{ "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", "enrichment": { "pass": 3, "engine": "claude", "producedAt": "2026-10-05T16:30:00Z", "ingestedAt": "2026-10-05T13:22:02+00:00", "fields": [ "agent_conduct", "ethics", "owners" ] }, "gate": { "passed": true, "version": "1.0", "at": "2026-10-06T19:52:00+00:00", "evidence": [ "completeness 1.00", "sense: Wikidata description", "2 live sources", "review by codex: pass" ] } }, "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": [], "agent_conduct": { "may": [ "Explain mutations in general terms with cited science.", "Report variant data from curated databases, stating clinical significance as classified." ], "must_not": [ "Interpret a person's genetic variants as a diagnosis.", "Disclose a person's genetic data without consent.", "Assist in engineering harmful mutations in pathogens.", "Use genetic variation to rank people." ], "requires_human": [ "Telling a person about a significant genetic finding." ] }, "ethics": { "considerations": [ "Genetic data reveals information about relatives too.", "Genetics has been misused to justify discrimination." ], "affected_parties": [ "Patients", "Relatives", "Research participants" ] }, "owners": { "steward": "Nobody owns a mutation; genetic data belongs to the person it describes.", "master_systems": [ "Genetic variant databases" ] } }, "sources": [ { "id": "wikidata", "title": "Wikidata item Q42918: mutation", "url": "https://www.wikidata.org/wiki/Q42918", "url_status": "live", "what_it_supports": "identity and sense of the item", "checked_by": "wikidata-api" }, { "id": "wikipedia-en", "title": "Wikipedia: Mutation", "url": "https://en.wikipedia.org/wiki/Mutation", "url_status": "live", "what_it_supports": "general description of the item", "checked_by": "wikidata-api sitelink" } ], "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 } }