{ "model": { "rank": 17309, "code": "thing-q863908", "model_id": "vr.tr.nucleic-acid-sequence", "name": "nucleic acid sequence", "purpose": "Let an agent explain nucleic acid sequences and their notation, describe functional sequence elements, support sequence analysis and database use, and relate sequences to genetics and medicine at a general level.", "family": "Thing Registry", "category": "Cross-cutting context", "status": "research-draft", "kind": "thing", "plane": "XCT", "domain": "XCT.QLT", "industry": "", "version": "", "url": "/models/thing/q863908/", "tier": 2, "score": 31, "payload": { "layer": "wikidata", "aliases": [ "RNA sequence", "polypurine tract", "Cap-independent translation element", "Simian virus 40 late polyadenylation signal", "regulatory sequence", "viral packaging sequences", "three prime untranslated region", "trans-regulatory element", "insulator elements", "ribonucleic acid regulatory sequences", "genetic operator regions", "five prime untranslated region", "transcription initiation site", "Coronavirus 5' UTR", "near-full-length sequence", "Restriction site", "expression library", "anticodon", "internal ribosome entry site", "mobile genetic element", "intergenic region", "scaffold/matrix attachment region", "Hybridization probe", "endogenous viral element", "DNA sequence", "GC rich sequence", "AT rich sequence", "Ribosomal protein leader", "Alphacoronavirus 5'UTR", "Arginine catabolic mobile element", "gene cassette", "Micropia", "5' flanking region", "3' flanking region", "whole-genome sequence", "transcription termination sequence", "coding region", "terminator", "sticky end", "recognition sequence" ], "aliasCount": 43, "merged": 43, "knownIn": 31, "facets": null, "markers": [], "lexicalClass": "", "senseRank": null, "alsoRegisteredAs": null, "source": { "dataset": "wikidata", "item": "Q863908", "url": "https://www.wikidata.org/wiki/Q863908", "license": "CC0 1.0" } }, "research": { "vercy": "1.0-draft", "publication": { "status": "research-draft", "adjudicationStatus": "unreviewed", "publishableCanonical": false, "generatedAt": "2026-09-12T00:30:19Z", "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": 2, "engine": "claude" }, "metaModel": { "id": "THING-Q863908", "registryId": "vr.tr.nucleic-acid-sequence", "name": "nucleic acid sequence", "version": "0.2.0-wave.2", "entryKind": "thing", "family": "Thing Registry", "domain": [ "XCT.QLT" ], "status": "research-draft" }, "canonicalUrl": "https://ver.cy/models/thing/q863908/", "model": { "registry_id": "vr.tr.nucleic-acid-sequence", "name": "nucleic acid sequence", "purpose": "Let an agent explain nucleic acid sequences and their notation, describe functional sequence elements, support sequence analysis and database use, and relate sequences to genetics and medicine at a general level.", "definition": "The order of nucleotides in a DNA or RNA molecule, represented as a string of the letters A, C, G and T or U, constituting the primary structure that encodes genes, regulatory sequences, packaging signals, polyadenylation signals and other functional elements; nucleic acid sequences are determined by sequencing, stored in databases, compared by alignment and analysed in bioinformatics, genetics and medicine.", "what_it_is_for": "The order of nucleotides in DNA or RNA.", "affordances": [ "explain notation and structure", "describe functional elements", "support analysis and databases", "relate to genetics and medicine" ], "distinguishing_features": [ "Four-letter alphabet", "Encodes function", "Sequenced and stored", "Comparable by alignment" ], "appearance": "Not physical as information; strings of letters representing molecules.", "visual_identification": [ "String of A, C, G, T or U", "Primary structure", "A protein sequence uses amino acid letters" ], "physical_properties": [], "families_and_kinds": [ "coding sequences", "regulatory sequences", "RNA sequences and elements such as translation elements", "viral sequences such as packaging signals", "repetitive and non-coding sequences" ], "related_models": [ { "relation": "is a kind of", "target": "primary structure", "why": "category" }, { "relation": "is related to", "target": "gene", "why": "sequences encoding genes" }, { "relation": "is related to", "target": "gene expression", "why": "regulatory sequences" }, { "relation": "is related to", "target": "DNA-binding protein", "why": "proteins recognising sequences" } ], "identifiers": [], "standards_and_regulation": [ "Sequence data formats and database standards", "Genetic data privacy laws", "Biosecurity screening of synthetic sequences" ], "failure_modes_and_hazards": [ "Sequencing and assembly errors", "Misinterpreting variants", "Privacy risks of genomic data" ], "in_scope": [], "out_of_scope": [], "characteristics": [] }, "sources": [], "structure": { "bundles": [ { "id": "understand", "name": "Understand", "description": "What a sequence is.", "rationale": "Biology.", "layers": [ { "id": "notation", "name": "Notation", "description": "Notation and structure.", "findings": [ { "id": "notation-finding", "name": "Notation", "description": "Notation.", "questions": [ { "text": "How are nucleic acid sequences written, and how do DNA and RNA sequences and their strands and directions relate?", "kind": "definition" }, { "text": "How do sequences relate to secondary and tertiary structure?", "kind": "definition" } ] } ] }, { "id": "elements", "name": "Elements", "description": "Functional elements.", "findings": [ { "id": "elements-finding", "name": "Elements", "description": "Elements.", "questions": [ { "text": "What are coding sequences, promoters, regulatory sequences, polyadenylation signals, packaging signals and other elements?", "kind": "definition" }, { "text": "Which entry fits a specific element?", "kind": "action" } ] } ] } ] }, { "id": "analyse", "name": "Analyse", "description": "Analysing sequences.", "rationale": "Bioinformatics.", "layers": [ { "id": "tools", "name": "Tools", "description": "Alignment and search.", "findings": [ { "id": "tools-finding", "name": "Tools", "description": "Tools.", "questions": [ { "text": "How are sequences aligned, searched and annotated with bioinformatics tools?", "kind": "provenance" }, { "text": "How can this sequence be analysed?", "kind": "action" } ] } ] }, { "id": "databases", "name": "Databases", "description": "Databases.", "findings": [ { "id": "databases-finding", "name": "Databases", "description": "Databases.", "questions": [ { "text": "Which databases store nucleic acid sequences, and what formats and identifiers are used?", "kind": "provenance" }, { "text": "Which entry fits a specific database?", "kind": "action" } ] } ] } ] }, { "id": "apply", "name": "Apply", "description": "Sequences in medicine and research.", "rationale": "General information.", "layers": [ { "id": "medicine", "name": "Medicine", "description": "Sequences and health.", "findings": [ { "id": "medicine-finding", "name": "Medicine", "description": "Medicine.", "questions": [ { "text": "How are sequence variants interpreted in medical genetics, and what limits apply?", "kind": "provenance" }, { "text": "Is the user asking about their own genetic data, which needs a clinician?", "kind": "boundary" } ] } ] }, { "id": "synthesis", "name": "Synthesis", "description": "Synthetic sequences.", "findings": [ { "id": "synthesis-finding", "name": "Synthesis", "description": "Synthesis.", "questions": [ { "text": "How are sequences synthesised for research, and which biosecurity screening rules apply?", "kind": "provenance" }, { "text": "Is the request seeking harmful capability, which must be declined?", "kind": "boundary" } ] } ] } ] }, { "id": "learn", "name": "Learn", "description": "History and teaching.", "rationale": "Education.", "layers": [ { "id": "history", "name": "History", "description": "History of sequencing.", "findings": [ { "id": "history-finding", "name": "History", "description": "History.", "questions": [ { "text": "How did sequencing develop from Sanger methods to high-throughput sequencing?", "kind": "provenance" }, { "text": "Which references are standard?", "kind": "provenance" } ] } ] }, { "id": "teach", "name": "Teach", "description": "Teaching.", "findings": [ { "id": "teach-finding", "name": "Teach", "description": "Teaching.", "questions": [ { "text": "How can sequence analysis be taught with exercises?", "kind": "action" }, { "text": "Which misconceptions arise?", "kind": "provenance" } ] } ] } ] } ] }, "openQuestions": [ "Should each element type be a separate entry?", "How should databases be linked?", "How should biosecurity rules 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 nucleic acid sequence, record what state it is in, and decide what may be done with it.", "whatItIs": "Let an agent explain nucleic acid sequences and their notation, describe functional sequence elements, support sequence analysis and database use, and relate sequences to genetics and medicine at a general level.", "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: RNA sequence, polypurine tract, Cap-independent translation element, Simian virus 40 late polyadenylation signal, regulatory sequence, viral packaging sequences, three prime untranslated region, trans-regulatory element, insulator elements, ribonucleic acid regulatory sequences, genetic operator regions, five prime untranslated region.", "43 finer distinctions are held as aliases rather than separate entries, because telling them apart needs a task that asks for it.", "Described in 31 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 nucleic acid sequence, 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": [ "RNA sequence", "polypurine tract", "Cap-independent translation element", "Simian virus 40 late polyadenylation signal", "regulatory sequence", "viral packaging sequences", "three prime untranslated region", "trans-regulatory element", "insulator elements", "ribonucleic acid regulatory sequences", "genetic operator regions", "five prime untranslated region" ] } ], "standing": "Described in 31 Wikipedia languages, which measures how widely it is written about rather than how important or how common it is. 43 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 nucleic acid sequence from another, and a nucleic acid sequence 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 nucleic acid sequence, 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 nucleic acid sequence, 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 nucleic acid sequence 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 nucleic acid sequence, 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 nucleic acid sequence, 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 nucleic acid sequence 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 nucleic acid sequence 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 nucleic acid sequence, 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 nucleic acid sequence, 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 nucleic acid sequence 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 nucleic acid sequence from the things most often confused with it.", "questions": [ { "id": "distinguishing-features-q01", "text": "What identifies and describes what distinguishes a nucleic acid sequence, 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 nucleic acid sequence, 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 nucleic acid sequence 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 nucleic acid sequence 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 nucleic acid sequence between them.", "questions": [ { "id": "stages-and-transitions-q01", "text": "What identifies and describes the lifecycle of a nucleic acid sequence, 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 nucleic acid sequence, 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 nucleic acid sequence 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 nucleic acid sequence, how often and by whom.", "findings": [ { "id": "observation-record", "name": "Observation record", "description": "How an observation of a nucleic acid sequence 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 nucleic acid sequence, 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 nucleic acid sequence, 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 nucleic acid sequence 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 nucleic acid sequence 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 nucleic acid sequence 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 nucleic acid sequence 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 nucleic acid sequence 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 nucleic acid sequence?", "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 nucleic acid sequence?", "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 nucleic acid sequence 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 nucleic acid sequence and how confident it is.", "questions": [ { "id": "claim-provenance-q01", "text": "What identifies and describes a claim about a nucleic acid sequence, 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 nucleic acid sequence, 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 nucleic acid sequence 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 nucleic acid sequence is retired without being erased.", "questions": [ { "id": "validity-and-supersession-q01", "text": "What identifies and describes the validity of a claim about a nucleic acid sequence, 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 nucleic acid sequence, 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 nucleic acid sequence 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 } } } }