{ "model": { "rank": 10393, "code": "thing-q121438", "model_id": "vr.tr.transposable-element", "name": "transposable element", "purpose": "Let an agent explain transposable elements and their classes, relay their roles in genome evolution, disease and biotechnology with attribution, and distinguish them from viruses and other repetitive DNA.", "family": "Thing Registry", "category": "Cross-cutting context", "status": "research-draft", "kind": "thing", "plane": "XCT", "domain": "XCT.QLT", "industry": "", "version": "", "url": "/models/thing/q121438/", "tier": 2, "score": 45, "payload": { "layer": "wikidata", "aliases": [ "retrotransposon", "Retrozyme", "SINE/VNTR/Alu", "long interspersed nuclear element", "LINE1", "Miniature Inverted-repeat Transposable Elements", "DNA transposon", "P element", "Insertion sequence", "Helitron", "Polintoviricetes" ], "aliasCount": 11, "merged": 11, "knownIn": 45, "facets": null, "markers": [], "lexicalClass": "", "senseRank": null, "alsoRegisteredAs": null, "source": { "dataset": "wikidata", "item": "Q121438", "url": "https://www.wikidata.org/wiki/Q121438", "license": "CC0 1.0" } }, "research": { "vercy": "1.0-draft", "publication": { "status": "research-draft", "adjudicationStatus": "unreviewed", "publishableCanonical": false, "generatedAt": "2026-09-13T00:11:44Z", "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": 3, "engine": "claude" }, "metaModel": { "id": "THING-Q121438", "registryId": "vr.tr.transposable-element", "name": "transposable element", "version": "0.2.0-wave.3", "entryKind": "thing", "family": "Thing Registry", "domain": [ "XCT.QLT" ], "status": "research-draft" }, "canonicalUrl": "https://ver.cy/models/thing/q121438/", "model": { "registry_id": "vr.tr.transposable-element", "name": "transposable element", "purpose": "Let an agent explain transposable elements and their classes, relay their roles in genome evolution, disease and biotechnology with attribution, and distinguish them from viruses and other repetitive DNA.", "definition": "A DNA sequence that can change its position within a genome, either by a cut-and-paste mechanism in DNA transposons or through an RNA intermediate in retrotransposons such as long interspersed nuclear elements including LINE1, short interspersed elements including Alu, and long terminal repeat elements, with derived forms such as miniature inverted-repeat transposable elements; transposable elements make up nearly half of the human genome, drive mutation and genome evolution, and are controlled by host silencing mechanisms.", "what_it_is_for": "Not applicable; a genomic element.", "affordances": [ "explain classes and mechanisms", "relay roles in evolution and disease", "relay biotechnology uses", "distinguish from related sequences" ], "distinguishing_features": [ "Mobility", "Two main classes", "Genome abundance", "Host silencing" ], "appearance": "Not visible; sequences identified in genome data.", "visual_identification": [ "DNA sequence that moves within the genome", "DNA transposons and retrotransposons including LINE, SINE and LTR elements", "Retroviruses are infectious; satellite DNA is repetitive but does not move" ], "physical_properties": [ { "quantity": "share of human genome", "typical_range": "about 45", "unit": "percent", "note": "" }, { "quantity": "LINE1 full length", "typical_range": "about 6", "unit": "kb", "note": "" } ], "families_and_kinds": [ "class I retrotransposons: LTR elements, LINEs such as LINE1, SINEs such as Alu and SVA", "class II DNA transposons including MITEs", "autonomous and non-autonomous elements", "unusual elements such as retrozymes" ], "related_models": [ { "relation": "is a kind of", "target": "mobile genetic element", "why": "in registry terms" }, { "relation": "is a kind of", "target": "DNA sequence", "why": "in registry terms" }, { "relation": "is silenced by", "target": "piRNA pathway", "why": "and DNA methylation" }, { "relation": "is used in", "target": "transposon mutagenesis", "why": "as a research tool" } ], "identifiers": [ { "scheme": "Dfam", "value_or_pattern": "database", "note": "transposable element families" }, { "scheme": "Repbase", "value_or_pattern": "database", "note": "" } ], "standards_and_regulation": [ "Transposable element classification systems", "Genetic engineering rules for transposon-based tools" ], "failure_modes_and_hazards": [ "Insertional mutations causing disease", "Confusing element classes", "Outdated genome share figures" ], "in_scope": [], "out_of_scope": [], "characteristics": [] }, "sources": [], "structure": { "bundles": [ { "id": "understand", "name": "Understand", "description": "What transposable elements are.", "rationale": "Science.", "layers": [ { "id": "definition", "name": "Definition", "description": "Definition and classes.", "findings": [ { "id": "definition-finding", "name": "Definition", "description": "Definition.", "questions": [ { "text": "What are transposable elements, and how are they classified?", "kind": "definition" }, { "text": "Is the sequence a transposable element, a virus or another repeat?", "kind": "boundary" } ] } ] }, { "id": "mechanism", "name": "Mechanism", "description": "Mechanisms.", "findings": [ { "id": "mechanism-finding", "name": "Mechanism", "description": "Mechanism.", "questions": [ { "text": "How do cut-and-paste and copy-and-paste transposition work?", "kind": "definition" }, { "text": "Which entry fits the specific class?", "kind": "action" } ] } ] } ] }, { "id": "genome", "name": "Genome", "description": "Genome roles.", "rationale": "Attribution.", "layers": [ { "id": "evolution", "name": "Evolution", "description": "Evolution.", "findings": [ { "id": "evolution-finding", "name": "Evolution", "description": "Evolution.", "questions": [ { "text": "How have transposable elements shaped genome evolution and regulation, with findings attributed?", "kind": "provenance" }, { "text": "Which sources are cited?", "kind": "provenance" } ] } ] }, { "id": "control", "name": "Control", "description": "Host control.", "findings": [ { "id": "control-finding", "name": "Control", "description": "Control.", "questions": [ { "text": "How do cells silence transposable elements?", "kind": "provenance" }, { "text": "Which entry fits piRNA?", "kind": "action" } ] } ] } ] }, { "id": "disease", "name": "Disease", "description": "Disease and tools.", "rationale": "Application.", "layers": [ { "id": "disease", "name": "Disease", "description": "Disease.", "findings": [ { "id": "disease-finding", "name": "Disease", "description": "Disease.", "questions": [ { "text": "How do transposable elements cause or contribute to disease, in general terms?", "kind": "provenance" }, { "text": "Is the user asking about a personal genetic result, which needs a clinician?", "kind": "boundary" } ] } ] }, { "id": "tools", "name": "Tools", "description": "Biotechnology.", "findings": [ { "id": "tools-finding", "name": "Tools", "description": "Tools.", "questions": [ { "text": "How are transposons used in mutagenesis, gene delivery and genome engineering?", "kind": "provenance" }, { "text": "Which entry fits the specific tool?", "kind": "action" } ] } ] } ] }, { "id": "context", "name": "Context", "description": "History and methods.", "rationale": "Context.", "layers": [ { "id": "history", "name": "History", "description": "History.", "findings": [ { "id": "history-finding", "name": "History", "description": "History.", "questions": [ { "text": "How did McClintock discover transposable elements, and how was the field received?", "kind": "provenance" }, { "text": "Which references are standard?", "kind": "provenance" } ] } ] }, { "id": "methods", "name": "Methods", "description": "Annotation methods.", "findings": [ { "id": "methods-finding", "name": "Methods", "description": "Methods.", "questions": [ { "text": "How are transposable elements annotated in genomes?", "kind": "provenance" }, { "text": "Which entry fits genome annotation?", "kind": "action" } ] } ] } ] } ] }, "openQuestions": [ "Should LINE1 and Alu be separate primary entries?", "How should databases be linked?", "The registry entry has merged aliases naming specific families; 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 transposable element, record what state it is in, and decide what may be done with it.", "whatItIs": "Let an agent explain transposable elements and their classes, relay their roles in genome evolution, disease and biotechnology with attribution, and distinguish them from viruses and other repetitive DNA.", "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: retrotransposon, Retrozyme, SINE/VNTR/Alu, long interspersed nuclear element, LINE1, Miniature Inverted-repeat Transposable Elements, DNA transposon, P element, Insertion sequence, Helitron, Polintoviricetes.", "11 finer distinctions are held as aliases rather than separate entries, because telling them apart needs a task that asks for it.", "Described in 45 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 transposable element, 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. 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": [ "retrotransposon", "Retrozyme", "SINE/VNTR/Alu", "long interspersed nuclear element", "LINE1", "Miniature Inverted-repeat Transposable Elements", "DNA transposon", "P element", "Insertion sequence", "Helitron", "Polintoviricetes" ] } ], "standing": "Described in 45 Wikipedia languages, which measures how widely it is written about rather than how important or how common it is. 11 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 transposable element from another, and a transposable element 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 transposable element, 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 transposable element, 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 transposable element 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 transposable element, 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 transposable element, 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 transposable element 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 transposable element 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 transposable element, 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 transposable element, 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 transposable element 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 transposable element from the things most often confused with it.", "questions": [ { "id": "distinguishing-features-q01", "text": "What identifies and describes what distinguishes a transposable element, 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 transposable element, 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 transposable element 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 transposable element 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 transposable element between them.", "questions": [ { "id": "stages-and-transitions-q01", "text": "What identifies and describes the lifecycle of a transposable element, 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 transposable element, 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 transposable element 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 transposable element, how often and by whom.", "findings": [ { "id": "observation-record", "name": "Observation record", "description": "How an observation of a transposable element 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 transposable element, 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 transposable element, 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 transposable element 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 transposable element 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 transposable element 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 transposable element 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 transposable element 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 transposable element?", "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 transposable element?", "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 transposable element 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 transposable element and how confident it is.", "questions": [ { "id": "claim-provenance-q01", "text": "What identifies and describes a claim about a transposable element, 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 transposable element, 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 transposable element 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 transposable element is retired without being erased.", "questions": [ { "id": "validity-and-supersession-q01", "text": "What identifies and describes the validity of a claim about a transposable element, 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 transposable element, 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 transposable element is known, and what must it refuse?", "kind": "action", "answer_data": [ "permitted actions", "preconditions", "refusals", "escalation" ] } ] } ] } ] } ] }, "statistics": { "bundles": 5, "layers": 10, "findings": 12, "questions": 32 } } } }