{ "model": { "rank": 2929, "code": "thing-q42918", "model_id": "vr.tr.mutation", "name": "mutation", "purpose": "Let an agent handle mutations by type, location, effect and evidence, with standard nomenclature, and avoid giving individual genetic advice.", "family": "Thing Registry", "category": "Activities and processes", "status": "research-draft", "kind": "thing", "plane": "ACT", "domain": "ACT.PRC", "industry": "", "version": "", "url": "/models/thing/q42918/", "tier": 2, "score": 94, "payload": { "layer": "wikidata", "aliases": [ "conserved signature indels", "gain of function", "random mutation", "DNA mutation", "Soft selective sweep", "spontaneous mutation", "beneficial mutation", "harmful mutation", "gene loss", "deleterious mutation", "founder mutation", "Transversion", "parthenocarpy", "point mutation", "frameshift mutation", "copy-number variation", "single gene mutation", "indel", "loss of function mutation", "insertion mutation", "driver mutation", "paramutation", "Revertant", "somatic mutation", "truncating mutation", "de novo mutation", "chromosomal rearrangement", "Induced mutation", "neutral mutation", "adaptive mutation", "germline mutation", "allelic imbalance", "trinucleotide repeat expansion", "sequence inversion", "sequence deletion", "base pair mismatch", "genetic suppression", "petite mutation", "gene duplication", "Synonymous substitution" ], "aliasCount": 138, "merged": 138, "knownIn": 94, "facets": null, "markers": [], "lexicalClass": "", "senseRank": null, "alsoRegisteredAs": null, "source": { "dataset": "wikidata", "item": "Q42918", "url": "https://www.wikidata.org/wiki/Q42918", "license": "CC0 1.0" } }, "research": { "vercy": "1.0-draft", "publication": { "status": "research-draft", "adjudicationStatus": "unreviewed", "publishableCanonical": false, "generatedAt": "2026-09-11T05:41:45Z", "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-Q42918", "registryId": "vr.tr.mutation", "name": "mutation", "version": "0.2.0-wave.1", "entryKind": "thing", "family": "Thing Registry", "domain": [ "ACT.PRC" ], "status": "research-draft" }, "canonicalUrl": "https://ver.cy/models/thing/q42918/", "model": { "registry_id": "vr.tr.mutation", "name": "mutation", "purpose": "Let an agent handle mutations by type, location, effect and evidence, with standard nomenclature, and avoid giving individual genetic advice.", "definition": "A change in the nucleotide sequence of an organism genome, arising spontaneously or from mutagens, ranging from single-base substitutions to insertions, deletions and larger rearrangements.", "what_it_is_for": "Mutations drive evolution and cause or influence many diseases; they are studied in genetics and medicine.", "affordances": [ "detect it, by sequencing", "name it, with HGVS nomenclature", "interpret its effect, with evidence", "study its evolutionary role" ], "distinguishing_features": [ "Change in DNA sequence", "Germline or somatic", "Effects range from none to severe", "Interpretation requires evidence and expert review" ], "appearance": "Not visible directly; seen as differences in sequence data or as traits.", "visual_identification": [ "Variant notation such as c.1521_1523del", "Sequence alignments showing differences", "Classifications such as pathogenic or benign" ], "physical_properties": [], "families_and_kinds": [ "point mutations", "insertions and deletions (indels)", "copy number variants", "structural rearrangements", "gain-of-function and loss-of-function mutations" ], "related_models": [ { "relation": "changes", "target": "DNA and protein", "why": "molecules" }, { "relation": "drives", "target": "evolution", "why": "variation" }, { "relation": "can cause", "target": "disease", "why": "genetic disease" }, { "relation": "is a kind of", "target": "sequence variant", "why": "variation" } ], "identifiers": [ { "scheme": "HGVS notation", "value_or_pattern": "for example NM_000492.4:c.1521_1523del", "note": "standard variant description" }, { "scheme": "ClinVar id", "value_or_pattern": "numeric", "note": "clinical interpretations" }, { "scheme": "dbSNP rs id", "value_or_pattern": "rs plus digits", "note": "variants" } ], "standards_and_regulation": [ "HGVS nomenclature", "ACMG/AMP variant classification guidelines", "Genetic data protection law" ], "failure_modes_and_hazards": [ "Over-interpreting variants of uncertain significance", "Individual genetic advice without a genetic counsellor", "Genetic discrimination" ], "in_scope": [], "out_of_scope": [], "characteristics": [] }, "sources": [], "structure": { "bundles": [ { "id": "description", "name": "Description", "description": "What changed.", "rationale": "Standard notation avoids ambiguity.", "layers": [ { "id": "notation", "name": "Notation", "description": "HGVS.", "findings": [ { "id": "notation-finding", "name": "Notation", "description": "Variant notation.", "questions": [ { "text": "What is the HGVS description, on which reference sequence?", "kind": "provenance" }, { "text": "Which gene is affected?", "kind": "definition" } ] } ] }, { "id": "type", "name": "Type", "description": "Substitution, indel.", "findings": [ { "id": "type-finding", "name": "Type", "description": "Variant type.", "questions": [ { "text": "What type of mutation is it?", "kind": "definition" }, { "text": "Is it germline or somatic?", "kind": "definition" } ] } ] } ] }, { "id": "effect", "name": "Effect", "description": "What it does.", "rationale": "Effect needs evidence.", "layers": [ { "id": "molecular", "name": "Molecular effect", "description": "On protein.", "findings": [ { "id": "molecular-finding", "name": "Molecular effect", "description": "Effect on product.", "questions": [ { "text": "What does it do to the gene product?", "kind": "definition" }, { "text": "How is that known?", "kind": "provenance" } ] } ] }, { "id": "clinical", "name": "Clinical significance", "description": "Classification.", "findings": [ { "id": "clinical-finding", "name": "Classification", "description": "Clinical classification.", "questions": [ { "text": "How is it classified, by which lab or database?", "kind": "provenance" }, { "text": "Has the classification changed?", "kind": "provenance" } ] } ] } ] }, { "id": "origin", "name": "Origin", "description": "How it arose.", "rationale": "Origin informs inheritance.", "layers": [ { "id": "cause", "name": "Cause", "description": "Spontaneous or induced.", "findings": [ { "id": "cause-finding", "name": "Cause", "description": "Cause.", "questions": [ { "text": "How did it arise?", "kind": "definition" }, { "text": "Is it inherited?", "kind": "boundary" } ] } ] }, { "id": "frequency", "name": "Frequency", "description": "Population.", "findings": [ { "id": "frequency-finding", "name": "Frequency", "description": "Population frequency.", "questions": [ { "text": "How common is it in populations, according to gnomAD or similar?", "kind": "measurement" }, { "text": "Which populations?", "kind": "boundary" } ] } ] } ] }, { "id": "handling", "name": "Handling", "description": "Advice and privacy.", "rationale": "Genetic information is sensitive.", "layers": [ { "id": "counselling", "name": "Counselling", "description": "Professional advice.", "findings": [ { "id": "counselling-finding", "name": "Referral", "description": "When to refer.", "questions": [ { "text": "Should the person be referred to genetic counselling?", "kind": "action" }, { "text": "What can the agent say in general terms?", "kind": "boundary" } ] } ] }, { "id": "privacy", "name": "Privacy", "description": "Genetic data.", "findings": [ { "id": "privacy-finding", "name": "Privacy", "description": "Genetic data rules.", "questions": [ { "text": "Is genetic data being shared lawfully?", "kind": "boundary" }, { "text": "Who else might be affected, such as relatives?", "kind": "boundary" } ] } ] } ] } ] }, "openQuestions": [ "Should variants be instances with HGVS and ClinVar ids?", "How should classification changes over time be recorded?", "How should agents direct people to genetic counselling?" ], "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 mutation, record what state it is in, and decide what may be done with it.", "whatItIs": "Let an agent handle mutations by type, location, effect and evidence, with standard nomenclature, and avoid giving individual genetic advice.", "characteristics": { "substance": "activity", "origin": "conceptual", "agency": "inert" }, "whatYouCanDoWithIt": [ "observed and measured" ], "distinguishingFeatures": [ "Names folded into this entry, which a task may need to split apart again: conserved signature indels, gain of function, random mutation, DNA mutation, Soft selective sweep, spontaneous mutation, beneficial mutation, harmful mutation, gene loss, deleterious mutation, founder mutation, Transversion.", "138 finer distinctions are held as aliases rather than separate entries, because telling them apart needs a task that asks for it.", "Described in 94 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 mutation, and on what evidence are they told apart?" ], "whatItIsMadeOf": "something that happens over time", "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": [ "conserved signature indels", "gain of function", "random mutation", "DNA mutation", "Soft selective sweep", "spontaneous mutation", "beneficial mutation", "harmful mutation", "gene loss", "deleterious mutation", "founder mutation", "Transversion" ] } ], "standing": "Described in 94 Wikipedia languages, which measures how widely it is written about rather than how important or how common it is. 138 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 mutation from another, and a mutation 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 mutation, 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 mutation, 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 mutation 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 mutation, 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 mutation, 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 mutation 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 mutation 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 mutation, 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 mutation, 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 mutation 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 mutation from the things most often confused with it.", "questions": [ { "id": "distinguishing-features-q01", "text": "What identifies and describes what distinguishes a mutation, 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 mutation, 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 mutation 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 mutation 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 mutation between them.", "questions": [ { "id": "stages-and-transitions-q01", "text": "What identifies and describes the lifecycle of a mutation, 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 mutation, 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 mutation 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 mutation, how often and by whom.", "findings": [ { "id": "observation-record", "name": "Observation record", "description": "How an observation of a mutation 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 mutation, 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 mutation, 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 mutation is known, and what must it refuse?", "kind": "action", "answer_data": [ "permitted actions", "preconditions", "refusals", "escalation" ] } ] } ] } ] }, { "id": "process-and-outcome", "name": "Process, inputs and outcome", "description": "How a mutation proceeds, what it needs and what it leaves behind.", "rationale": "An activity is known by its steps and its results, and both have to be recordable while it is still running.", "layers": [ { "id": "steps-and-sequence", "name": "Steps and sequence", "description": "The steps of a mutation, their order and what may run in parallel.", "findings": [ { "id": "steps-and-preconditions", "name": "Steps, preconditions and completion", "description": "What has to be true before each step of a mutation and what marks it done.", "questions": [ { "id": "steps-and-preconditions-q01", "text": "What identifies and describes a step of a mutation, and in what units or vocabulary?", "kind": "definition", "answer_data": [ "identifiers", "types and classes", "values with units", "explicit unknowns" ] }, { "id": "steps-and-preconditions-q02", "text": "Who or what asserted this about a step of a mutation, by which method, and when was it true?", "kind": "provenance", "answer_data": [ "authority", "method", "evidence", "event time", "knowledge time" ] }, { "id": "steps-and-preconditions-q03", "text": "What may an agent decide or do once a step of a mutation is known, and what must it refuse?", "kind": "action", "answer_data": [ "permitted actions", "preconditions", "refusals", "escalation" ] } ] } ] }, { "id": "inputs-and-results", "name": "Inputs, resources and results", "description": "What a mutation consumes and what it produces.", "findings": [ { "id": "inputs-and-outputs", "name": "Inputs, outputs and side effects", "description": "The resources a mutation takes and the results it leaves, wanted or not.", "questions": [ { "id": "inputs-and-outputs-q01", "text": "What identifies and describes the inputs and results of a mutation, and in what units or vocabulary?", "kind": "definition", "answer_data": [ "identifiers", "types and classes", "values with units", "explicit unknowns" ] }, { "id": "inputs-and-outputs-q02", "text": "Who or what asserted this about the inputs and results of a mutation, by which method, and when was it true?", "kind": "provenance", "answer_data": [ "authority", "method", "evidence", "event time", "knowledge time" ] }, { "id": "inputs-and-outputs-q03", "text": "What may an agent decide or do once the inputs and results of a mutation 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 mutation 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 mutation 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 mutation 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 mutation 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 mutation?", "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 mutation?", "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 mutation 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 mutation and how confident it is.", "questions": [ { "id": "claim-provenance-q01", "text": "What identifies and describes a claim about a mutation, 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 mutation, 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 mutation 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 mutation is retired without being erased.", "questions": [ { "id": "validity-and-supersession-q01", "text": "What identifies and describes the validity of a claim about a mutation, 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 mutation, 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 mutation is known, and what must it refuse?", "kind": "action", "answer_data": [ "permitted actions", "preconditions", "refusals", "escalation" ] } ] } ] } ] } ] }, "statistics": { "bundles": 6, "layers": 12, "findings": 14, "questions": 38 } } } }