{
  "vercy": "1.0-draft",
  "publication": {
    "status": "research-draft",
    "adjudicationStatus": "unreviewed",
    "publishableCanonical": false,
    "generatedAt": "2026-10-21T20:24:21Z",
    "providers": [
      "Claude"
    ],
    "breadth": "researched by Claude against the sources listed below",
    "pass": 2,
    "wave": 5,
    "engine": "claude",
    "gate": {
      "passed": true,
      "version": "1.0",
      "at": "2026-10-21T20:39:55+00:00",
      "evidence": [
        "completeness 1.00",
        "sense: Wikidata description",
        "7 live sources",
        "review by codex: pass"
      ]
    }
  },
  "metaModel": {
    "id": "THING-Q4915012",
    "registryId": "vr.tr.biological-pathway",
    "name": "biological pathway",
    "version": "0.2.0-wave.5",
    "entryKind": "thing",
    "family": "Thing Registry",
    "domain": [
      "ACT.PRC"
    ],
    "status": "research-draft"
  },
  "canonicalUrl": "https://ver.cy/models/thing/q4915012/",
  "model": {
    "registry_id": "vr.tr.biological-pathway",
    "name": "biological pathway",
    "purpose": "Let an agent describe biological pathways, find them in curated databases with identifiers, and explain their components and roles in health and disease.",
    "definition": "A set of interconnected molecular reactions and interactions in a cell or organism, such as metabolic, signalling or gene-regulatory pathways, delineated as a model for studying how biomolecules work together to produce a function.",
    "what_it_is_for": "Organising knowledge of molecular mechanisms for research, drug discovery and data analysis.",
    "affordances": [
      "identify a pathway and its database records",
      "list components and steps",
      "explain pathway enrichment analysis in general terms",
      "link pathways to diseases and drugs with sources"
    ],
    "distinguishing_features": [
      "A model: manually curated or computationally inferred, with boundaries set by each database and purpose.",
      "Metabolic pathways transform molecules; signalling pathways transmit information; regulatory pathways control gene expression.",
      "The same pathway can be represented differently in different databases."
    ],
    "appearance": null,
    "visual_identification": [
      "Shown as diagrams of molecules connected by reactions and interactions"
    ],
    "physical_properties": [],
    "families_and_kinds": [
      "metabolic pathway",
      "signalling pathway",
      "gene-regulatory pathway",
      "disease pathway"
    ],
    "related_models": [
      {
        "relation": "is a kind of",
        "target": "biological process model",
        "why": "model"
      },
      {
        "relation": "contains",
        "target": "biochemical reaction",
        "why": "steps"
      },
      {
        "relation": "is described in",
        "target": "pathway database",
        "why": "Reactome, KEGG, WikiPathways"
      },
      {
        "relation": "is related to",
        "target": "Gene Ontology biological process",
        "why": "annotation"
      }
    ],
    "identifiers": [
      {
        "scheme": "Reactome stable ID",
        "value_or_pattern": "R-HSA-<number>, optionally .<version>",
        "note": "human pathways; check the record type is Pathway"
      },
      {
        "scheme": "KEGG pathway ID",
        "value_or_pattern": "map##### or hsa#####",
        "note": ""
      },
      {
        "scheme": "WikiPathways ID",
        "value_or_pattern": "WP<number>, for example WP732",
        "note": "revision recorded separately"
      }
    ],
    "standards_and_regulation": [
      "BioPAX and SBGN exchange and notation standards",
      "Systems Biology Markup Language (SBML)"
    ],
    "failure_modes_and_hazards": [
      "Over-interpreting enrichment results",
      "Mixing pathway versions and species"
    ],
    "agent_conduct": {
      "may": [
        "describe pathways with database identifiers"
      ],
      "must_not": [
        "present pathway models as complete reality",
        "give medical advice from pathway data"
      ],
      "requires_human": []
    },
    "ethics": {
      "considerations": [
        "accuracy",
        "open data"
      ],
      "affected_parties": [
        "researchers"
      ]
    },
    "owners": {
      "steward": "nobody as a concept; each database curates its own pathway models",
      "master_systems": [
        "Reactome",
        "KEGG",
        "WikiPathways"
      ]
    },
    "facets_not_applicable": {
      "properties": "A molecular model has no physical properties.",
      "hazards": "A model poses no hazards; misinterpretation risks are listed as failure modes."
    },
    "in_scope": [],
    "out_of_scope": [],
    "characteristics": []
  },
  "sources": [
    {
      "id": "SRC-001",
      "title": "Q4915012",
      "publisher": "Wikidata",
      "url": "https://www.wikidata.org/wiki/Q4915012",
      "what_it_supports": "identity of the registry item, labels and sitelinks",
      "url_status": "live"
    },
    {
      "id": "SRC-002",
      "title": "Biological pathway",
      "publisher": "Wikipedia",
      "url": "https://en.wikipedia.org/wiki/Biological_pathway",
      "what_it_supports": "general description of the subject",
      "url_status": "live"
    },
    {
      "id": "SRC-003",
      "title": "Biological Pathways Fact Sheet",
      "publisher": "National Human Genome Research Institute",
      "url": "https://www.genome.gov/about-genomics/fact-sheets/Biological-Pathways-Fact-Sheet",
      "what_it_supports": "Definition, metabolic and regulatory kinds, interconnected boundaries and disease and drug research applications.",
      "url_status": "live"
    },
    {
      "id": "SRC-004",
      "title": "Explain the identifiers associated with entities and events",
      "publisher": "Reactome",
      "url": "https://release.reactome.org/documentation/faq/37-general-website/201-identifiers",
      "what_it_supports": "Stable identifier structure, versions, species codes and manually annotated versus computationally inferred events.",
      "url_status": "live"
    },
    {
      "id": "SRC-005",
      "title": "KEGG PATHWAY Database",
      "publisher": "KEGG",
      "url": "https://www.genome.jp/kegg/pathway.html",
      "what_it_supports": "Pathway categories, reference and organism-specific maps, and prefix-plus-five-digit identifiers.",
      "url_status": "live"
    },
    {
      "id": "SRC-006",
      "title": "WikiPathways identifier registry",
      "publisher": "Bioregistry",
      "url": "https://www.bioregistry.io/registry/wikipathways",
      "what_it_supports": "Variable-length WikiPathways identifiers and revision-qualified forms.",
      "url_status": "unverified"
    },
    {
      "id": "SRC-007",
      "title": "BioPAX Level 3 Documentation",
      "publisher": "BioPAX community",
      "url": "https://www.biopax.org/release/biopax-level3-documentation.pdf",
      "what_it_supports": "Pathway exchange, molecular context and the complementary roles of BioPAX, SBGN and SBML.",
      "url_status": "live"
    },
    {
      "id": "SRC-008",
      "title": "SBML Specifications",
      "publisher": "SBML community",
      "url": "https://sbml.org/documents/specifications/",
      "what_it_supports": "SBML as a model representation standard, including quantitative and qualitative model types.",
      "url_status": "live"
    }
  ],
  "structure": {
    "bundles": [
      {
        "id": "identity",
        "name": "Identity",
        "description": "Which pathway.",
        "rationale": "Identifiers make pathways traceable.",
        "layers": [
          {
            "id": "database-record",
            "name": "Database record",
            "description": "Database and ID.",
            "findings": [
              {
                "id": "pathway-record",
                "name": "Pathway record",
                "description": "Database, ID and version.",
                "questions": [
                  {
                    "text": "Which database record describes the pathway?",
                    "kind": "provenance"
                  },
                  {
                    "text": "Which version and species?",
                    "kind": "provenance"
                  }
                ]
              }
            ]
          },
          {
            "id": "kind",
            "name": "Kind",
            "description": "Metabolic, signalling, regulatory.",
            "findings": [
              {
                "id": "pathway-kind",
                "name": "Pathway kind",
                "description": "Kind.",
                "questions": [
                  {
                    "text": "What kind of pathway is it?",
                    "kind": "definition"
                  },
                  {
                    "text": "Which process does it serve?",
                    "kind": "definition"
                  }
                ]
              }
            ]
          }
        ]
      },
      {
        "id": "components",
        "name": "Components",
        "description": "Parts and steps.",
        "rationale": "Components define the model.",
        "layers": [
          {
            "id": "participants",
            "name": "Participants",
            "description": "Genes, proteins, metabolites.",
            "findings": [
              {
                "id": "participant",
                "name": "Participant",
                "description": "Molecule and role.",
                "questions": [
                  {
                    "text": "Which molecules take part?",
                    "kind": "provenance"
                  },
                  {
                    "text": "In which roles?",
                    "kind": "definition"
                  }
                ]
              }
            ]
          },
          {
            "id": "reactions",
            "name": "Reactions",
            "description": "Steps and interactions.",
            "findings": [
              {
                "id": "reaction",
                "name": "Reaction",
                "description": "Reaction, direction, catalysts and regulators, compartment and cell context, experimental or inferred evidence.",
                "questions": [
                  {
                    "text": "Which reactions make up the pathway?",
                    "kind": "provenance"
                  },
                  {
                    "text": "What evidence supports each?",
                    "kind": "provenance"
                  }
                ]
              }
            ]
          }
        ]
      },
      {
        "id": "analysis",
        "name": "Analysis",
        "description": "Using pathways in data analysis.",
        "rationale": "Analyses need care.",
        "layers": [
          {
            "id": "enrichment",
            "name": "Enrichment",
            "description": "Pathway enrichment.",
            "findings": [
              {
                "id": "enrichment-result",
                "name": "Enrichment result",
                "description": "Method and statistics.",
                "questions": [
                  {
                    "text": "Which method and database version were used?",
                    "kind": "provenance"
                  },
                  {
                    "text": "What correction for multiple testing?",
                    "kind": "measurement"
                  }
                ]
              }
            ]
          },
          {
            "id": "modelling",
            "name": "Modelling",
            "description": "Quantitative models.",
            "findings": [
              {
                "id": "model",
                "name": "Model",
                "description": "Format and parameters.",
                "questions": [
                  {
                    "text": "Is there a quantitative model?",
                    "kind": "provenance"
                  },
                  {
                    "text": "In which format?",
                    "kind": "provenance"
                  }
                ]
              }
            ]
          }
        ]
      },
      {
        "id": "biomedical-relevance",
        "name": "Biomedical relevance",
        "description": "Disease and drugs.",
        "rationale": "Links need sources.",
        "layers": [
          {
            "id": "disease",
            "name": "Disease",
            "description": "Pathway in disease.",
            "findings": [
              {
                "id": "disease-link",
                "name": "Disease link",
                "description": "Disease and evidence.",
                "questions": [
                  {
                    "text": "Which diseases involve the pathway?",
                    "kind": "provenance"
                  },
                  {
                    "text": "What is the evidence?",
                    "kind": "provenance"
                  }
                ]
              }
            ]
          },
          {
            "id": "drugs",
            "name": "Drugs",
            "description": "Drug targets.",
            "findings": [
              {
                "id": "drug-target",
                "name": "Drug target",
                "description": "Drug and target.",
                "questions": [
                  {
                    "text": "Which drugs act on the pathway?",
                    "kind": "provenance"
                  },
                  {
                    "text": "At which step?",
                    "kind": "provenance"
                  }
                ]
              }
            ]
          }
        ]
      }
    ]
  },
  "openQuestions": [
    "The registry merges specific processes and ecological dispersal pathways; they need registry corrections."
  ],
  "statistics": {
    "bundles": 4,
    "layers": 8,
    "findings": 8,
    "questions": 16
  }
}