{
  "vercy": "1.0-draft",
  "publication": {
    "status": "research-draft",
    "adjudicationStatus": "unreviewed",
    "publishableCanonical": false,
    "generatedAt": "2026-09-11T14:24:29Z",
    "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": "2026-10-05T13:29:18+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-Q45948",
    "registryId": "vr.tr.organelle",
    "name": "organelle",
    "version": "0.2.0-wave.1",
    "entryKind": "thing",
    "family": "Thing Registry",
    "domain": [
      "PHY.LIV"
    ],
    "status": "research-draft"
  },
  "canonicalUrl": "https://ver.cy/models/thing/q45948/",
  "model": {
    "registry_id": "vr.tr.organelle",
    "name": "organelle",
    "purpose": "Let an agent explain organelles by structure, function, origin and research, for learners and researchers.",
    "definition": "A specialised structure within a cell that performs a particular function, such as the nucleus, mitochondria, chloroplasts, endoplasmic reticulum, Golgi apparatus, lysosomes and vacuoles; mitochondria and plastids are semiautonomous with their own DNA, and new organelles such as the nitrogen-fixing nitroplast continue to be described.",
    "what_it_is_for": "Cell biology education and research.",
    "affordances": [
      "describe organelle functions",
      "explain endosymbiotic origins",
      "compare plant, animal and protist organelles",
      "find imaging and ontology resources"
    ],
    "distinguishing_features": [
      "Compartmentalised function",
      "Often membrane-bound",
      "Some have own DNA",
      "Vary among organisms"
    ],
    "appearance": "Microscopic compartments seen in light and electron micrographs.",
    "visual_identification": [
      "Membrane-bound compartments",
      "Mitochondria and chloroplasts",
      "Ribosomes are complexes often not counted as membrane organelles"
    ],
    "physical_properties": [
      {
        "quantity": "Characteristic length",
        "unit": "micrometre",
        "typical_range": "",
        "note": "Measure the longest dimension using calibrated microscopy because size depends on organelle type and cellular state."
      },
      {
        "quantity": "Volume",
        "unit": "cubic micrometre",
        "typical_range": "",
        "note": "Estimate volume from segmented three-dimensional microscopy images with the organelle boundary explicitly defined."
      },
      {
        "quantity": "Surface area",
        "unit": "square micrometre",
        "typical_range": "",
        "note": "Measure the defined outer boundary from reconstructed microscopy images while distinguishing it from internal membrane surfaces."
      }
    ],
    "families_and_kinds": [
      "nucleus",
      "mitochondria and plastids",
      "endomembrane system",
      "lysosomes, peroxisomes and vacuoles",
      "protist organelles such as trichocysts and extrusomes"
    ],
    "related_models": [
      {
        "relation": "is a kind of",
        "target": "cellular anatomical entity",
        "why": "category"
      },
      {
        "relation": "is part of",
        "target": "cell",
        "why": "unit"
      },
      {
        "relation": "includes",
        "target": "mitochondrion",
        "why": "example"
      },
      {
        "relation": "is related to",
        "target": "cellular respiration",
        "why": "process"
      }
    ],
    "identifiers": [],
    "standards_and_regulation": [
      "Gene Ontology cellular component terms"
    ],
    "failure_modes_and_hazards": [
      "Oversimplified textbook diagrams",
      "Confusing organelles across kingdoms"
    ],
    "in_scope": [],
    "out_of_scope": [],
    "characteristics": [],
    "agent_conduct": {
      "may": [
        "Explain organelles and their functions, citing scientific sources.",
        "Help researchers find literature and imaging data."
      ],
      "must_not": [
        "Present early findings on new organelles as established.",
        "Present mitochondrial health supplements as proven therapies."
      ],
      "requires_human": [
        "Interpreting organelle-related findings for a patient's diagnosis or treatment."
      ]
    },
    "ethics": {
      "considerations": [
        "Research claims must not overstate findings, especially when health products are sold on them.",
        "Cell lines and tissues used to study organelles come from donors whose consent should be respected."
      ],
      "affected_parties": [
        "Students and the public",
        "Patients",
        "Tissue donors"
      ]
    },
    "owners": {
      "steward": "Nobody: a biological structure; researchers answer for their claims.",
      "master_systems": []
    }
  },
  "sources": [
    {
      "id": "wikidata",
      "title": "Wikidata item Q45948: organelle",
      "url": "https://www.wikidata.org/wiki/Q45948",
      "url_status": "live",
      "what_it_supports": "identity and sense of the item",
      "checked_by": "wikidata-api"
    },
    {
      "id": "wikipedia-en",
      "title": "Wikipedia: Organelle",
      "url": "https://en.wikipedia.org/wiki/Organelle",
      "url_status": "live",
      "what_it_supports": "general description of the item",
      "checked_by": "wikidata-api sitelink"
    }
  ],
  "structure": {
    "bundles": [
      {
        "id": "function",
        "name": "Function",
        "description": "What organelles do.",
        "rationale": "Each has a role.",
        "layers": [
          {
            "id": "roles",
            "name": "Roles",
            "description": "Functions.",
            "findings": [
              {
                "id": "roles-finding",
                "name": "Roles",
                "description": "Functions.",
                "questions": [
                  {
                    "text": "What does this organelle do in the cell?",
                    "kind": "definition"
                  },
                  {
                    "text": "How does it interact with others?",
                    "kind": "definition"
                  }
                ]
              }
            ]
          },
          {
            "id": "compare",
            "name": "Compare",
            "description": "Across organisms.",
            "findings": [
              {
                "id": "compare-finding",
                "name": "Compare",
                "description": "Comparison.",
                "questions": [
                  {
                    "text": "Which organelles are found in plant cells but not animal cells?",
                    "kind": "definition"
                  },
                  {
                    "text": "Which unusual organelles do protists have?",
                    "kind": "provenance"
                  }
                ]
              }
            ]
          }
        ]
      },
      {
        "id": "origin",
        "name": "Origin",
        "description": "Evolution.",
        "rationale": "Some organelles were once bacteria.",
        "layers": [
          {
            "id": "endosymbiosis",
            "name": "Endosymbiosis",
            "description": "Origins.",
            "findings": [
              {
                "id": "endosymbiosis-finding",
                "name": "Endosymbiosis",
                "description": "Endosymbiosis.",
                "questions": [
                  {
                    "text": "What evidence supports the endosymbiotic origin of mitochondria and plastids?",
                    "kind": "provenance"
                  },
                  {
                    "text": "Who proposed the theory?",
                    "kind": "provenance"
                  }
                ]
              }
            ]
          },
          {
            "id": "new",
            "name": "New",
            "description": "Newly described organelles.",
            "findings": [
              {
                "id": "new-finding",
                "name": "New",
                "description": "New organelles.",
                "questions": [
                  {
                    "text": "What is the nitroplast, and how was it described, according to recent studies?",
                    "kind": "provenance"
                  },
                  {
                    "text": "Is its status as an organelle accepted?",
                    "kind": "boundary"
                  }
                ]
              }
            ]
          }
        ]
      },
      {
        "id": "methods",
        "name": "Methods",
        "description": "Studying organelles.",
        "rationale": "Imaging reveals structure.",
        "layers": [
          {
            "id": "imaging",
            "name": "Imaging",
            "description": "Microscopy.",
            "findings": [
              {
                "id": "imaging-finding",
                "name": "Imaging",
                "description": "Microscopy.",
                "questions": [
                  {
                    "text": "Which microscopy methods show this organelle?",
                    "kind": "definition"
                  },
                  {
                    "text": "Which stains or markers are used?",
                    "kind": "provenance"
                  }
                ]
              }
            ]
          },
          {
            "id": "ontology",
            "name": "Ontology",
            "description": "Terminology.",
            "findings": [
              {
                "id": "ontology-finding",
                "name": "Ontology",
                "description": "Ontology.",
                "questions": [
                  {
                    "text": "Which Gene Ontology term describes this organelle?",
                    "kind": "provenance"
                  },
                  {
                    "text": "Which databases list proteins localised there?",
                    "kind": "provenance"
                  }
                ]
              }
            ]
          }
        ]
      },
      {
        "id": "health",
        "name": "Health",
        "description": "Disease links.",
        "rationale": "General information only.",
        "layers": [
          {
            "id": "disorders",
            "name": "Disorders",
            "description": "Organelle disorders.",
            "findings": [
              {
                "id": "disorders-finding",
                "name": "Disorders",
                "description": "Organelle disorders.",
                "questions": [
                  {
                    "text": "Which disorders involve mitochondria or lysosomes, according to medical sources?",
                    "kind": "provenance"
                  },
                  {
                    "text": "How strong is the evidence?",
                    "kind": "boundary"
                  }
                ]
              }
            ]
          },
          {
            "id": "personal",
            "name": "Personal",
            "description": "Personal questions.",
            "findings": [
              {
                "id": "personal-finding",
                "name": "Personal",
                "description": "Personal advice limits.",
                "questions": [
                  {
                    "text": "Is the user asking about their own diagnosis?",
                    "kind": "boundary"
                  },
                  {
                    "text": "How should the agent refer them to a clinician?",
                    "kind": "action"
                  }
                ]
              }
            ]
          }
        ]
      }
    ]
  },
  "openQuestions": [
    "Should each organelle be a separate entry?",
    "How should Gene Ontology be linked?",
    "How should newly described organelles be tracked?"
  ],
  "statistics": {
    "bundles": 4,
    "layers": 8,
    "findings": 8,
    "questions": 16
  }
}