{
  "vercy": "1.0-draft",
  "publication": {
    "status": "research-draft",
    "adjudicationStatus": "unreviewed",
    "publishableCanonical": false,
    "generatedAt": "2026-09-11T12:04:03Z",
    "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": 1,
    "engine": "claude",
    "enrichment": {
      "pass": 3,
      "engine": "claude",
      "producedAt": "2026-10-05T17:00:00Z",
      "ingestedAt": "2026-10-05T13:30:24+00:00",
      "fields": [
        "agent_conduct",
        "ethics",
        "owners"
      ]
    },
    "gate": {
      "passed": true,
      "version": "1.0",
      "at": "2026-10-07T10:10:31+00:00",
      "evidence": [
        "completeness 1.00",
        "sense: Wikidata description",
        "2 live sources",
        "review by codex: pass"
      ]
    }
  },
  "metaModel": {
    "id": "THING-Q4713306",
    "registryId": "vr.tr.alcohol-oxidoreductase",
    "name": "alcohol oxidoreductase",
    "version": "0.2.0-wave.1",
    "entryKind": "thing",
    "family": "Thing Registry",
    "domain": [
      "PHY.MAT"
    ],
    "status": "research-draft"
  },
  "canonicalUrl": "https://ver.cy/models/thing/q4713306/",
  "model": {
    "registry_id": "vr.tr.alcohol-oxidoreductase",
    "name": "alcohol oxidoreductase",
    "purpose": "Let an agent handle alcohol oxidoreductases by EC class, reaction, cofactor, biological role and data sources.",
    "definition": "A group of oxidoreductase enzymes that act on the CH-OH group of donors, classified under EC 1.1, including alcohol dehydrogenase, lactate dehydrogenase and glucose-6-phosphate dehydrogenase, usually using NAD+ or NADP+ as acceptor.",
    "what_it_is_for": "Metabolism, biochemistry, diagnostics and biotechnology.",
    "affordances": [
      "classify an enzyme by EC number",
      "describe the reaction and cofactor",
      "find enzyme data in databases",
      "relate enzymes to metabolism and disease in general terms"
    ],
    "distinguishing_features": [
      "Oxidise alcohol groups",
      "Mostly use NAD(P)+",
      "Very large class",
      "Central to metabolism"
    ],
    "appearance": "Proteins, not visible; described by structures and reactions.",
    "visual_identification": [
      "EC numbers beginning 1.1",
      "Dehydrogenases using NAD+ or NADP+",
      "Oxidases acting on other groups belong elsewhere"
    ],
    "physical_properties": [
      {
        "quantity": "Molecular mass",
        "unit": "kDa",
        "typical_range": "",
        "note": "Determine mass from the specific enzyme sequence or mass spectrometry, distinguishing individual subunits from assembled complexes."
      },
      {
        "quantity": "Isoelectric point",
        "unit": "pH units",
        "typical_range": "",
        "note": "Measure the pH at which the specified enzyme has zero net charge using isoelectric focusing."
      },
      {
        "quantity": "Hydrodynamic radius",
        "unit": "nm",
        "typical_range": "",
        "note": "Measure the effective solution radius using a suitable diffusion-based method while recording buffer conditions and aggregation state."
      }
    ],
    "families_and_kinds": [
      "EC 1.1.1 with NAD+ or NADP+ as acceptor",
      "EC 1.1.2 with a cytochrome as acceptor",
      "EC 1.1.3 with oxygen as acceptor",
      "EC 1.1.5 with a quinone as acceptor",
      "other acceptors"
    ],
    "related_models": [
      {
        "relation": "is a kind of",
        "target": "oxidoreductase",
        "why": "category"
      },
      {
        "relation": "includes",
        "target": "alcohol dehydrogenase",
        "why": "example"
      },
      {
        "relation": "uses",
        "target": "NAD+",
        "why": "cofactor"
      },
      {
        "relation": "is classified by",
        "target": "EC number",
        "why": "scheme"
      }
    ],
    "identifiers": [
      {
        "scheme": "EC number",
        "value_or_pattern": "1.1",
        "note": "enzyme subclass"
      }
    ],
    "standards_and_regulation": [
      "IUBMB enzyme nomenclature"
    ],
    "failure_modes_and_hazards": [
      "Confusing EC subclasses",
      "Over-interpreting diagnostic enzyme tests"
    ],
    "in_scope": [],
    "out_of_scope": [],
    "characteristics": [],
    "agent_conduct": {
      "may": [
        "Report enzymes in this group with their EC numbers from enzyme nomenclature databases.",
        "Explain their reactions and roles in metabolism."
      ],
      "must_not": [
        "Confuse EC subclasses or assign wrong EC numbers.",
        "Interpret a person's enzyme test results as a diagnosis."
      ],
      "requires_human": [
        "Medical decisions based on enzyme tests."
      ]
    },
    "ethics": {
      "considerations": [
        "Accurate classification underpins research and diagnostics."
      ],
      "affected_parties": [
        "Researchers and students",
        "Patients undergoing tests"
      ]
    },
    "owners": {
      "steward": "Nobody owns the group; enzyme nomenclature is kept by the scientific community.",
      "master_systems": [
        "Enzyme nomenclature lists"
      ]
    }
  },
  "sources": [
    {
      "id": "wikidata",
      "title": "Wikidata item Q4713306: alcohol oxidoreductase",
      "url": "https://www.wikidata.org/wiki/Q4713306",
      "url_status": "live",
      "what_it_supports": "identity and sense of the item",
      "checked_by": "wikidata-api"
    },
    {
      "id": "wikipedia-en",
      "title": "Wikipedia: Alcohol oxidoreductase",
      "url": "https://en.wikipedia.org/wiki/Alcohol_oxidoreductase",
      "url_status": "live",
      "what_it_supports": "general description of the item",
      "checked_by": "wikidata-api sitelink"
    }
  ],
  "structure": {
    "bundles": [
      {
        "id": "classification",
        "name": "Classification",
        "description": "EC numbers.",
        "rationale": "EC numbers identify.",
        "layers": [
          {
            "id": "ec",
            "name": "EC",
            "description": "Number.",
            "findings": [
              {
                "id": "ec-finding",
                "name": "EC",
                "description": "EC number.",
                "questions": [
                  {
                    "text": "What is the full EC number of this enzyme?",
                    "kind": "provenance"
                  },
                  {
                    "text": "Which acceptor subclass is it in?",
                    "kind": "definition"
                  }
                ]
              }
            ]
          },
          {
            "id": "names",
            "name": "Names",
            "description": "Systematic names.",
            "findings": [
              {
                "id": "names-finding",
                "name": "Names",
                "description": "Names.",
                "questions": [
                  {
                    "text": "What are its systematic and accepted names?",
                    "kind": "provenance"
                  },
                  {
                    "text": "Has it been reclassified?",
                    "kind": "provenance"
                  }
                ]
              }
            ]
          }
        ]
      },
      {
        "id": "reaction",
        "name": "Reaction",
        "description": "Chemistry.",
        "rationale": "Reactions define enzymes.",
        "layers": [
          {
            "id": "substrate",
            "name": "Substrate",
            "description": "Donor.",
            "findings": [
              {
                "id": "substrate-finding",
                "name": "Substrate",
                "description": "Substrates.",
                "questions": [
                  {
                    "text": "Which alcohol substrate does it oxidise, and what is the product?",
                    "kind": "definition"
                  },
                  {
                    "text": "What is its substrate specificity?",
                    "kind": "measurement"
                  }
                ]
              }
            ]
          },
          {
            "id": "cofactor",
            "name": "Cofactor",
            "description": "Acceptor.",
            "findings": [
              {
                "id": "cofactor-finding",
                "name": "Cofactor",
                "description": "Cofactor.",
                "questions": [
                  {
                    "text": "Which cofactor or acceptor does it use?",
                    "kind": "definition"
                  },
                  {
                    "text": "What are its kinetic parameters?",
                    "kind": "measurement"
                  }
                ]
              }
            ]
          }
        ]
      },
      {
        "id": "biology",
        "name": "Biology",
        "description": "Role.",
        "rationale": "Enzymes serve pathways.",
        "layers": [
          {
            "id": "pathway",
            "name": "Pathway",
            "description": "Metabolism.",
            "findings": [
              {
                "id": "pathway-finding",
                "name": "Pathway",
                "description": "Pathways.",
                "questions": [
                  {
                    "text": "Which metabolic pathway does it participate in?",
                    "kind": "provenance"
                  },
                  {
                    "text": "In which organisms?",
                    "kind": "provenance"
                  }
                ]
              }
            ]
          },
          {
            "id": "health",
            "name": "Health",
            "description": "Deficiency.",
            "findings": [
              {
                "id": "health-finding",
                "name": "Health",
                "description": "Health links.",
                "questions": [
                  {
                    "text": "Is a deficiency of this enzyme linked to a condition, according to medical sources?",
                    "kind": "provenance"
                  },
                  {
                    "text": "Is the user asking about their own health?",
                    "kind": "boundary"
                  }
                ]
              }
            ]
          }
        ]
      },
      {
        "id": "data",
        "name": "Data",
        "description": "Databases.",
        "rationale": "Databases hold details.",
        "layers": [
          {
            "id": "databases",
            "name": "Databases",
            "description": "BRENDA and UniProt.",
            "findings": [
              {
                "id": "databases-finding",
                "name": "Databases",
                "description": "Databases.",
                "questions": [
                  {
                    "text": "Which database entries describe this enzyme?",
                    "kind": "provenance"
                  },
                  {
                    "text": "Is a structure available in the PDB?",
                    "kind": "provenance"
                  }
                ]
              }
            ]
          },
          {
            "id": "applications",
            "name": "Applications",
            "description": "Biotech.",
            "findings": [
              {
                "id": "applications-finding",
                "name": "Applications",
                "description": "Applications.",
                "questions": [
                  {
                    "text": "How is the enzyme used in diagnostics or biocatalysis?",
                    "kind": "provenance"
                  },
                  {
                    "text": "Which products use it?",
                    "kind": "provenance"
                  }
                ]
              }
            ]
          }
        ]
      }
    ]
  },
  "openQuestions": [
    "Should each enzyme be a separate entry?",
    "How should BRENDA and UniProt be linked?",
    "How should EC reclassification be tracked?"
  ],
  "statistics": {
    "bundles": 4,
    "layers": 8,
    "findings": 8,
    "questions": 16
  }
}