{ "model": { "rank": 8075, "code": "thing-q210538", "model_id": "vr.tr.dna-repair", "name": "DNA repair", "purpose": "Let an agent explain DNA repair pathways and their biological and medical significance, support learning and research, and provide general information on repair-related conditions without individual medical advice.", "family": "Thing Registry", "category": "Activities and processes", "status": "research-draft", "kind": "thing", "plane": "ACT", "domain": "ACT.PRC", "industry": "", "version": "", "url": "/models/thing/q210538/", "tier": 2, "score": 52, "payload": { "layer": "wikidata", "aliases": [ "translesion synthesis", "photoreactivation", "recombinational DNA repair", "meiotic mismatch repair", "recombinational repair", "protein-DNA covalent cross-linking repair", "base-excision repair", "double-strand break repair", "single strand break repair", "pyrimidine dimer repair", "interstrand cross-link repair", "UV-damage excision repair", "mitochondrial DNA repair", "DNA replication proofreading", "non-photoreactive DNA repair", "viral DNA repair", "nucleotide-excision repair", "DNA mismatch repair", "excision repair", "DNA end-joining repair", "postreplication repair", "pyrimidine dimer repair by nucleotide-excision repair", "transcription-coupled nucleotide-excision repair", "global genome nucleotide-excision repair", "nucleotide-excision repair involved in interstrand cross-link repair", "mismatch repair involved in maintenance of fidelity involved in DNA-dependent DNA replication", "error-free postreplication DNA repair" ], "aliasCount": 27, "merged": 27, "knownIn": 52, "facets": null, "markers": [], "lexicalClass": "", "senseRank": null, "alsoRegisteredAs": null, "source": { "dataset": "wikidata", "item": "Q210538", "url": "https://www.wikidata.org/wiki/Q210538", "license": "CC0 1.0" } }, "research": { "vercy": "1.0-draft", "publication": { "status": "research-draft", "adjudicationStatus": "unreviewed", "publishableCanonical": false, "generatedAt": "2026-09-11T15:52:29Z", "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-Q210538", "registryId": "vr.tr.dna-repair", "name": "DNA repair", "version": "0.2.0-wave.1", "entryKind": "thing", "family": "Thing Registry", "domain": [ "ACT.PRC" ], "status": "research-draft" }, "canonicalUrl": "https://ver.cy/models/thing/q210538/", "model": { "registry_id": "vr.tr.dna-repair", "name": "DNA repair", "purpose": "Let an agent explain DNA repair pathways and their biological and medical significance, support learning and research, and provide general information on repair-related conditions without individual medical advice.", "definition": "The collection of cellular processes that identify and correct damage to DNA, including base and nucleotide excision repair, mismatch repair, double-strand break repair by homologous recombination and non-homologous end joining, photoreactivation and translesion synthesis; defects in DNA repair underlie cancer predisposition syndromes and ageing, and repair pathways are targets of cancer therapy.", "what_it_is_for": "Maintaining genome integrity.", "affordances": [ "explain repair pathways and when they act", "relate repair defects to diseases", "explain repair as a therapy target", "find research resources" ], "distinguishing_features": [ "Detects and corrects DNA damage", "Multiple pathways", "Essential for genome stability", "Medically important" ], "appearance": "Not visible; molecular processes shown in diagrams.", "visual_identification": [ "Pathways named by damage type", "Enzymes such as ligases and polymerases", "DNA replication is a separate process" ], "physical_properties": [], "families_and_kinds": [ "excision repair pathways", "mismatch repair", "double-strand break repair", "direct reversal such as photoreactivation", "damage tolerance such as translesion synthesis" ], "related_models": [ { "relation": "is a kind of", "target": "DNA metabolic process", "why": "category" }, { "relation": "is a kind of", "target": "cellular response to DNA damage stimulus", "why": "category" }, { "relation": "acts on", "target": "DNA", "why": "substrate" }, { "relation": "is related to", "target": "restriction enzyme", "why": "DNA-modifying enzymes" } ], "identifiers": [ { "scheme": "Gene Ontology", "value_or_pattern": "GO:0006281 DNA repair", "note": "ontology" } ], "standards_and_regulation": [ "Research ethics and biosafety rules", "Clinical guidelines for hereditary cancer syndromes" ], "failure_modes_and_hazards": [ "Agents giving individual genetic or medical advice", "Oversimplifying pathway roles" ], "in_scope": [], "out_of_scope": [], "characteristics": [] }, "sources": [], "structure": { "bundles": [ { "id": "pathways", "name": "Pathways", "description": "How repair works.", "rationale": "Damage type selects pathway.", "layers": [ { "id": "which", "name": "Which", "description": "Pathway for damage.", "findings": [ { "id": "which-finding", "name": "Which", "description": "Pathway selection.", "questions": [ { "text": "Which repair pathway handles this type of DNA damage?", "kind": "definition" }, { "text": "Which key proteins are involved?", "kind": "provenance" } ] } ] }, { "id": "steps", "name": "Steps", "description": "Mechanism.", "findings": [ { "id": "steps-finding", "name": "Steps", "description": "Mechanism.", "questions": [ { "text": "What are the steps of this repair pathway?", "kind": "definition" }, { "text": "How is fidelity ensured?", "kind": "definition" } ] } ] } ] }, { "id": "disease", "name": "Disease", "description": "When repair fails.", "rationale": "General information.", "layers": [ { "id": "syndromes", "name": "Syndromes", "description": "Repair defects.", "findings": [ { "id": "syndromes-finding", "name": "Syndromes", "description": "Repair defects.", "questions": [ { "text": "Which conditions result from defects in this pathway, according to medical genetics sources?", "kind": "provenance" }, { "text": "Is the user asking about their own genetic results?", "kind": "boundary" } ] } ] }, { "id": "cancer", "name": "Cancer", "description": "Cancer link.", "findings": [ { "id": "cancer-finding", "name": "Cancer", "description": "Cancer.", "questions": [ { "text": "How do repair defects contribute to cancer development?", "kind": "definition" }, { "text": "Where can genetic counselling be found?", "kind": "provenance" } ] } ] } ] }, { "id": "therapy", "name": "Therapy", "description": "Targeting repair.", "rationale": "Repair as a target.", "layers": [ { "id": "drugs", "name": "Drugs", "description": "Repair inhibitors.", "findings": [ { "id": "drugs-finding", "name": "Drugs", "description": "Repair inhibitors.", "questions": [ { "text": "How do therapies such as PARP inhibitors exploit repair defects, in general terms?", "kind": "provenance" }, { "text": "Which are approved?", "kind": "provenance" } ] } ] }, { "id": "radiation", "name": "Radiation", "description": "Radiotherapy.", "findings": [ { "id": "radiation-finding", "name": "Radiation", "description": "Radiotherapy.", "questions": [ { "text": "How does DNA repair affect responses to radiotherapy and chemotherapy?", "kind": "definition" }, { "text": "What research is under way?", "kind": "provenance" } ] } ] } ] }, { "id": "learn", "name": "Learn", "description": "Study.", "rationale": "Resources exist.", "layers": [ { "id": "history", "name": "History", "description": "Discovery.", "findings": [ { "id": "history-finding", "name": "History", "description": "Discovery.", "questions": [ { "text": "How were DNA repair mechanisms discovered, and who was recognised?", "kind": "provenance" }, { "text": "Which experiments were key?", "kind": "provenance" } ] } ] }, { "id": "resources", "name": "Resources", "description": "Databases.", "findings": [ { "id": "resources-finding", "name": "Resources", "description": "Databases.", "questions": [ { "text": "Which databases and reviews cover DNA repair genes?", "kind": "provenance" }, { "text": "Which GO terms apply?", "kind": "provenance" } ] } ] } ] } ] }, "openQuestions": [ "Should each pathway be a separate entry?", "How should gene databases be linked?", "How should clinical guidance 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 DNA repair, record what state it is in, and decide what may be done with it.", "whatItIs": "Let an agent explain DNA repair pathways and their biological and medical significance, support learning and research, and provide general information on repair-related conditions without individual medical 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: translesion synthesis, photoreactivation, recombinational DNA repair, meiotic mismatch repair, recombinational repair, protein-DNA covalent cross-linking repair, base-excision repair, double-strand break repair, single strand break repair, pyrimidine dimer repair, interstrand cross-link repair, UV-damage excision repair.", "27 finer distinctions are held as aliases rather than separate entries, because telling them apart needs a task that asks for it.", "Described in 52 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 DNA repair, 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": [ "translesion synthesis", "photoreactivation", "recombinational DNA repair", "meiotic mismatch repair", "recombinational repair", "protein-DNA covalent cross-linking repair", "base-excision repair", "double-strand break repair", "single strand break repair", "pyrimidine dimer repair", "interstrand cross-link repair", "UV-damage excision repair" ] } ], "standing": "Described in 52 Wikipedia languages, which measures how widely it is written about rather than how important or how common it is. 27 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 DNA repair from another, and a DNA repair 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 DNA repair, 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 DNA repair, 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 DNA repair 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 DNA repair, 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 DNA repair, 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 DNA repair 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 DNA repair 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 DNA repair, 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 DNA repair, 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 DNA repair 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 DNA repair from the things most often confused with it.", "questions": [ { "id": "distinguishing-features-q01", "text": "What identifies and describes what distinguishes a DNA repair, 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 DNA repair, 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 DNA repair 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 DNA repair 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 DNA repair between them.", "questions": [ { "id": "stages-and-transitions-q01", "text": "What identifies and describes the lifecycle of a DNA repair, 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 DNA repair, 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 DNA repair 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 DNA repair, how often and by whom.", "findings": [ { "id": "observation-record", "name": "Observation record", "description": "How an observation of a DNA repair 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 DNA repair, 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 DNA repair, 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 DNA repair 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 DNA repair 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 DNA repair, 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 DNA repair and what marks it done.", "questions": [ { "id": "steps-and-preconditions-q01", "text": "What identifies and describes a step of a DNA repair, 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 DNA repair, 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 DNA repair 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 DNA repair consumes and what it produces.", "findings": [ { "id": "inputs-and-outputs", "name": "Inputs, outputs and side effects", "description": "The resources a DNA repair 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 DNA repair, 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 DNA repair, 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 DNA repair 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 DNA repair 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 DNA repair 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 DNA repair 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 DNA repair 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 DNA repair?", "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 DNA repair?", "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 DNA repair 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 DNA repair and how confident it is.", "questions": [ { "id": "claim-provenance-q01", "text": "What identifies and describes a claim about a DNA repair, 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 DNA repair, 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 DNA repair 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 DNA repair is retired without being erased.", "questions": [ { "id": "validity-and-supersession-q01", "text": "What identifies and describes the validity of a claim about a DNA repair, 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 DNA repair, 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 DNA repair 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 } } } }