{ "model": { "rank": 16234, "code": "thing-q387981", "model_id": "vr.tr.allele-frequency", "name": "allele frequency", "purpose": "Let an agent explain allele frequency and how it is estimated and changes, compute frequencies and Hardy-Weinberg expectations, and apply the concept to evolution, conservation and resistance management.", "family": "Thing Registry", "category": "Cross-cutting context", "status": "research-draft", "kind": "thing", "plane": "XCT", "domain": "XCT.QTY", "industry": "", "version": "", "url": "/models/thing/q387981/", "tier": 2, "score": 32, "payload": { "layer": "wikidata", "aliases": [ "resistance allele frequency" ], "aliasCount": 1, "merged": 1, "knownIn": 32, "facets": null, "markers": [], "lexicalClass": "", "senseRank": null, "alsoRegisteredAs": null, "source": { "dataset": "wikidata", "item": "Q387981", "url": "https://www.wikidata.org/wiki/Q387981", "license": "CC0 1.0" } }, "research": { "vercy": "1.0-draft", "publication": { "status": "research-draft", "adjudicationStatus": "unreviewed", "publishableCanonical": false, "generatedAt": "2026-09-11T22:44:49Z", "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-Q387981", "registryId": "vr.tr.allele-frequency", "name": "allele frequency", "version": "0.2.0-wave.2", "entryKind": "thing", "family": "Thing Registry", "domain": [ "XCT.QTY" ], "status": "research-draft" }, "canonicalUrl": "https://ver.cy/models/thing/q387981/", "model": { "registry_id": "vr.tr.allele-frequency", "name": "allele frequency", "purpose": "Let an agent explain allele frequency and how it is estimated and changes, compute frequencies and Hardy-Weinberg expectations, and apply the concept to evolution, conservation and resistance management.", "definition": "The proportion of copies of a particular allele among all copies of a gene in a population, ranging from zero to one, used in population genetics to describe genetic variation and to track evolutionary change through selection, drift, mutation and migration, including cases such as resistance allele frequencies in pests and pathogens; allele frequencies are estimated from samples and modelled with principles such as Hardy-Weinberg equilibrium.", "what_it_is_for": "Measuring genetic variation in populations.", "affordances": [ "explain allele frequency", "compute frequencies and expectations", "explain evolutionary change", "apply to conservation and resistance" ], "distinguishing_features": [ "Population-level", "Proportion", "Evolution indicator", "Sample-estimated" ], "appearance": "Not physical; proportions in population data.", "visual_identification": [ "Proportion of an allele in a population", "Between zero and one", "Genotype frequency counts individuals, not alleles" ], "physical_properties": [], "families_and_kinds": [ "allele frequencies in natural populations", "resistance allele frequencies", "allele frequencies in human populations", "frequencies under Hardy-Weinberg equilibrium", "frequency changes under selection and drift" ], "related_models": [ { "relation": "is a kind of", "target": "frequency", "why": "category" }, { "relation": "is a kind of", "target": "abundance", "why": "category" }, { "relation": "is related to", "target": "dominance", "why": "allele expression" }, { "relation": "is related to", "target": "relative quantity", "why": "a proportion" } ], "identifiers": [], "standards_and_regulation": [ "Population genetics reporting conventions", "Ethics for human genetic data", "Resistance monitoring programmes" ], "failure_modes_and_hazards": [ "Confusing allele and genotype frequencies", "Small sample bias", "Misuse of human population data for discrimination" ], "in_scope": [], "out_of_scope": [], "characteristics": [] }, "sources": [], "structure": { "bundles": [ { "id": "define", "name": "Define", "description": "What allele frequency is.", "rationale": "Concepts.", "layers": [ { "id": "concept", "name": "Concept", "description": "Definition.", "findings": [ { "id": "concept-finding", "name": "Concept", "description": "Concept.", "questions": [ { "text": "What is allele frequency, and how does it differ from genotype frequency?", "kind": "definition" }, { "text": "How is it estimated from a sample?", "kind": "action" } ] } ] }, { "id": "hardy", "name": "Hardy-Weinberg", "description": "Equilibrium expectations.", "findings": [ { "id": "hardy-finding", "name": "Hardy-Weinberg", "description": "Equilibrium.", "questions": [ { "text": "What genotype frequencies does Hardy-Weinberg equilibrium predict from these allele frequencies, and what assumptions does it make?", "kind": "action" }, { "text": "What does deviation indicate?", "kind": "definition" } ] } ] } ] }, { "id": "change", "name": "Change", "description": "How frequencies change.", "rationale": "Evolution.", "layers": [ { "id": "forces", "name": "Forces", "description": "Evolutionary forces.", "findings": [ { "id": "forces-finding", "name": "Forces", "description": "Forces.", "questions": [ { "text": "How do selection, drift, mutation and migration change allele frequencies over generations?", "kind": "definition" }, { "text": "How is frequency change modelled?", "kind": "definition" } ] } ] }, { "id": "resistance", "name": "Resistance", "description": "Resistance alleles.", "findings": [ { "id": "resistance-finding", "name": "Resistance", "description": "Resistance.", "questions": [ { "text": "How are resistance allele frequencies in pests and pathogens monitored and managed?", "kind": "provenance" }, { "text": "Which strategies slow resistance?", "kind": "provenance" } ] } ] } ] }, { "id": "apply", "name": "Apply", "description": "Applications.", "rationale": "Practice.", "layers": [ { "id": "conservation", "name": "Conservation", "description": "Conservation genetics.", "findings": [ { "id": "conservation-finding", "name": "Conservation", "description": "Conservation.", "questions": [ { "text": "How are allele frequencies used in conservation to assess diversity and inbreeding?", "kind": "provenance" }, { "text": "Which entry fits a specific species?", "kind": "action" } ] } ] }, { "id": "human", "name": "Human", "description": "Human populations.", "findings": [ { "id": "human-finding", "name": "Human", "description": "Human populations.", "questions": [ { "text": "How are allele frequencies used in human genetics, and which ethical safeguards apply?", "kind": "provenance" }, { "text": "Is the presentation free of deterministic or discriminatory framing?", "kind": "boundary" } ] } ] } ] }, { "id": "learn", "name": "Learn", "description": "Teaching and history.", "rationale": "Education.", "layers": [ { "id": "teach", "name": "Teach", "description": "Teaching population genetics.", "findings": [ { "id": "teach-finding", "name": "Teach", "description": "Teaching.", "questions": [ { "text": "How can allele frequency be taught with simulations?", "kind": "action" }, { "text": "Which misconceptions arise?", "kind": "provenance" } ] } ] }, { "id": "history", "name": "History", "description": "History.", "findings": [ { "id": "history-finding", "name": "History", "description": "History.", "questions": [ { "text": "How did population genetics develop the concept from Hardy, Weinberg, Fisher and Wright onward?", "kind": "provenance" }, { "text": "Which references are standard?", "kind": "provenance" } ] } ] } ] } ] }, "openQuestions": [ "Should Hardy-Weinberg be a separate entry?", "How should frequency databases be linked?", "How should ethics guidance be linked?" ], "statistics": { "bundles": 4, "layers": 8, "findings": 8, "questions": 16 } }, "draft": { "generator": "vr.draft.v3", "status": "draft-generated", "researched": false, "archetype": "unit, quantity or measure", "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 allele frequency, record what state it is in, and decide what may be done with it.", "whatItIs": "Let an agent explain allele frequency and how it is estimated and changes, compute frequencies and Hardy-Weinberg expectations, and apply the concept to evolution, conservation and resistance management.", "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: resistance allele frequency.", "1 finer distinctions are held as aliases rather than separate entries, because telling them apart needs a task that asks for it.", "Described in 32 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 allele frequency, 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: a unit is a convention. What is seen is an instrument reading in it." ], "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": [ "resistance allele frequency" ] } ], "standing": "Described in 32 Wikipedia languages, which measures how widely it is written about rather than how important or how common it is. 1 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 allele frequency from another, and a allele frequency 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 allele frequency, 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 allele frequency, 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 allele frequency 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 allele frequency, 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 allele frequency, 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 allele frequency 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 allele frequency 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 allele frequency, 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 allele frequency, 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 allele frequency 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 allele frequency from the things most often confused with it.", "questions": [ { "id": "distinguishing-features-q01", "text": "What identifies and describes what distinguishes a allele frequency, 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 allele frequency, 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 allele frequency 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 allele frequency 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 allele frequency between them.", "questions": [ { "id": "stages-and-transitions-q01", "text": "What identifies and describes the lifecycle of a allele frequency, 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 allele frequency, 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 allele frequency 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 allele frequency, how often and by whom.", "findings": [ { "id": "observation-record", "name": "Observation record", "description": "How an observation of a allele frequency 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 allele frequency, 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 allele frequency, 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 allele frequency is known, and what must it refuse?", "kind": "action", "answer_data": [ "permitted actions", "preconditions", "refusals", "escalation" ] } ] } ] } ] }, { "id": "definition-and-realisation", "name": "Definition, dimension and realisation", "description": "What allele frequency is defined as and how it is realised in practice.", "rationale": "A unit is not the quantity it measures, and its definition has a history that older data still depends on.", "layers": [ { "id": "definition", "name": "Definition and dimension", "description": "The defining relation and the quantity it measures.", "findings": [ { "id": "definition-record", "name": "Definition, body and date", "description": "What defines it now, and what defined it before.", "questions": [ { "id": "definition-record-q01", "text": "How is allele frequency defined, by which body, and since when?", "kind": "definition" }, { "id": "definition-record-q02", "text": "What was the previous definition, and what data still depends on it?", "kind": "provenance" } ] } ] }, { "id": "conversion", "name": "Conversion and compatibility", "description": "Relations to other units, exact or approximate.", "findings": [ { "id": "conversion-record", "name": "Conversions and their exactness", "description": "Factors, and whether each is exact by definition.", "questions": [ { "id": "conversion-record-q01", "text": "What conversions relate allele frequency to other units, and which are exact by definition?", "kind": "measurement" }, { "id": "conversion-record-q02", "text": "Where does rounding a conversion change a decision, and how should that be recorded?", "kind": "action" } ] } ] } ] }, { "id": "provenance-and-evidence", "name": "Provenance, evidence and time", "description": "Where every claim about a allele frequency 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 allele frequency and how confident it is.", "questions": [ { "id": "claim-provenance-q01", "text": "What identifies and describes a claim about a allele frequency, 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 allele frequency, 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 allele frequency 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 allele frequency is retired without being erased.", "questions": [ { "id": "validity-and-supersession-q01", "text": "What identifies and describes the validity of a claim about a allele frequency, 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 allele frequency, 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 allele frequency is known, and what must it refuse?", "kind": "action", "answer_data": [ "permitted actions", "preconditions", "refusals", "escalation" ] } ] } ] } ] } ] }, "statistics": { "bundles": 4, "layers": 8, "findings": 10, "questions": 28 } } } }