{
  "vercy": "1.0-draft",
  "publication": {
    "status": "research-draft",
    "adjudicationStatus": "unreviewed",
    "publishableCanonical": false,
    "generatedAt": "2026-09-13T12:55:08Z",
    "providers": [
      "Claude"
    ],
    "breadth": "written by Claude from model knowledge without web access - no source was read, every claim is a lead to verify",
    "pass": 2,
    "wave": 4,
    "engine": "claude",
    "enrichment": {
      "pass": 3,
      "engine": "claude",
      "producedAt": "2026-10-06T10:00:00Z",
      "ingestedAt": "2026-10-06T07:12:59+00:00",
      "fields": [
        "agent_conduct",
        "ethics",
        "owners"
      ]
    },
    "revisions": [
      {
        "at": "2026-10-06T22:43:39+00:00",
        "engine": "codex",
        "fields": [
          "definition",
          "distinguishing_features",
          "visual_identification"
        ],
        "answering_review": "8086cb1ee31bfa6ca7e52e681f24524046cfe2788a33a3042649555104451599"
      }
    ],
    "gate": {
      "passed": true,
      "version": "1.0",
      "at": "2026-10-07T10:10:28+00:00",
      "evidence": [
        "completeness 1.00",
        "sense: Wikidata description",
        "2 live sources",
        "review by codex: pass"
      ]
    }
  },
  "metaModel": {
    "id": "THING-Q22274727",
    "registryId": "vr.tr.secondary-metabolic-process",
    "name": "secondary metabolic process",
    "version": "0.2.0-wave.4",
    "entryKind": "thing",
    "family": "Thing Registry",
    "domain": [
      "ACT.PRC"
    ],
    "status": "research-draft"
  },
  "canonicalUrl": "https://ver.cy/models/thing/q22274727/",
  "model": {
    "registry_id": "vr.tr.secondary-metabolic-process",
    "name": "secondary metabolic process",
    "purpose": "Let an agent explain secondary metabolic processes as an ontology class, relay biochemistry, gene clusters and examples from biology references, describe applications in medicine and agriculture, and distinguish secondary from primary metabolism and the ontology term from specific pathways.",
    "definition": "A metabolic process, in the Gene Ontology sense, that produces or transforms secondary metabolites, compounds not necessarily required for growth and maintenance of cells but important for defence, signalling and ecological interaction, including the biosynthesis of pheromones, fungal products such as fumagillin, helvolic acid and ochratoxin A, and sterol intermediates such as protostadienol; secondary metabolism underlies antibiotics, toxins, pigments and many drugs.",
    "what_it_is_for": "Not applicable; a biological process class.",
    "affordances": [
      "explain the class",
      "relay biochemistry and examples",
      "describe applications",
      "distinguish related terms"
    ],
    "distinguishing_features": [
      "The compounds involved are not necessarily required for growth and maintenance of cells.",
      "Secondary metabolites have ecological roles.",
      "Genes involved in secondary metabolism can occur in clusters.",
      "Secondary metabolism is a source of drugs."
    ],
    "appearance": "Not a visible object; biochemical pathways.",
    "visual_identification": [
      "It concerns the metabolism of specialised compounds not necessarily required for growth and maintenance of cells.",
      "Examples include pheromone, fumagillin, helvolic acid, ochratoxin A and protostadienol metabolic processes.",
      "Primary metabolism supplies energy and building blocks, while this ontology term describes a class rather than one pathway."
    ],
    "physical_properties": [
      {
        "quantity": "major classes",
        "typical_range": "terpenoids, alkaloids, polyketides, non-ribosomal peptides, phenylpropanoids",
        "unit": "list",
        "note": ""
      },
      {
        "quantity": "known plant secondary metabolites",
        "typical_range": "over 200000",
        "unit": "count",
        "note": "estimates"
      }
    ],
    "families_and_kinds": [
      "secondary metabolite biosynthetic processes",
      "pheromone metabolic processes",
      "fungal polyketide and terpenoid processes such as fumagillin and helvolic acid",
      "mycotoxin processes such as ochratoxin A",
      "sterol and triterpenoid intermediates such as protostadienol",
      "plant secondary metabolism"
    ],
    "related_models": [
      {
        "relation": "is a kind of",
        "target": "metabolism",
        "why": "in registry terms"
      },
      {
        "relation": "produces",
        "target": "secondary metabolite",
        "why": "as its product"
      },
      {
        "relation": "is contrasted with",
        "target": "primary metabolism",
        "why": "for growth and energy"
      },
      {
        "relation": "is defined in",
        "target": "Gene Ontology",
        "why": "as a biological process term"
      }
    ],
    "identifiers": [
      {
        "scheme": "GO",
        "value_or_pattern": "GO:0019748",
        "note": "secondary metabolic process"
      }
    ],
    "standards_and_regulation": [
      "Gene Ontology term definitions",
      "Food safety limits for mycotoxins such as ochratoxin A"
    ],
    "failure_modes_and_hazards": [
      "Confusing the ontology class with a single pathway",
      "Registry aliases naming obscure compound processes",
      "Mycotoxin contamination of food"
    ],
    "in_scope": [],
    "out_of_scope": [],
    "characteristics": [],
    "agent_conduct": {
      "may": [
        "Explain secondary metabolism and the Gene Ontology class in general terms.",
        "Annotate genes to the class following ontology rules and evidence codes."
      ],
      "must_not": [
        "Present the ontology class as a single pathway.",
        "Give procedures for producing toxic secondary metabolites such as mycotoxins.",
        "Annotate a gene to the class without supporting evidence.",
        "Present traces of a mycotoxin in food as harmless without data."
      ],
      "requires_human": [
        "Using annotations to guide engineering of organisms that produce toxins."
      ]
    },
    "ethics": {
      "considerations": [
        "Mycotoxins contaminate food and harm health, especially in poorer regions.",
        "Ontology errors spread through many downstream analyses."
      ],
      "affected_parties": [
        "Consumers of contaminated food",
        "Farmers",
        "Researchers"
      ]
    },
    "owners": {
      "steward": "The Gene Ontology consortium maintains the class.",
      "master_systems": [
        "Gene Ontology"
      ]
    }
  },
  "sources": [
    {
      "id": "wikidata",
      "title": "Wikidata item Q22274727: secondary metabolic process",
      "url": "https://www.wikidata.org/wiki/Q22274727",
      "url_status": "live",
      "what_it_supports": "identity and sense of the item",
      "checked_by": "wikidata-api"
    },
    {
      "id": "wikipedia-en",
      "title": "Wikipedia: Secondary metabolism",
      "url": "https://en.wikipedia.org/wiki/Secondary_metabolism",
      "url_status": "live",
      "what_it_supports": "general description of the item",
      "checked_by": "wikidata-api sitelink"
    }
  ],
  "structure": {
    "bundles": [
      {
        "id": "understand",
        "name": "Understand",
        "description": "What secondary metabolism is.",
        "rationale": "Science.",
        "layers": [
          {
            "id": "definition",
            "name": "Definition",
            "description": "Definition.",
            "findings": [
              {
                "id": "definition-finding",
                "name": "Definition",
                "description": "Definition.",
                "questions": [
                  {
                    "text": "What is a secondary metabolic process, and how does it differ from primary metabolism?",
                    "kind": "definition"
                  },
                  {
                    "text": "Is the question about the ontology class, a compound class or a specific pathway?",
                    "kind": "boundary"
                  }
                ]
              }
            ]
          },
          {
            "id": "examples",
            "name": "Examples",
            "description": "Examples.",
            "findings": [
              {
                "id": "examples-finding",
                "name": "Examples",
                "description": "Examples.",
                "questions": [
                  {
                    "text": "What are pheromone, fumagillin, helvolic acid, ochratoxin A and protostadienol processes?",
                    "kind": "definition"
                  },
                  {
                    "text": "Which entry fits the specific compound?",
                    "kind": "action"
                  }
                ]
              }
            ]
          }
        ]
      },
      {
        "id": "biology",
        "name": "Biology",
        "description": "Biochemistry and genetics.",
        "rationale": "Science.",
        "layers": [
          {
            "id": "pathways",
            "name": "Pathways",
            "description": "Pathways.",
            "findings": [
              {
                "id": "pathways-finding",
                "name": "Pathways",
                "description": "Pathways.",
                "questions": [
                  {
                    "text": "How do polyketide, terpenoid, alkaloid and peptide pathways build secondary metabolites?",
                    "kind": "provenance"
                  },
                  {
                    "text": "Which references are standard?",
                    "kind": "provenance"
                  }
                ]
              }
            ]
          },
          {
            "id": "clusters",
            "name": "Clusters",
            "description": "Gene clusters.",
            "findings": [
              {
                "id": "clusters-finding",
                "name": "Clusters",
                "description": "Clusters.",
                "questions": [
                  {
                    "text": "How are biosynthetic gene clusters organised and regulated?",
                    "kind": "provenance"
                  },
                  {
                    "text": "Which sources are cited?",
                    "kind": "provenance"
                  }
                ]
              }
            ]
          }
        ]
      },
      {
        "id": "use",
        "name": "Use",
        "description": "Applications.",
        "rationale": "Application.",
        "layers": [
          {
            "id": "medicine",
            "name": "Medicine",
            "description": "Medicine.",
            "findings": [
              {
                "id": "medicine-finding",
                "name": "Medicine",
                "description": "Medicine.",
                "questions": [
                  {
                    "text": "How do secondary metabolites provide antibiotics and drugs?",
                    "kind": "provenance"
                  },
                  {
                    "text": "Which entry fits natural product drug discovery?",
                    "kind": "action"
                  }
                ]
              }
            ]
          },
          {
            "id": "agriculture",
            "name": "Agriculture",
            "description": "Agriculture and food.",
            "findings": [
              {
                "id": "agriculture-finding",
                "name": "Agriculture",
                "description": "Agriculture.",
                "questions": [
                  {
                    "text": "How do mycotoxins and plant defence compounds matter in agriculture and food safety?",
                    "kind": "provenance"
                  },
                  {
                    "text": "Which entry fits mycotoxin?",
                    "kind": "action"
                  }
                ]
              }
            ]
          }
        ]
      },
      {
        "id": "context",
        "name": "Context",
        "description": "Ontology and ecology.",
        "rationale": "Context.",
        "layers": [
          {
            "id": "ontology",
            "name": "Ontology",
            "description": "Gene Ontology.",
            "findings": [
              {
                "id": "ontology-finding",
                "name": "Ontology",
                "description": "Ontology.",
                "questions": [
                  {
                    "text": "How does the Gene Ontology organise metabolic process terms?",
                    "kind": "provenance"
                  },
                  {
                    "text": "Which entry fits Gene Ontology?",
                    "kind": "action"
                  }
                ]
              }
            ]
          },
          {
            "id": "ecology",
            "name": "Ecology",
            "description": "Ecology.",
            "findings": [
              {
                "id": "ecology-finding",
                "name": "Ecology",
                "description": "Ecology.",
                "questions": [
                  {
                    "text": "What ecological roles do secondary metabolites play in defence and signalling?",
                    "kind": "provenance"
                  },
                  {
                    "text": "Which entry fits chemical ecology?",
                    "kind": "action"
                  }
                ]
              }
            ]
          }
        ]
      }
    ]
  },
  "openQuestions": [
    "Should secondary metabolite and mycotoxin be the primary linked entries?",
    "How should ontology and biochemistry sources be linked?",
    "The registry entry has merged aliases naming specific compound processes; should they be split off?"
  ],
  "statistics": {
    "bundles": 4,
    "layers": 8,
    "findings": 8,
    "questions": 16
  }
}