |
| CATH-Gene3D hierarchy — Class/Architecture/Topology/Homologous-superfamily (CC-BY 4.0) | 8,151 | data/traits/structure/{class,architecture,topology,homologous_superfamily}/cath/ |
| Reactome pathways — Homo sapiens reference set (CC0) | 2,883 | data/traits/function/pathway/reactome/ |
| CARD/ARO — antibiotic-resistance determinants + mechanisms (CC-BY 4.0) | 7,451 | data/traits/function/resistance/aro/ |
| TCDB transport classification — Class/Subclass/Family (CC-BY-SA 3.0; 946 families ChEBI-grounded) | 2,285 | data/traits/function/transport/tcdb/ |
| COG 2020 orthologous groups + 26 functional categories (US Gov public domain) | 4,903 | data/traits/function/ortholog_group/cog/ |
| Rhea reactions — enzymatic reactions + ChEBI participants (CC-BY 4.0; EC via rhea2ec) | 18,558 | data/traits/function/enzymatic_activity/rhea/ |
| ExPASy ENZYME — complete EC hierarchy (CC-BY 4.0; GO/RHEA mapped, KEGG direct, DR examples) | 7,375 | data/traits/function/enzymatic_activity/ec/ |
| RepeatsDB — structural tandem-repeat Class/Topology/Fold/Clan (CC-BY 4.0) | 122 | data/traits/sequence_structure/structural_repeat/repeatsdb/ |
| NCBIfam (ex-TIGRFAMs) — prokaryotic family HMMs (US-gov public domain) | 38,394 | data/traits/structure/domain/ncbifam/ |
| CDD — NCBI-curated conserved domains + PRK clusters + KOG ortholog groups (US-gov public domain) | 38,218 | data/traits/{structure/domain,function/ortholog_group}/cdd/ |
| IDEAL — ProS (protean segment) trait; 1,448 IDPs as examples (CC-BY 4.0) | 1 | data/traits/sequence/disorder/ |
| ELM (Eukaryotic Linear Motif) — targeting/cleavage/motif classes (⚠ non-commercial) | 353 | data/traits/sequence/{targeting_signal,cleavage_site,ptm_site,motif}/elm/ |
| MEROPS peptidase families — S/C/A/M/… catalytic classes (EBI; academic) | 370 | data/traits/structure/domain/merops/ |
| Curated RiPP leader-peptide classes — lanthipeptide/lasso/sactipeptide/… (CC0) | 20 | data/traits/sequence/leader_peptide/ |
| Total | 277,697 |
Curation model
Every record is a stand-alone YAML with an identifier (source-anchored CURIE when possible), label + definition with provenance, trait_axis + trait_category, parent_traits / xrefs / synonyms, an optional sequence_pattern, optional canonical_examples (UniProtKB exemplars), optional evidence-backed causal_graphs (every edge cites ≥1 reference), and an append-only curation_history. Seeded records land as SEEDED; curator review flips them to REVIEWED.