{
  "vercy": "1.0-draft",
  "publication": {
    "status": "research-draft",
    "adjudicationStatus": "unreviewed",
    "publishableCanonical": false,
    "generatedAt": "2026-09-13T19:28:43Z",
    "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": "2026-10-06T11:00:00Z",
      "ingestedAt": "2026-10-06T07:37:39+00:00",
      "fields": [
        "agent_conduct",
        "ethics",
        "owners"
      ]
    },
    "revisions": [
      {
        "at": "2026-10-06T22:48:54+00:00",
        "engine": "codex",
        "fields": [
          "definition",
          "visual_identification"
        ],
        "answering_review": "275572b8e53424e721454af695a0d4c17c2c3ab1543a798a04b3992b2042f9ac"
      },
      {
        "at": "2026-10-07T11:30:10+00:00",
        "engine": "codex",
        "fields": [
          "definition",
          "visual_identification"
        ],
        "answering_review": "f7d9b8def766dd3a21918f11e24cf8215c571dcb1f118ad5ccab4ab7ded65e81"
      }
    ],
    "gate": {
      "passed": true,
      "version": "1.0",
      "at": "2026-10-07T12:16:32+00:00",
      "evidence": [
        "completeness 1.00",
        "sense: Wikidata description",
        "2 live sources",
        "review by codex: pass"
      ]
    }
  },
  "metaModel": {
    "id": "THING-Q3333419",
    "registryId": "vr.tr.primary-metabolite",
    "name": "primary metabolite",
    "version": "0.2.0-wave.4",
    "entryKind": "thing",
    "family": "Thing Registry",
    "domain": [
      "PHY.MAT"
    ],
    "status": "research-draft"
  },
  "canonicalUrl": "https://ver.cy/models/thing/q3333419/",
  "model": {
    "registry_id": "vr.tr.primary-metabolite",
    "name": "primary metabolite",
    "purpose": "Let an agent explain primary metabolites, relay pathways, examples and industrial production from biochemistry sources, describe the compounds the registry aliases name as examples, and distinguish primary from secondary metabolites, from metabolic enzymes and from nutrients as dietary inputs.",
    "definition": "A primary metabolite is an intermediate or end product of metabolism directly involved in normal growth, development and reproduction, including products of central pathways such as glycolysis, the citric acid cycle and amino acid, lipid and nucleotide synthesis; examples include sugars, amino acids, fatty acids such as stearic acid, acyl-CoA intermediates, phospholipids such as phosphatidylglycerols and folate derivatives such as polyglutamated tetrahydrofolates, while classification of examples such as pentosans and thiosulfate requires an identified organism and metabolic context; secondary metabolites generally have more specialised roles, including ecological functions that can be essential for survival in particular environments.",
    "what_it_is_for": "Not applicable; a class of biomolecules.",
    "affordances": [
      "explain the class",
      "relay pathways and examples",
      "describe named compounds",
      "distinguish related concepts"
    ],
    "distinguishing_features": [
      "Essential for life",
      "Central pathways",
      "Conserved across organisms",
      "Industrial fermentation targets"
    ],
    "appearance": "Not a visible object; molecules.",
    "visual_identification": [
      "A primary metabolite is identified by its direct role in growth, development or reproduction in the relevant organism and metabolic context.",
      "Examples include stearic acid, trans-3-enoyl-CoA, phosphatidylglycerol and polyglutamated tetrahydrofolate, while pentosan and thiosulfate require organism-specific and metabolic context.",
      "Secondary metabolites generally serve specialised roles that can be essential for survival in particular environments, enzymes catalyse reactions and nutrients are consumed inputs."
    ],
    "physical_properties": [
      {
        "quantity": "examples",
        "typical_range": "glucose, amino acids, nucleotides, fatty acids",
        "unit": "list",
        "note": ""
      },
      {
        "quantity": "industrial products",
        "typical_range": "citric acid, glutamate, ethanol",
        "unit": "list",
        "note": ""
      },
      {
        "quantity": "registry parent",
        "typical_range": "metabolite",
        "unit": "note",
        "note": ""
      }
    ],
    "families_and_kinds": [
      "carbohydrates and polysaccharides",
      "amino acids",
      "lipids and acyl groups",
      "nucleotides",
      "cofactors such as folates",
      "inorganic metabolites"
    ],
    "related_models": [
      {
        "relation": "is a kind of",
        "target": "metabolite",
        "why": "in registry terms"
      },
      {
        "relation": "is produced by",
        "target": "central metabolism",
        "why": ""
      },
      {
        "relation": "is contrasted with",
        "target": "secondary metabolite",
        "why": ""
      },
      {
        "relation": "is catalogued in",
        "target": "ChEBI",
        "why": "and KEGG"
      }
    ],
    "identifiers": [],
    "standards_and_regulation": [
      "No regulation; food and fermentation product rules apply to industrial metabolites"
    ],
    "failure_modes_and_hazards": [
      "Blurry boundary with secondary metabolites",
      "Registry aliases naming very specific compounds",
      "Confusing metabolites and nutrients"
    ],
    "in_scope": [],
    "out_of_scope": [],
    "characteristics": [],
    "agent_conduct": {
      "may": [
        "Explain primary metabolites and how they differ from secondary metabolites.",
        "Give examples from central metabolic pathways with sources."
      ],
      "must_not": [
        "Present the boundary with secondary metabolites as sharper than it is.",
        "Make health claims about supplements based on their status as metabolites.",
        "Confuse primary metabolites with primary metabolism disorders."
      ],
      "requires_human": [
        "Using metabolite data in decisions about a person's diet or treatment."
      ]
    },
    "ethics": {
      "considerations": [
        "Metabolic science is often used to sell unproven supplements.",
        "Clear teaching of basic biochemistry protects people from health fraud."
      ],
      "affected_parties": [
        "Students",
        "Consumers",
        "Researchers"
      ]
    },
    "owners": {
      "steward": "Nobody owns the concept; it belongs to biochemistry as shared knowledge.",
      "master_systems": []
    }
  },
  "sources": [
    {
      "id": "wikidata",
      "title": "Wikidata item Q3333419: primary metabolite",
      "url": "https://www.wikidata.org/wiki/Q3333419",
      "url_status": "live",
      "what_it_supports": "identity and sense of the item",
      "checked_by": "wikidata-api"
    },
    {
      "id": "wikipedia-en",
      "title": "Wikipedia: Primary metabolite",
      "url": "https://en.wikipedia.org/wiki/Primary_metabolite",
      "url_status": "live",
      "what_it_supports": "general description of the item",
      "checked_by": "wikidata-api sitelink"
    }
  ],
  "structure": {
    "bundles": [
      {
        "id": "understand",
        "name": "Understand",
        "description": "What a primary metabolite is.",
        "rationale": "Science.",
        "layers": [
          {
            "id": "definition",
            "name": "Definition",
            "description": "Definition.",
            "findings": [
              {
                "id": "definition-finding",
                "name": "Definition",
                "description": "Definition.",
                "questions": [
                  {
                    "text": "What is a primary metabolite, and how does it differ from secondary metabolites, enzymes and nutrients?",
                    "kind": "definition"
                  },
                  {
                    "text": "Is the question about biochemistry, a specific compound or industry?",
                    "kind": "boundary"
                  }
                ]
              }
            ]
          },
          {
            "id": "examples",
            "name": "Examples",
            "description": "Named compounds.",
            "findings": [
              {
                "id": "examples-finding",
                "name": "Examples",
                "description": "Examples.",
                "questions": [
                  {
                    "text": "What are the stearoyl group, enoyl-CoA intermediates, phosphatidylglycerols, polyglutamated folates, pentosans and thiosulfate?",
                    "kind": "definition"
                  },
                  {
                    "text": "Which entry fits the specific compound?",
                    "kind": "action"
                  }
                ]
              }
            ]
          }
        ]
      },
      {
        "id": "biochemistry",
        "name": "Biochemistry",
        "description": "Pathways.",
        "rationale": "Science.",
        "layers": [
          {
            "id": "central",
            "name": "Central",
            "description": "Central metabolism.",
            "findings": [
              {
                "id": "central-finding",
                "name": "Central",
                "description": "Central.",
                "questions": [
                  {
                    "text": "How do glycolysis, the citric acid cycle and biosynthetic pathways produce primary metabolites?",
                    "kind": "provenance"
                  },
                  {
                    "text": "Which references are standard?",
                    "kind": "provenance"
                  }
                ]
              }
            ]
          },
          {
            "id": "databases",
            "name": "Databases",
            "description": "Databases.",
            "findings": [
              {
                "id": "databases-finding",
                "name": "Databases",
                "description": "Databases.",
                "questions": [
                  {
                    "text": "How are metabolites catalogued in ChEBI, KEGG and HMDB?",
                    "kind": "provenance"
                  },
                  {
                    "text": "Which sources are cited?",
                    "kind": "provenance"
                  }
                ]
              }
            ]
          }
        ]
      },
      {
        "id": "applications",
        "name": "Applications",
        "description": "Applications.",
        "rationale": "Application.",
        "layers": [
          {
            "id": "industry",
            "name": "Industry",
            "description": "Industrial fermentation.",
            "findings": [
              {
                "id": "industry-finding",
                "name": "Industry",
                "description": "Industry.",
                "questions": [
                  {
                    "text": "How are primary metabolites produced industrially by fermentation?",
                    "kind": "provenance"
                  },
                  {
                    "text": "Which entry fits industrial fermentation?",
                    "kind": "action"
                  }
                ]
              }
            ]
          },
          {
            "id": "metabolomics",
            "name": "Metabolomics",
            "description": "Metabolomics.",
            "findings": [
              {
                "id": "metabolomics-finding",
                "name": "Metabolomics",
                "description": "Metabolomics.",
                "questions": [
                  {
                    "text": "How does metabolomics measure primary metabolites?",
                    "kind": "provenance"
                  },
                  {
                    "text": "Which entry fits metabolomics?",
                    "kind": "action"
                  }
                ]
              }
            ]
          }
        ]
      },
      {
        "id": "context",
        "name": "Context",
        "description": "Classification.",
        "rationale": "Context.",
        "layers": [
          {
            "id": "secondary",
            "name": "Secondary",
            "description": "Secondary metabolites.",
            "findings": [
              {
                "id": "secondary-finding",
                "name": "Secondary",
                "description": "Secondary.",
                "questions": [
                  {
                    "text": "How do secondary metabolites differ, and where is the boundary debated?",
                    "kind": "provenance"
                  },
                  {
                    "text": "Which entry fits secondary metabolite?",
                    "kind": "action"
                  }
                ]
              }
            ]
          },
          {
            "id": "history",
            "name": "History",
            "description": "History.",
            "findings": [
              {
                "id": "history-finding",
                "name": "History",
                "description": "History.",
                "questions": [
                  {
                    "text": "How did the distinction between primary and secondary metabolism arise?",
                    "kind": "provenance"
                  },
                  {
                    "text": "Which entry fits the history of biochemistry?",
                    "kind": "action"
                  }
                ]
              }
            ]
          }
        ]
      }
    ]
  },
  "openQuestions": [
    "Should the named compounds be linked individually?",
    "How should biochemistry databases be linked?",
    "The registry entry has merged aliases naming specific compounds; should they be split off?"
  ],
  "statistics": {
    "bundles": 4,
    "layers": 8,
    "findings": 8,
    "questions": 16
  }
}