{ "model": { "rank": 4128, "code": "thing-q104053", "model_id": "vr.tr.phenotype", "name": "phenotype", "purpose": "Let an agent explain phenotype and its relation to genotype and environment, describe how phenotypes are measured and classified, relate phenotype to medicine and breeding in general terms, and support learning in genetics.", "family": "Thing Registry", "category": "Cross-cutting context", "status": "research-draft", "kind": "thing", "plane": "XCT", "domain": "XCT.QLT", "industry": "", "version": "", "url": "/models/thing/q104053/", "tier": 2, "score": 78, "payload": { "layer": "wikidata", "aliases": [ "Familial sleep traits", "eye color determined by the player", "Gombo syndrome", "genetic endocrine growth disease", "molecular phenotype", "behavioral phenotype", "multicellularity", "anoxia tolerance", "cytotype", "hydraulic trait", "reproductive trait", "unicellularity", "wild type", "natural competence", "endophenotype", "prototrophy", "eye color", "Pollination syndrome", "cold hardiness", "eggshell", "auxotrophy", "spandrel", "senescence-associated secretory phenotype", "diazotrophy", "Norms of reaction", "color changing eyes", "broad autism phenotype", "growth disorder" ], "aliasCount": 28, "merged": 29, "knownIn": 78, "facets": null, "markers": [], "lexicalClass": "", "senseRank": null, "alsoRegisteredAs": null, "source": { "dataset": "wikidata", "item": "Q104053", "url": "https://www.wikidata.org/wiki/Q104053", "license": "CC0 1.0" } }, "research": { "vercy": "1.0-draft", "publication": { "status": "research-draft", "adjudicationStatus": "unreviewed", "publishableCanonical": false, "generatedAt": "2026-09-12T03:00:55Z", "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": 2, "engine": "claude" }, "metaModel": { "id": "THING-Q104053", "registryId": "vr.tr.phenotype", "name": "phenotype", "version": "0.2.0-wave.2", "entryKind": "thing", "family": "Thing Registry", "domain": [ "XCT.QLT" ], "status": "research-draft" }, "canonicalUrl": "https://ver.cy/models/thing/q104053/", "model": { "registry_id": "vr.tr.phenotype", "name": "phenotype", "purpose": "Let an agent explain phenotype and its relation to genotype and environment, describe how phenotypes are measured and classified, relate phenotype to medicine and breeding in general terms, and support learning in genetics.", "definition": "The set of observable characteristics of an organism, including morphology, physiology, behaviour and molecular traits, resulting from the interaction of its genotype with the environment, and used in genetics, medicine and breeding to describe traits from eye colour and sleep patterns to disease syndromes and cellular molecular profiles; phenotypes are described with standardised ontologies and are the basis for linking genes to traits.", "what_it_is_for": "Observable traits of an organism.", "affordances": [ "explain phenotype and genotype", "describe measurement and classification", "relate to medicine and breeding", "support learning" ], "distinguishing_features": [ "Observable", "Genotype-environment product", "Multi-level", "Ontology-described" ], "appearance": "Not physical as a concept; observed traits of organisms.", "visual_identification": [ "Observable characteristics", "Genotype plus environment", "Genotype is the genetic makeup; a trait is a single characteristic" ], "physical_properties": [], "families_and_kinds": [ "morphological phenotypes", "physiological and molecular phenotypes", "behavioural phenotypes", "clinical phenotypes and syndromes", "phenotypes in breeding and agriculture" ], "related_models": [ { "relation": "is a kind of", "target": "quality", "why": "category" }, { "relation": "is related to", "target": "Ehlers-Danlos syndrome", "why": "a clinical phenotype" }, { "relation": "is related to", "target": "speciation", "why": "phenotypic divergence" }, { "relation": "is related to", "target": "male", "why": "sex as a phenotypic category" } ], "identifiers": [], "standards_and_regulation": [ "Phenotype ontologies such as the Human Phenotype Ontology", "Clinical classification standards", "Breeding and variety registration standards" ], "failure_modes_and_hazards": [ "Genetic determinism", "Agents interpreting personal genetic results", "Confusing phenotype with genotype" ], "in_scope": [], "out_of_scope": [], "characteristics": [] }, "sources": [], "structure": { "bundles": [ { "id": "understand", "name": "Understand", "description": "What phenotype is.", "rationale": "Genetics.", "layers": [ { "id": "concept", "name": "Concept", "description": "Concept.", "findings": [ { "id": "concept-finding", "name": "Concept", "description": "Concept.", "questions": [ { "text": "What is a phenotype, and how do genotype, environment and their interaction produce it?", "kind": "definition" }, { "text": "Which level of phenotype is meant?", "kind": "boundary" } ] } ] }, { "id": "levels", "name": "Levels", "description": "Levels of phenotype.", "findings": [ { "id": "levels-finding", "name": "Levels", "description": "Levels.", "questions": [ { "text": "How do morphological, physiological, molecular and behavioural phenotypes differ?", "kind": "definition" }, { "text": "Which entry fits a specific trait?", "kind": "action" } ] } ] } ] }, { "id": "measure", "name": "Measure", "description": "Measurement and classification.", "rationale": "Practice.", "layers": [ { "id": "phenotyping", "name": "Phenotyping", "description": "Phenotyping.", "findings": [ { "id": "phenotyping-finding", "name": "Phenotyping", "description": "Phenotyping.", "questions": [ { "text": "How are phenotypes measured in research, clinics and breeding programmes?", "kind": "provenance" }, { "text": "Which entry fits phenotyping methods?", "kind": "action" } ] } ] }, { "id": "ontologies", "name": "Ontologies", "description": "Ontologies.", "findings": [ { "id": "ontologies-finding", "name": "Ontologies", "description": "Ontologies.", "questions": [ { "text": "How do phenotype ontologies standardise descriptions for research and diagnosis?", "kind": "provenance" }, { "text": "Which entry fits a specific ontology?", "kind": "action" } ] } ] } ] }, { "id": "apply", "name": "Apply", "description": "Applications.", "rationale": "General information.", "layers": [ { "id": "medicine", "name": "Medicine", "description": "Clinical phenotypes.", "findings": [ { "id": "medicine-finding", "name": "Medicine", "description": "Medicine.", "questions": [ { "text": "How are clinical phenotypes used in diagnosis and in linking genes to disease, in general terms?", "kind": "provenance" }, { "text": "Is the user asking about their own genetic results, which need a clinician?", "kind": "boundary" } ] } ] }, { "id": "breeding", "name": "Breeding", "description": "Breeding and evolution.", "findings": [ { "id": "breeding-finding", "name": "Breeding", "description": "Breeding.", "questions": [ { "text": "How are phenotypes used in selective breeding and studied in evolution?", "kind": "provenance" }, { "text": "Which entry fits selective breeding?", "kind": "action" } ] } ] } ] }, { "id": "learn", "name": "Learn", "description": "History and teaching.", "rationale": "Education.", "layers": [ { "id": "history", "name": "History", "description": "History.", "findings": [ { "id": "history-finding", "name": "History", "description": "History.", "questions": [ { "text": "How did the genotype-phenotype distinction develop from Johannsen onward?", "kind": "provenance" }, { "text": "Which references are standard?", "kind": "provenance" } ] } ] }, { "id": "teach", "name": "Teach", "description": "Teaching.", "findings": [ { "id": "teach-finding", "name": "Teach", "description": "Teaching.", "questions": [ { "text": "How can phenotype be taught without genetic determinism?", "kind": "action" }, { "text": "Which misconceptions arise?", "kind": "provenance" } ] } ] } ] } ] }, "openQuestions": [ "Should clinical phenotypes be a separate entry?", "How should ontologies be linked?", "How should genetics resources be linked?" ], "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. This entry carries no facets of its own, so they were inferred from its domain - a guess about a whole domain applied to one thing.", "facetsInferred": true, "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 phenotype, record what state it is in, and decide what may be done with it.", "whatItIs": "Let an agent explain phenotype and its relation to genotype and environment, describe how phenotypes are measured and classified, relate phenotype to medicine and breeding in general terms, and support learning in genetics.", "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: Familial sleep traits, eye color determined by the player, Gombo syndrome, genetic endocrine growth disease, molecular phenotype, behavioral phenotype, multicellularity, anoxia tolerance, cytotype, hydraulic trait, reproductive trait, unicellularity.", "29 finer distinctions are held as aliases rather than separate entries, because telling them apart needs a task that asks for it.", "Described in 78 Wikipedia languages, which is a measure of how widely the thing is known, not of how important it is." ], "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 phenotype, 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.", "These come from the domain this entry sits in rather than from the entry itself, so treat them as a first guess about the whole domain applied to one thing." ], "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": [ "Familial sleep traits", "eye color determined by the player", "Gombo syndrome", "genetic endocrine growth disease", "molecular phenotype", "behavioral phenotype", "multicellularity", "anoxia tolerance", "cytotype", "hydraulic trait", "reproductive trait", "unicellularity" ] } ], "standing": "Described in 78 Wikipedia languages, which measures how widely it is written about rather than how important or how common it is. 29 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 phenotype from another, and a phenotype 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 phenotype, 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 phenotype, 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 phenotype 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 phenotype, 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 phenotype, 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 phenotype 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 phenotype 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 phenotype, 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 phenotype, 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 phenotype 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 phenotype from the things most often confused with it.", "questions": [ { "id": "distinguishing-features-q01", "text": "What identifies and describes what distinguishes a phenotype, 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 phenotype, 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 phenotype 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 phenotype 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 phenotype between them.", "questions": [ { "id": "stages-and-transitions-q01", "text": "What identifies and describes the lifecycle of a phenotype, 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 phenotype, 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 phenotype 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 phenotype, how often and by whom.", "findings": [ { "id": "observation-record", "name": "Observation record", "description": "How an observation of a phenotype 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 phenotype, 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 phenotype, 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 phenotype 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 phenotype 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 phenotype 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 phenotype 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 phenotype 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 phenotype?", "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 phenotype?", "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 phenotype 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 phenotype and how confident it is.", "questions": [ { "id": "claim-provenance-q01", "text": "What identifies and describes a claim about a phenotype, 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 phenotype, 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 phenotype 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 phenotype is retired without being erased.", "questions": [ { "id": "validity-and-supersession-q01", "text": "What identifies and describes the validity of a claim about a phenotype, 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 phenotype, 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 phenotype 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 } } } }