{ "model": { "rank": 1654, "code": "thing-cell", "model_id": "vr.tr.cell", "name": "cell", "purpose": "(biology) the basic structural and functional unit of all organisms; they may exist as independent units of life (as in monads) or may form colonies or tissues as in higher plants and animals", "family": "Thing Registry", "category": "Cross-cutting context", "status": "research-draft", "kind": "thing", "plane": "XCT", "domain": "XCT.TOP", "industry": "", "version": "", "url": "/models/thing/cell/", "tier": 2, "score": 133, "payload": { "layer": "wordnet", "aliases": [ "recombinant", "blastomere", "egg", "nit", "spawn", "roe", "silkworm seed", "flagellated cell", "choanocyte", "collar cell", "fiber", "fibre", "skin cell", "epidermal cell", "melanoblast", "melanocyte", "prickle cell", "epithelial cell", "columnar cell", "columnar epithelial cell", "spongioblast", "cuboidal cell", "cuboidal epithelial cell", "goblet cell", "hair cell", "squamous cell", "beta cell", "taste cell", "gustatory cell", "ganglion cell", "gangliocyte", "somatic cell", "vegetative cell", "neoplastic cell", "cancer cell", "blastema", "zygote", "fertilized ovum", "heterozygote", "homozygote" ], "aliasCount": 195, "merged": 133, "knownIn": 0, "facets": { "substance": "abstract", "origin": "conceptual", "agency": "inert", "mobility": "not-applicable", "scale": "not-applicable", "affordances": [ "observable" ] }, "markers": [], "lexicalClass": "noun.Tops", "senseRank": 1, "alsoRegisteredAs": null, "source": { "dataset": "oewn:2024", "synset": "oewn-00006484-n", "ili": "i35560", "license": "CC BY 4.0" } }, "research": { "vercy": "1.0-draft", "publication": { "status": "research-draft", "adjudicationStatus": "unreviewed", "publishableCanonical": false, "generatedAt": "2026-09-11T05:07:43Z", "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": 1, "engine": "claude" }, "metaModel": { "id": "THING-CELL", "registryId": "vr.tr.cell", "name": "cell", "version": "0.2.0-wave.1", "entryKind": "thing", "family": "Thing Registry", "domain": [ "XCT.TOP" ], "status": "research-draft" }, "canonicalUrl": "https://ver.cy/models/thing/cell/", "model": { "registry_id": "vr.tr.cell", "name": "cell", "purpose": "Let an agent handle cells by type, organism, structure and state, as the unit underlying biology, medicine and biotechnology.", "definition": "In biology, the basic structural and functional unit of all organisms, bounded by a membrane, containing genetic material, and able to exist alone or as part of a multicellular body.", "what_it_is_for": "Cells are the units of life; people study, culture and engineer them for medicine, research and industry.", "affordances": [ "observe it, under a microscope", "culture it, in laboratories under biosafety rules", "count and classify it, for diagnosis", "engineer it, in regulated biotechnology" ], "distinguishing_features": [ "Membrane-bound unit of life", "Prokaryotic cells lack a nucleus; eukaryotic cells have one", "Specialised cell types in multicellular organisms", "Other senses of cell (battery, prison, spreadsheet) are different entries" ], "appearance": "Microscopic units, typically 1-100 micrometres, with a membrane and internal structures visible under staining; eggs and some algae are larger.", "visual_identification": [ "Microscopy with stains shows membrane, nucleus and organelles", "Shape and size suggest type; markers confirm it", "Eggs, roe and spawn are cells or clusters of them in everyday language" ], "physical_properties": [ { "quantity": "diameter", "typical_range": "1-100", "unit": "micrometres", "note": "bacteria about 1-2, human cells 10-30" }, { "quantity": "cells in a human body", "typical_range": "about 3.7 x 10^13", "unit": "cells", "note": "" } ], "families_and_kinds": [ "prokaryotic and eukaryotic cells", "animal, plant, fungal cells", "specialised types: neurons, blood cells, gametes", "stem cells", "cell lines in culture" ], "related_models": [ { "relation": "is part of", "target": "organism", "why": "organisms are made of cells" }, { "relation": "is studied by", "target": "biology", "why": "cell biology" }, { "relation": "contains", "target": "DNA", "why": "genetic material" }, { "relation": "is confused with", "target": "battery cell and other cells", "why": "homonyms" } ], "identifiers": [ { "scheme": "Cell Ontology id", "value_or_pattern": "CL: plus digits", "note": "cell types" }, { "scheme": "Cellosaurus accession", "value_or_pattern": "CVCL_ plus code", "note": "cell lines" } ], "standards_and_regulation": [ "Biosafety rules for cell culture", "Regulation of human tissues and cells, such as EU Directive 2004/23/EC", "Stem cell research regulations" ], "failure_modes_and_hazards": [ "Misidentified or contaminated cell lines", "Biosafety lapses with infected cultures", "Ethical breaches in human cell research" ], "in_scope": [], "out_of_scope": [], "characteristics": [] }, "sources": [], "structure": { "bundles": [ { "id": "type", "name": "Type", "description": "What kind of cell.", "rationale": "Cell type decides function and handling.", "layers": [ { "id": "classification", "name": "Classification", "description": "Prokaryote, eukaryote, cell type.", "findings": [ { "id": "classification-finding", "name": "Cell type", "description": "The cell type.", "questions": [ { "text": "What type of cell is this, by Cell Ontology term?", "kind": "definition" }, { "text": "From which organism and tissue?", "kind": "provenance" } ] } ] }, { "id": "markers", "name": "Markers", "description": "How type is confirmed.", "findings": [ { "id": "markers-finding", "name": "Markers", "description": "Markers used.", "questions": [ { "text": "Which markers confirm the type?", "kind": "measurement" }, { "text": "How reliable is that identification?", "kind": "measurement" } ] } ] } ] }, { "id": "structure-and-function", "name": "Structure and function", "description": "What it has and does.", "rationale": "Structure explains function.", "layers": [ { "id": "structure", "name": "Structure", "description": "Membrane and organelles.", "findings": [ { "id": "structure-finding", "name": "Structure", "description": "Structures present.", "questions": [ { "text": "Which structures does it have?", "kind": "definition" }, { "text": "How large is it?", "kind": "measurement" } ] } ] }, { "id": "function", "name": "Function", "description": "Role in the organism.", "findings": [ { "id": "function-finding", "name": "Function", "description": "What it does.", "questions": [ { "text": "What is its function?", "kind": "definition" }, { "text": "How does it divide or die?", "kind": "definition" } ] } ] } ] }, { "id": "culture-and-research", "name": "Culture and research", "description": "Working with cells.", "rationale": "Cultured cells need authentication and biosafety.", "layers": [ { "id": "culture", "name": "Culture", "description": "Growing cells.", "findings": [ { "id": "culture-finding", "name": "Culture conditions", "description": "Culture conditions.", "questions": [ { "text": "Under what conditions is it cultured?", "kind": "definition" }, { "text": "Has the cell line been authenticated?", "kind": "provenance" } ] } ] }, { "id": "biosafety", "name": "Biosafety", "description": "Containment.", "findings": [ { "id": "biosafety-finding", "name": "Biosafety level", "description": "Required containment.", "questions": [ { "text": "Which biosafety level applies?", "kind": "boundary" }, { "text": "Could it carry pathogens?", "kind": "boundary" } ] } ] } ] }, { "id": "ethics-and-medicine", "name": "Ethics and medicine", "description": "Human cells and therapy.", "rationale": "Human cells raise consent and regulatory questions.", "layers": [ { "id": "consent", "name": "Consent", "description": "Donor consent.", "findings": [ { "id": "consent-finding", "name": "Consent", "description": "Consent for human cells.", "questions": [ { "text": "Was donor consent obtained, and for what uses?", "kind": "provenance" }, { "text": "Is the donor identity protected?", "kind": "boundary" } ] } ] }, { "id": "therapy", "name": "Therapy", "description": "Cell therapies.", "findings": [ { "id": "therapy-finding", "name": "Therapy status", "description": "Regulatory status.", "questions": [ { "text": "Is a cell therapy approved, or experimental?", "kind": "provenance" }, { "text": "Where should people get reliable information?", "kind": "action" } ] } ] } ] } ] }, "openQuestions": [ "Should cell types be separate entries using the Cell Ontology?", "How should cell lines be linked to Cellosaurus?", "The registry entry has merged aliases such as roe and silkworm seed; should they be split off?" ], "statistics": { "bundles": 4, "layers": 8, "findings": 8, "questions": 16 } }, "draft": { "generator": "vr.draft.v3", "status": "draft-generated", "researched": false, "archetype": "abstract concept", "method": "Written from the archetype playbook - what this kind of thing needs beyond identity and provenance - and from the structure that recurred across 6,333 models already researched by two engines. Applied to this entry by rule. No source was read for this thing and no claim here is researched.", "facetsInferred": false, "nextPass": "A researcher replaces this draft with a sourced specification. Treat every sentence below as a proposal to argue with.", "purpose": "Give an agent a durable, checkable way to recognise a cell, record what state it is in, and decide what may be done with it.", "whatItIs": "(biology) the basic structural and functional unit of all organisms; they may exist as independent units of life (as in monads) or may form colonies or tissues as in higher plants and animals", "characteristics": { "substance": "abstract", "origin": "conceptual", "agency": "inert" }, "whatYouCanDoWithIt": [ "observed and measured" ], "distinguishingFeatures": [ "Names folded into this entry, which a task may need to split apart again: recombinant, blastomere, egg, nit, spawn, roe, silkworm seed, flagellated cell, choanocyte, collar cell, fiber, fibre.", "133 finer distinctions are held as aliases rather than separate entries, because telling them apart needs a task that asks for it." ], "openQuestionsForResearch": [ "Which of the bundles below does a real task actually need, and which are ceremony?", "What does this thing have that the facets do not capture at all?", "Which neighbouring kind is most often confused with a cell, and on what evidence are they told apart?" ], "whatItIsMadeOf": "an abstraction with no physical instance", "physicalCharacter": [ "Does nothing on its own; everything it does, something else did to it." ], "whatCanBeDoneWithIt": [ "observe it, measure it, record its state" ], "howItIsRecognised": [ "Nothing to see. What is recognised is an instance of it, and which instances count is exactly what is argued about." ], "relatedModels": [ { "relation": "covers", "note": "Finer kinds folded into this entry because telling them apart needs a task that asks for it. Each is a model waiting to be split out when one does.", "targets": [ "recombinant", "blastomere", "egg", "nit", "spawn", "roe", "silkworm seed", "flagellated cell", "choanocyte", "collar cell", "fiber", "fibre" ] } ], "standing": "133 finer distinctions are held inside this entry as names rather than as separate models.", "structure": { "bundles": [ { "id": "identity-and-classification", "name": "Identity, naming and classification", "description": "How an agent tells one cell from another, and a cell from things that resemble it.", "rationale": "Recognition comes before every other claim. Without stable identity nothing else in the model can be trusted to be about the same thing twice.", "layers": [ { "id": "naming-and-identifiers", "name": "Names and identifiers", "description": "The names this thing goes by and the identifiers that survive translation and time.", "findings": [ { "id": "preferred-name-and-aliases", "name": "Preferred name, aliases and local names", "description": "Which name to use, which names mean the same thing, and which merely sound similar.", "questions": [ { "id": "preferred-name-and-aliases-q01", "text": "What identifies and describes the name of a cell, and in what units or vocabulary?", "kind": "definition", "answer_data": [ "identifiers", "types and classes", "values with units", "explicit unknowns" ] }, { "id": "preferred-name-and-aliases-q02", "text": "Who or what asserted this about the name of a cell, by which method, and when was it true?", "kind": "provenance", "answer_data": [ "authority", "method", "evidence", "event time", "knowledge time" ] }, { "id": "preferred-name-and-aliases-q03", "text": "What may an agent decide or do once the name of a cell is known, and what must it refuse?", "kind": "action", "answer_data": [ "permitted actions", "preconditions", "refusals", "escalation" ] } ] }, { "id": "stable-identifiers", "name": "Stable identifiers and external keys", "description": "Identifiers that keep pointing at this kind of thing across systems and languages.", "questions": [ { "id": "stable-identifiers-q01", "text": "What identifies and describes an identifier for a cell, and in what units or vocabulary?", "kind": "definition", "answer_data": [ "identifiers", "types and classes", "values with units", "explicit unknowns" ] }, { "id": "stable-identifiers-q02", "text": "Who or what asserted this about an identifier for a cell, by which method, and when was it true?", "kind": "provenance", "answer_data": [ "authority", "method", "evidence", "event time", "knowledge time" ] }, { "id": "stable-identifiers-q03", "text": "What may an agent decide or do once an identifier for a cell is known, and what must it refuse?", "kind": "action", "answer_data": [ "permitted actions", "preconditions", "refusals", "escalation" ] } ] } ] }, { "id": "classification-and-granularity", "name": "Classification and granularity", "description": "Where a cell sits among kinds, and how finely a task needs to cut it.", "findings": [ { "id": "kind-and-parents", "name": "Kind, parents and neighbouring kinds", "description": "The classes this thing belongs to and the ones it is next to.", "questions": [ { "id": "kind-and-parents-q01", "text": "What identifies and describes the kind of a cell, and in what units or vocabulary?", "kind": "definition", "answer_data": [ "identifiers", "types and classes", "values with units", "explicit unknowns" ] }, { "id": "kind-and-parents-q02", "text": "Who or what asserted this about the kind of a cell, by which method, and when was it true?", "kind": "provenance", "answer_data": [ "authority", "method", "evidence", "event time", "knowledge time" ] }, { "id": "kind-and-parents-q03", "text": "What may an agent decide or do once the kind of a cell is known, and what must it refuse?", "kind": "action", "answer_data": [ "permitted actions", "preconditions", "refusals", "escalation" ] } ] }, { "id": "distinguishing-features", "name": "Distinguishing features", "description": "What separates a cell from the things most often confused with it.", "questions": [ { "id": "distinguishing-features-q01", "text": "What identifies and describes what distinguishes a cell, and in what units or vocabulary?", "kind": "definition", "answer_data": [ "identifiers", "types and classes", "values with units", "explicit unknowns" ] }, { "id": "distinguishing-features-q02", "text": "Who or what asserted this about what distinguishes a cell, by which method, and when was it true?", "kind": "provenance", "answer_data": [ "authority", "method", "evidence", "event time", "knowledge time" ] }, { "id": "distinguishing-features-q03", "text": "What may an agent decide or do once what distinguishes a cell is known, and what must it refuse?", "kind": "action", "answer_data": [ "permitted actions", "preconditions", "refusals", "escalation" ] } ] } ] } ] }, { "id": "state-and-lifecycle", "name": "State and lifecycle", "description": "The states a cell passes through and the events that move it between them.", "rationale": "Most decisions about a thing depend on what state it is in now, which is a claim with a time on it, not a property.", "layers": [ { "id": "lifecycle-stages", "name": "Lifecycle stages", "description": "From coming into existence to ceasing to be one of these.", "findings": [ { "id": "stages-and-transitions", "name": "Stages and transitions", "description": "The stages worth naming and what moves a cell between them.", "questions": [ { "id": "stages-and-transitions-q01", "text": "What identifies and describes the lifecycle of a cell, and in what units or vocabulary?", "kind": "definition", "answer_data": [ "identifiers", "types and classes", "values with units", "explicit unknowns" ] }, { "id": "stages-and-transitions-q02", "text": "Who or what asserted this about the lifecycle of a cell, by which method, and when was it true?", "kind": "provenance", "answer_data": [ "authority", "method", "evidence", "event time", "knowledge time" ] }, { "id": "stages-and-transitions-q03", "text": "What may an agent decide or do once the lifecycle of a cell is known, and what must it refuse?", "kind": "action", "answer_data": [ "permitted actions", "preconditions", "refusals", "escalation" ] } ] } ] }, { "id": "observations-and-status", "name": "Observations and current status", "description": "What is observed about a cell, how often and by whom.", "findings": [ { "id": "observation-record", "name": "Observation record", "description": "How an observation of a cell is recorded so that it can be superseded rather than overwritten.", "questions": [ { "id": "observation-record-q01", "text": "What identifies and describes an observation of a cell, and in what units or vocabulary?", "kind": "definition", "answer_data": [ "identifiers", "types and classes", "values with units", "explicit unknowns" ] }, { "id": "observation-record-q02", "text": "Who or what asserted this about an observation of a cell, by which method, and when was it true?", "kind": "provenance", "answer_data": [ "authority", "method", "evidence", "event time", "knowledge time" ] }, { "id": "observation-record-q03", "text": "What may an agent decide or do once an observation of a cell is known, and what must it refuse?", "kind": "action", "answer_data": [ "permitted actions", "preconditions", "refusals", "escalation" ] } ] } ] } ] }, { "id": "definitions-in-contest", "name": "Definitions and who holds them", "description": "What cell is taken to mean, and by whom.", "rationale": "When a field disagrees about a concept, the disagreement is the content. A model that picks one definition silently destroys the information.", "layers": [ { "id": "competing-definitions", "name": "Competing definitions", "description": "The main readings and the traditions behind them.", "findings": [ { "id": "definition-map", "name": "Definitions and their holders", "description": "Each definition with the school or body that holds it.", "questions": [ { "id": "definition-map-q01", "text": "Which definitions of cell are in use, and which tradition or body holds each?", "kind": "definition" }, { "id": "definition-map-q02", "text": "What turns on the difference between them in practice?", "kind": "boundary" } ] } ] }, { "id": "operationalisation", "name": "Operationalisation", "description": "How it is measured or applied when it has to be.", "findings": [ { "id": "operational-record", "name": "Measures and proxies", "description": "Instruments and indicators used to stand in for it.", "questions": [ { "id": "operational-record-q01", "text": "How is cell operationalised or measured in practice, and by what instrument?", "kind": "measurement" }, { "id": "operational-record-q02", "text": "What does that operationalisation leave out, and when does that matter?", "kind": "boundary" } ] } ] } ] }, { "id": "instances-and-use", "name": "Instances, use and consequence", "description": "What counts as an instance of cell and what follows from calling something that.", "rationale": "Applying a concept is an act with consequences, so a model must say what the label licenses and what it does not.", "layers": [ { "id": "instances", "name": "What counts as an instance", "description": "Clear cases, borderline cases and non-cases.", "findings": [ { "id": "instance-tests", "name": "Tests for an instance", "description": "What would settle whether something falls under it.", "questions": [ { "id": "instance-tests-q01", "text": "What would settle whether something is an instance of cell?", "kind": "boundary" }, { "id": "instance-tests-q02", "text": "Which borderline cases are argued about, and on what grounds?", "kind": "definition" } ] } ] }, { "id": "consequence", "name": "Consequence of application", "description": "Rights, duties or decisions that follow from the label.", "findings": [ { "id": "consequence-record", "name": "What the label licenses", "description": "What an agent may do once something is classified this way.", "questions": [ { "id": "consequence-record-q01", "text": "What follows practically once something is treated as cell?", "kind": "action" }, { "id": "consequence-record-q02", "text": "What must an agent not infer from the label alone?", "kind": "action" } ] } ] } ] }, { "id": "provenance-and-evidence", "name": "Provenance, evidence and time", "description": "Where every claim about a cell came from and when it held.", "rationale": "A claim without a source and a time cannot be superseded, only overwritten, and an agent that overwrites loses the ability to explain itself.", "layers": [ { "id": "source-and-authority", "name": "Source and authority", "description": "Who said it, on what evidence, and how strongly.", "findings": [ { "id": "claim-provenance", "name": "Claim provenance and confidence", "description": "The authority behind each claim about a cell and how confident it is.", "questions": [ { "id": "claim-provenance-q01", "text": "What identifies and describes a claim about a cell, and in what units or vocabulary?", "kind": "definition", "answer_data": [ "identifiers", "types and classes", "values with units", "explicit unknowns" ] }, { "id": "claim-provenance-q02", "text": "Who or what asserted this about a claim about a cell, by which method, and when was it true?", "kind": "provenance", "answer_data": [ "authority", "method", "evidence", "event time", "knowledge time" ] }, { "id": "claim-provenance-q03", "text": "What may an agent decide or do once a claim about a cell is known, and what must it refuse?", "kind": "action", "answer_data": [ "permitted actions", "preconditions", "refusals", "escalation" ] } ] } ] }, { "id": "time-and-versions", "name": "Time, versions and supersession", "description": "When a claim was true, when it was learnt, and what replaced it.", "findings": [ { "id": "validity-and-supersession", "name": "Validity period and supersession", "description": "How an old claim about a cell is retired without being erased.", "questions": [ { "id": "validity-and-supersession-q01", "text": "What identifies and describes the validity of a claim about a cell, and in what units or vocabulary?", "kind": "definition", "answer_data": [ "identifiers", "types and classes", "values with units", "explicit unknowns" ] }, { "id": "validity-and-supersession-q02", "text": "Who or what asserted this about the validity of a claim about a cell, by which method, and when was it true?", "kind": "provenance", "answer_data": [ "authority", "method", "evidence", "event time", "knowledge time" ] }, { "id": "validity-and-supersession-q03", "text": "What may an agent decide or do once the validity of a claim about a cell is known, and what must it refuse?", "kind": "action", "answer_data": [ "permitted actions", "preconditions", "refusals", "escalation" ] } ] } ] } ] } ] }, "statistics": { "bundles": 5, "layers": 10, "findings": 12, "questions": 32 } } } }