{ "model": { "rank": 15738, "code": "thing-q874745", "model_id": "vr.tr.dna-methylation", "name": "DNA methylation", "purpose": "Let an agent explain DNA methylation and its roles, relay mechanisms, enzymes, measurement and significance from molecular biology references, describe its dynamics in development and disease in general terms, and distinguish DNA methylation from histone modification, RNA methylation and genetic mutation.", "family": "Thing Registry", "category": "Activities and processes", "status": "research-draft", "kind": "thing", "plane": "ACT", "domain": "ACT.PRC", "industry": "", "version": "", "url": "/models/thing/q874745/", "tier": 2, "score": 33, "payload": { "layer": "wikidata", "aliases": [ "DNA methylation involved in gamete generation", "DNA methylation involved in embryo development", "DNA methylation on cytosine", "DNA methylation on adenine" ], "aliasCount": 4, "merged": 4, "knownIn": 33, "facets": null, "markers": [], "lexicalClass": "", "senseRank": null, "alsoRegisteredAs": null, "source": { "dataset": "wikidata", "item": "Q874745", "url": "https://www.wikidata.org/wiki/Q874745", "license": "CC0 1.0" } }, "research": { "vercy": "1.0-draft", "publication": { "status": "research-draft", "adjudicationStatus": "unreviewed", "publishableCanonical": false, "generatedAt": "2026-09-13T14:03:52Z", "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": 4, "engine": "claude" }, "metaModel": { "id": "THING-Q874745", "registryId": "vr.tr.dna-methylation", "name": "DNA methylation", "version": "0.2.0-wave.4", "entryKind": "thing", "family": "Thing Registry", "domain": [ "ACT.PRC" ], "status": "research-draft" }, "canonicalUrl": "https://ver.cy/models/thing/q874745/", "model": { "registry_id": "vr.tr.dna-methylation", "name": "DNA methylation", "purpose": "Let an agent explain DNA methylation and its roles, relay mechanisms, enzymes, measurement and significance from molecular biology references, describe its dynamics in development and disease in general terms, and distinguish DNA methylation from histone modification, RNA methylation and genetic mutation.", "definition": "The addition of methyl groups to DNA, mainly at cytosine in CpG sites in mammals and also at adenine in bacteria and some eukaryotes, an epigenetic mark that regulates gene expression, genomic imprinting, X inactivation and transposon silencing, reprogrammed during gamete generation and embryo development and altered in cancer and ageing; DNA methylation is measured by bisulfite sequencing and related methods and underlies epigenetic clocks.", "what_it_is_for": "Not applicable; an epigenetic process.", "affordances": [ "explain mechanisms", "relay measurement and roles", "describe development and disease", "distinguish related modifications" ], "distinguishing_features": [ "Epigenetic mark", "Heritable through division", "Reprogrammed in development", "Disease relevance" ], "appearance": "Not a visible object; methyl groups on DNA bases.", "visual_identification": [ "Methyl groups added to DNA bases", "Cytosine methylation at CpG, adenine methylation, methylation in gamete generation and embryo development", "Histone modification marks proteins; RNA methylation marks RNA; mutations change sequence" ], "physical_properties": [ { "quantity": "mammalian CpG methylation", "typical_range": "about 70-80", "unit": "percent", "note": "of CpGs" }, { "quantity": "main enzymes", "typical_range": "DNMT1, DNMT3A, DNMT3B", "unit": "list", "note": "" }, { "quantity": "demethylation enzymes", "typical_range": "TET family", "unit": "list", "note": "" } ], "families_and_kinds": [ "cytosine methylation at CpG sites", "non-CpG methylation in neurons and stem cells", "adenine methylation in bacteria and some eukaryotes", "methylation dynamics in gamete generation", "methylation dynamics in embryo development", "aberrant methylation in cancer and ageing" ], "related_models": [ { "relation": "is a kind of", "target": "DNA methylation or demethylation", "why": "in registry terms" }, { "relation": "is a kind of", "target": "macromolecule methylation", "why": "in registry terms" }, { "relation": "is a kind of", "target": "DNA alkylation", "why": "in registry terms" }, { "relation": "is contrasted with", "target": "histone modification", "why": "another epigenetic mark" } ], "identifiers": [ { "scheme": "GO", "value_or_pattern": "GO:0006306", "note": "DNA methylation" } ], "standards_and_regulation": [ "No regulation; standards for methylation assays and clinical tests" ], "failure_modes_and_hazards": [ "Overinterpreting epigenetic clocks and direct-to-consumer tests", "Agents giving personal medical advice", "Confusing methylation with mutation" ], "in_scope": [], "out_of_scope": [], "characteristics": [] }, "sources": [], "structure": { "bundles": [ { "id": "understand", "name": "Understand", "description": "What DNA methylation is.", "rationale": "Science.", "layers": [ { "id": "definition", "name": "Definition", "description": "Definition.", "findings": [ { "id": "definition-finding", "name": "Definition", "description": "Definition.", "questions": [ { "text": "What is DNA methylation, and how does it differ from histone modification, RNA methylation and mutation?", "kind": "definition" }, { "text": "Is the question about the mechanism, development, disease or a personal test?", "kind": "boundary" } ] } ] }, { "id": "forms", "name": "Forms", "description": "Forms.", "findings": [ { "id": "forms-finding", "name": "Forms", "description": "Forms.", "questions": [ { "text": "What are cytosine and adenine methylation, and what are the GO subprocesses for gametes and embryos?", "kind": "definition" }, { "text": "Which entry fits the specific form?", "kind": "action" } ] } ] } ] }, { "id": "mechanism", "name": "Mechanism", "description": "Mechanism and measurement.", "rationale": "Science.", "layers": [ { "id": "enzymes", "name": "Enzymes", "description": "Enzymes.", "findings": [ { "id": "enzymes-finding", "name": "Enzymes", "description": "Enzymes.", "questions": [ { "text": "How do DNMT and TET enzymes add, maintain and remove methylation?", "kind": "provenance" }, { "text": "Which references are standard?", "kind": "provenance" } ] } ] }, { "id": "measurement", "name": "Measurement", "description": "Measurement.", "findings": [ { "id": "measurement-finding", "name": "Measurement", "description": "Measurement.", "questions": [ { "text": "How is methylation measured by bisulfite sequencing, arrays and nanopore methods?", "kind": "measurement" }, { "text": "Which sources are cited?", "kind": "provenance" } ] } ] } ] }, { "id": "biology", "name": "Biology", "description": "Development and disease.", "rationale": "Clinical.", "layers": [ { "id": "development", "name": "Development", "description": "Development.", "findings": [ { "id": "development-finding", "name": "Development", "description": "Development.", "questions": [ { "text": "How is methylation reprogrammed in gametes and embryos, and how does it drive imprinting and X inactivation?", "kind": "provenance" }, { "text": "Which entry fits genomic imprinting?", "kind": "action" } ] } ] }, { "id": "disease", "name": "Disease", "description": "Disease and ageing.", "findings": [ { "id": "disease-finding", "name": "Disease", "description": "Disease.", "questions": [ { "text": "How is methylation altered in cancer and ageing, and what are epigenetic clocks, with findings attributed?", "kind": "provenance" }, { "text": "Is the user asking about a personal test result, which needs a clinician?", "kind": "boundary" } ] } ] } ] }, { "id": "context", "name": "Context", "description": "Evolution and history.", "rationale": "Context.", "layers": [ { "id": "evolution", "name": "Evolution", "description": "Across life.", "findings": [ { "id": "evolution-finding", "name": "Evolution", "description": "Evolution.", "questions": [ { "text": "How does methylation differ across bacteria, plants and animals?", "kind": "provenance" }, { "text": "Which entry fits epigenetics?", "kind": "action" } ] } ] }, { "id": "history", "name": "History", "description": "History.", "findings": [ { "id": "history-finding", "name": "History", "description": "History.", "questions": [ { "text": "How was DNA methylation discovered and its role established?", "kind": "provenance" }, { "text": "Which entry fits the history of epigenetics?", "kind": "action" } ] } ] } ] } ] }, "openQuestions": [ "Should epigenetic clock and genomic imprinting be separate primary entries?", "How should molecular biology references be linked?", "The registry entry has merged aliases naming GO subprocesses; should they be split off?" ], "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 methylation, record what state it is in, and decide what may be done with it.", "whatItIs": "Let an agent explain DNA methylation and its roles, relay mechanisms, enzymes, measurement and significance from molecular biology references, describe its dynamics in development and disease in general terms, and distinguish DNA methylation from histone modification, RNA methylation and genetic mutation.", "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: DNA methylation involved in gamete generation, DNA methylation involved in embryo development, DNA methylation on cytosine, DNA methylation on adenine.", "4 finer distinctions are held as aliases rather than separate entries, because telling them apart needs a task that asks for it.", "Described in 33 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 methylation, 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": [ "DNA methylation involved in gamete generation", "DNA methylation involved in embryo development", "DNA methylation on cytosine", "DNA methylation on adenine" ] } ], "standing": "Described in 33 Wikipedia languages, which measures how widely it is written about rather than how important or how common it is. 4 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 methylation from another, and a DNA methylation 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 methylation, 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 methylation, 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 methylation 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 methylation, 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 methylation, 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 methylation 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 methylation 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 methylation, 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 methylation, 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 methylation 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 methylation from the things most often confused with it.", "questions": [ { "id": "distinguishing-features-q01", "text": "What identifies and describes what distinguishes a DNA methylation, 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 methylation, 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 methylation 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 methylation 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 methylation between them.", "questions": [ { "id": "stages-and-transitions-q01", "text": "What identifies and describes the lifecycle of a DNA methylation, 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 methylation, 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 methylation 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 methylation, how often and by whom.", "findings": [ { "id": "observation-record", "name": "Observation record", "description": "How an observation of a DNA methylation 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 methylation, 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 methylation, 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 methylation 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 methylation 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 methylation, 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 methylation and what marks it done.", "questions": [ { "id": "steps-and-preconditions-q01", "text": "What identifies and describes a step of a DNA methylation, 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 methylation, 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 methylation 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 methylation consumes and what it produces.", "findings": [ { "id": "inputs-and-outputs", "name": "Inputs, outputs and side effects", "description": "The resources a DNA methylation 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 methylation, 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 methylation, 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 methylation 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 methylation 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 methylation 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 methylation 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 methylation 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 methylation?", "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 methylation?", "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 methylation 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 methylation and how confident it is.", "questions": [ { "id": "claim-provenance-q01", "text": "What identifies and describes a claim about a DNA methylation, 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 methylation, 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 methylation 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 methylation is retired without being erased.", "questions": [ { "id": "validity-and-supersession-q01", "text": "What identifies and describes the validity of a claim about a DNA methylation, 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 methylation, 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 methylation 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 } } } }