{
  "vercy": "1.0-draft",
  "publication": {
    "status": "research-draft",
    "adjudicationStatus": "unreviewed",
    "publishableCanonical": false,
    "generatedAt": "2026-09-12T19:59:28Z",
    "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": 3,
    "engine": "claude",
    "enrichment": {
      "pass": 3,
      "engine": "claude",
      "producedAt": "2026-10-06T10:00:00Z",
      "ingestedAt": "2026-10-06T06:58:34+00:00",
      "fields": [
        "agent_conduct",
        "ethics",
        "owners"
      ]
    },
    "gate": {
      "passed": true,
      "version": "1.0",
      "at": "2026-10-06T19:52:02+00:00",
      "evidence": [
        "completeness 1.00",
        "sense: Wikidata description",
        "2 live sources",
        "review by codex: pass"
      ]
    }
  },
  "metaModel": {
    "id": "THING-Q79899",
    "registryId": "vr.tr.cytoplasm",
    "name": "cytoplasm",
    "version": "0.2.0-wave.3",
    "entryKind": "thing",
    "family": "Thing Registry",
    "domain": [
      "PHY.LIV"
    ],
    "status": "research-draft"
  },
  "canonicalUrl": "https://ver.cy/models/thing/q79899/",
  "model": {
    "registry_id": "vr.tr.cytoplasm",
    "name": "cytoplasm",
    "purpose": "Let an agent explain the cytoplasm and its components, distinguish cytoplasm from cytosol, nucleus and specialised regions, relay facts from cell biology references, and route detailed biochemical questions to the relevant entries.",
    "definition": "The material within a living cell enclosed by the cell membrane, excluding the nucleus in eukaryotes: the cytosol, a water-based solution of ions, small molecules and proteins, together with the organelles, cytoskeleton and inclusions suspended in it; the site of most metabolism, protein synthesis and transport within the cell.",
    "what_it_is_for": "Not for anything; the internal medium of the cell.",
    "affordances": [
      "explain composition and organisation",
      "distinguish cytoplasm from cytosol and nucleoplasm",
      "explain roles in metabolism and transport",
      "route to organelle and pathway entries"
    ],
    "distinguishing_features": [
      "Bounded by the cell membrane",
      "Excludes the nucleus in eukaryotes",
      "Contains cytosol, organelles and cytoskeleton",
      "Crowded, gel-like and dynamic"
    ],
    "appearance": "Not visible to the eye; under the microscope a translucent gel with organelles and granules.",
    "visual_identification": [
      "Everything inside the membrane except the nucleus",
      "Cytosol plus organelles and cytoskeleton",
      "The nucleoplasm and the extracellular matrix are outside it"
    ],
    "physical_properties": [
      {
        "quantity": "water content",
        "typical_range": "about 70-80",
        "unit": "percent",
        "note": ""
      },
      {
        "quantity": "pH",
        "typical_range": "about 7.2",
        "unit": "pH",
        "note": "cytosol"
      },
      {
        "quantity": "fraction of cell volume",
        "typical_range": "about 50-80",
        "unit": "percent",
        "note": "varies by cell type"
      }
    ],
    "families_and_kinds": [
      "cytosol",
      "organelles such as mitochondria and endoplasmic reticulum",
      "cytoskeleton",
      "inclusions such as glycogen and lipid droplets",
      "specialised regions such as the cell cortex, sarcoplasm and ooplasm",
      "prokaryotic cytoplasm without membrane-bound organelles"
    ],
    "related_models": [
      {
        "relation": "is a kind of",
        "target": "cellular component",
        "why": "part of the cell"
      },
      {
        "relation": "contains",
        "target": "organelle",
        "why": "suspended structures"
      },
      {
        "relation": "is contrasted with",
        "target": "cell nucleus",
        "why": "excluded from the cytoplasm"
      },
      {
        "relation": "is bounded by",
        "target": "cell membrane",
        "why": "the outer limit"
      }
    ],
    "identifiers": [
      {
        "scheme": "Gene Ontology",
        "value_or_pattern": "GO:0005737",
        "note": "cytoplasm"
      },
      {
        "scheme": "UBERON or CL terms",
        "value_or_pattern": "per context",
        "note": "cell ontology"
      }
    ],
    "standards_and_regulation": [
      "Gene Ontology and cell ontology definitions"
    ],
    "failure_modes_and_hazards": [
      "Confusing cytoplasm with cytosol",
      "Treating it as a uniform fluid",
      "Outdated textbook simplifications"
    ],
    "in_scope": [],
    "out_of_scope": [],
    "characteristics": [],
    "agent_conduct": {
      "may": [
        "Explain the composition of cytoplasm and its role in cell function.",
        "Describe how cytoplasm differs between prokaryotic and eukaryotic cells."
      ],
      "must_not": [
        "Confuse cytoplasm with cytosol or with the contents of the nucleus.",
        "Present simplified textbook models as complete descriptions of the cell.",
        "Use the term to lend false scientific weight to health products."
      ],
      "requires_human": [
        "Use of human cells or tissue in research."
      ]
    },
    "ethics": {
      "considerations": [
        "Accurate basic biology underpins trust in medicine and science teaching.",
        "Cell research uses material from donors who must consent."
      ],
      "affected_parties": [
        "Students",
        "Researchers",
        "Cell and tissue donors"
      ]
    },
    "owners": {
      "steward": "Nobody owns the concept; it belongs to biology.",
      "master_systems": []
    }
  },
  "sources": [
    {
      "id": "wikidata",
      "title": "Wikidata item Q79899: cytoplasm",
      "url": "https://www.wikidata.org/wiki/Q79899",
      "url_status": "live",
      "what_it_supports": "identity and sense of the item",
      "checked_by": "wikidata-api"
    },
    {
      "id": "wikipedia-en",
      "title": "Wikipedia: Cytoplasm",
      "url": "https://en.wikipedia.org/wiki/Cytoplasm",
      "url_status": "live",
      "what_it_supports": "general description of the item",
      "checked_by": "wikidata-api sitelink"
    }
  ],
  "structure": {
    "bundles": [
      {
        "id": "structure",
        "name": "Structure",
        "description": "What the cytoplasm is.",
        "rationale": "Definition.",
        "layers": [
          {
            "id": "definition",
            "name": "Definition",
            "description": "Definition and boundaries.",
            "findings": [
              {
                "id": "definition-finding",
                "name": "Definition",
                "description": "Definition.",
                "questions": [
                  {
                    "text": "What does the cytoplasm include and exclude, and how does it differ from the cytosol?",
                    "kind": "definition"
                  },
                  {
                    "text": "Is the question about the cytoplasm, the cytosol or the nucleus?",
                    "kind": "boundary"
                  }
                ]
              }
            ]
          },
          {
            "id": "components",
            "name": "Components",
            "description": "Components.",
            "findings": [
              {
                "id": "components-finding",
                "name": "Components",
                "description": "Components.",
                "questions": [
                  {
                    "text": "What organelles, cytoskeleton and inclusions does it contain, and how are they organised?",
                    "kind": "definition"
                  },
                  {
                    "text": "Which entry fits a specific organelle?",
                    "kind": "action"
                  }
                ]
              }
            ]
          }
        ]
      },
      {
        "id": "function",
        "name": "Function",
        "description": "What happens there.",
        "rationale": "Physiology.",
        "layers": [
          {
            "id": "metabolism",
            "name": "Metabolism",
            "description": "Metabolism and synthesis.",
            "findings": [
              {
                "id": "metabolism-finding",
                "name": "Metabolism",
                "description": "Metabolism.",
                "questions": [
                  {
                    "text": "Which metabolic and synthetic processes take place in the cytoplasm?",
                    "kind": "provenance"
                  },
                  {
                    "text": "Which entry fits a specific pathway?",
                    "kind": "action"
                  }
                ]
              }
            ]
          },
          {
            "id": "transport",
            "name": "Transport",
            "description": "Transport and signalling.",
            "findings": [
              {
                "id": "transport-finding",
                "name": "Transport",
                "description": "Transport.",
                "questions": [
                  {
                    "text": "How do transport, streaming and signalling work in the cytoplasm?",
                    "kind": "provenance"
                  },
                  {
                    "text": "Which references are standard?",
                    "kind": "provenance"
                  }
                ]
              }
            ]
          }
        ]
      },
      {
        "id": "properties",
        "name": "Properties",
        "description": "Physical properties.",
        "rationale": "Physics.",
        "layers": [
          {
            "id": "composition",
            "name": "Composition",
            "description": "Composition.",
            "findings": [
              {
                "id": "composition-finding",
                "name": "Composition",
                "description": "Composition.",
                "questions": [
                  {
                    "text": "What is the composition of the cytoplasm, and how is it measured?",
                    "kind": "measurement"
                  },
                  {
                    "text": "How does it vary by cell type?",
                    "kind": "measurement"
                  }
                ]
              }
            ]
          },
          {
            "id": "physics",
            "name": "Physics",
            "description": "Crowding and phases.",
            "findings": [
              {
                "id": "physics-finding",
                "name": "Physics",
                "description": "Physics.",
                "questions": [
                  {
                    "text": "What do studies say about crowding, viscosity and phase separation, with findings attributed?",
                    "kind": "provenance"
                  },
                  {
                    "text": "Which entry fits biomolecular condensates?",
                    "kind": "action"
                  }
                ]
              }
            ]
          }
        ]
      },
      {
        "id": "study",
        "name": "Study",
        "description": "Comparison and teaching.",
        "rationale": "Study.",
        "layers": [
          {
            "id": "comparison",
            "name": "Comparison",
            "description": "Prokaryotes and specialised cells.",
            "findings": [
              {
                "id": "comparison-finding",
                "name": "Comparison",
                "description": "Comparison.",
                "questions": [
                  {
                    "text": "How does the cytoplasm differ in prokaryotes, muscle cells and eggs?",
                    "kind": "provenance"
                  },
                  {
                    "text": "Which entry fits the specific cell type?",
                    "kind": "action"
                  }
                ]
              }
            ]
          },
          {
            "id": "teach",
            "name": "Teach",
            "description": "Teaching.",
            "findings": [
              {
                "id": "teach-finding",
                "name": "Teach",
                "description": "Teaching.",
                "questions": [
                  {
                    "text": "How is the cytoplasm taught, and which misconceptions arise?",
                    "kind": "provenance"
                  },
                  {
                    "text": "Which entry fits cell biology?",
                    "kind": "action"
                  }
                ]
              }
            ]
          }
        ]
      }
    ]
  },
  "openQuestions": [
    "Should cytosol be a separate entry?",
    "How should ontology terms be linked?",
    "The registry entry has merged aliases for specialised regions; should they be split off?"
  ],
  "statistics": {
    "bundles": 4,
    "layers": 8,
    "findings": 8,
    "questions": 16
  }
}