{ "model": { "rank": 16699, "code": "thing-q898273", "model_id": "vr.tr.protein-domain", "name": "protein domain", "purpose": "Let an agent handle protein domains by family, structure, function and databases, for research and bioinformatics.", "family": "Thing Registry", "category": "Cross-cutting context", "status": "research-draft", "kind": "thing", "plane": "XCT", "domain": "XCT.QLT", "industry": "", "version": "", "url": "/models/thing/q898273/", "tier": 2, "score": 32, "payload": { "layer": "wikidata", "aliases": [ "Krueppel-associated box", "paratope", "catalytic domain", "Krueppel-associated box-related", "membrane spanning domain", "Heptad repeat", "Light-Oxygen-Voltage-sensing domain", "bromodomain", "Ubiquitin-binding domains", "saposin B type domain", "Nucleotidyl transferase domain", "Helicase, superfamily 3, single-stranded DNA/RNA virus", "UBX domain", "Somatomedin B domain", "Sugar isomerase (SIS) domain", "ephrin receptor ligand binding domain", "Cyclophilin-type peptidyl-prolyl cis-trans isomerase domain", "JmjC domain", "CS domain", "Bacterial transcription activator, effector binding", "Acyl transferase", "Mammalian uncoordinated homology 13, domain 2", "UvrD-like helicase, ATP-binding domain", "FAD/NAD(P)-binding domain", "Flavodoxin/nitric oxide synthase", "tRNA methyltransferase TRMD/TRM10-type domain", "Cytidyltransferase-like domain", "PDZ domain", "Spen paralogue and orthologue SPOC, C-terminal", "Bacterial bifunctional deaminase-reductase, C-terminal", "SpoVT-AbrB domain", "HRDC domain", "Multicopper oxidase, type 3", "Helicase superfamily 1/2, ATP-binding domain", "RNA polymerase Rpb7, N-terminal", "Multihaem cytochrome", "PUA domain", "cytochrome c oxidase subunit III-like", "Nitrate/nitrite sensing protein", "tRNA-binding domain" ], "aliasCount": 1371, "merged": 1372, "knownIn": 32, "facets": null, "markers": [], "lexicalClass": "", "senseRank": null, "alsoRegisteredAs": null, "source": { "dataset": "wikidata", "item": "Q898273", "url": "https://www.wikidata.org/wiki/Q898273", "license": "CC0 1.0" } }, "research": { "vercy": "1.0-draft", "publication": { "status": "research-draft", "adjudicationStatus": "unreviewed", "publishableCanonical": false, "generatedAt": "2026-09-11T09:54:47Z", "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-Q898273", "registryId": "vr.tr.protein-domain", "name": "protein domain", "version": "0.2.0-wave.1", "entryKind": "thing", "family": "Thing Registry", "domain": [ "XCT.QLT" ], "status": "research-draft" }, "canonicalUrl": "https://ver.cy/models/thing/q898273/", "model": { "registry_id": "vr.tr.protein-domain", "name": "protein domain", "purpose": "Let an agent handle protein domains by family, structure, function and databases, for research and bioinformatics.", "definition": "A conserved part of a protein sequence and structure that can fold, function and evolve independently, such as kinase domains, zinc fingers or transmembrane domains; proteins often combine several domains.", "what_it_is_for": "Understanding protein function and evolution.", "affordances": [ "identify domains in a protein sequence", "look up domain families in databases", "relate domains to function", "compare domain architectures" ], "distinguishing_features": [ "Independent folding unit", "Conserved across proteins", "Associated with functions", "Combined in multidomain proteins" ], "appearance": "Folded regions in protein structures, shown in models and diagrams.", "visual_identification": [ "Domain annotations on sequences", "Families such as Pfam entries", "Internet domains are a different sense" ], "physical_properties": [ { "quantity": "typical length", "typical_range": "about 50-250", "unit": "amino acids", "note": "" } ], "families_and_kinds": [ "catalytic domains", "binding domains such as zinc fingers", "transmembrane domains", "signalling domains such as SH2", "repeat domains" ], "related_models": [ { "relation": "is a kind of", "target": "amino acid sequence", "why": "category" }, { "relation": "is part of", "target": "protein", "why": "whole" }, { "relation": "is catalogued in", "target": "InterPro and Pfam", "why": "databases" }, { "relation": "is confused with", "target": "internet domain", "why": "another sense" } ], "identifiers": [ { "scheme": "Pfam ID", "value_or_pattern": "PFxxxxx", "note": "domain family" }, { "scheme": "InterPro ID", "value_or_pattern": "IPRxxxxxx", "note": "integrated entry" } ], "standards_and_regulation": [], "failure_modes_and_hazards": [ "Over-interpreting predicted domains", "Outdated annotations" ], "in_scope": [], "out_of_scope": [], "characteristics": [] }, "sources": [], "structure": { "bundles": [ { "id": "identity", "name": "Identity", "description": "Which domain.", "rationale": "Databases identify domains.", "layers": [ { "id": "family", "name": "Family", "description": "Database entry.", "findings": [ { "id": "family-finding", "name": "Family", "description": "Domain family.", "questions": [ { "text": "Which domain family is it, according to InterPro or Pfam?", "kind": "provenance" }, { "text": "What is its identifier?", "kind": "provenance" } ] } ] }, { "id": "location", "name": "Location", "description": "Sequence position.", "findings": [ { "id": "location-finding", "name": "Location", "description": "Location.", "questions": [ { "text": "Where is the domain in the protein sequence?", "kind": "measurement" }, { "text": "How confident is the prediction?", "kind": "boundary" } ] } ] } ] }, { "id": "structure", "name": "Structure", "description": "Fold.", "rationale": "Structure informs function.", "layers": [ { "id": "fold", "name": "Fold", "description": "Structure.", "findings": [ { "id": "fold-finding", "name": "Fold", "description": "Fold.", "questions": [ { "text": "What fold does the domain adopt?", "kind": "definition" }, { "text": "Is the structure experimental or predicted?", "kind": "provenance" } ] } ] }, { "id": "architecture", "name": "Architecture", "description": "Multidomain.", "findings": [ { "id": "architecture-finding", "name": "Architecture", "description": "Domain architecture.", "questions": [ { "text": "Which other domains does the protein contain?", "kind": "provenance" }, { "text": "How are they arranged?", "kind": "definition" } ] } ] } ] }, { "id": "function", "name": "Function", "description": "Role.", "rationale": "Domains carry functions.", "layers": [ { "id": "role", "name": "Role", "description": "Activity.", "findings": [ { "id": "role-finding", "name": "Role", "description": "Function.", "questions": [ { "text": "What function is associated with this domain?", "kind": "provenance" }, { "text": "Is it experimentally shown?", "kind": "boundary" } ] } ] }, { "id": "variants", "name": "Variants", "description": "Mutations.", "findings": [ { "id": "variants-finding", "name": "Variants", "description": "Variants.", "questions": [ { "text": "Do known variants in the domain affect function?", "kind": "provenance" }, { "text": "Which database records them?", "kind": "provenance" } ] } ] } ] }, { "id": "evolution", "name": "Evolution", "description": "History.", "rationale": "Domains evolve.", "layers": [ { "id": "conservation", "name": "Conservation", "description": "Across species.", "findings": [ { "id": "conservation-finding", "name": "Conservation", "description": "Conservation.", "questions": [ { "text": "How conserved is the domain across species?", "kind": "measurement" }, { "text": "Which alignment shows it?", "kind": "provenance" } ] } ] }, { "id": "shuffling", "name": "Shuffling", "description": "Recombination.", "findings": [ { "id": "shuffling-finding", "name": "Shuffling", "description": "Domain shuffling.", "questions": [ { "text": "How did the domain spread to different proteins?", "kind": "provenance" }, { "text": "Which studies discuss it?", "kind": "provenance" } ] } ] } ] } ] }, "openQuestions": [ "Should domain families be separate entries?", "How should InterPro data be linked?", "How should predicted versus experimental structures be marked?" ], "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 protein domain, record what state it is in, and decide what may be done with it.", "whatItIs": "Let an agent handle protein domains by family, structure, function and databases, for research and bioinformatics.", "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: Krueppel-associated box, paratope, catalytic domain, Krueppel-associated box-related, membrane spanning domain, Heptad repeat, Light-Oxygen-Voltage-sensing domain, bromodomain, Ubiquitin-binding domains, saposin B type domain, Nucleotidyl transferase domain, Helicase, superfamily 3, single-stranded DNA/RNA virus.", "1372 finer distinctions are held as aliases rather than separate entries, because telling them apart needs a task that asks for it.", "Described in 32 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 protein domain, 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": [ "Krueppel-associated box", "paratope", "catalytic domain", "Krueppel-associated box-related", "membrane spanning domain", "Heptad repeat", "Light-Oxygen-Voltage-sensing domain", "bromodomain", "Ubiquitin-binding domains", "saposin B type domain", "Nucleotidyl transferase domain", "Helicase, superfamily 3, single-stranded DNA/RNA virus" ] } ], "standing": "Described in 32 Wikipedia languages, which measures how widely it is written about rather than how important or how common it is. 1372 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 protein domain from another, and a protein domain 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 protein domain, 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 protein domain, 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 protein domain 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 protein domain, 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 protein domain, 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 protein domain 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 protein domain 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 protein domain, 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 protein domain, 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 protein domain 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 protein domain from the things most often confused with it.", "questions": [ { "id": "distinguishing-features-q01", "text": "What identifies and describes what distinguishes a protein domain, 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 protein domain, 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 protein domain 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 protein domain 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 protein domain between them.", "questions": [ { "id": "stages-and-transitions-q01", "text": "What identifies and describes the lifecycle of a protein domain, 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 protein domain, 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 protein domain 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 protein domain, how often and by whom.", "findings": [ { "id": "observation-record", "name": "Observation record", "description": "How an observation of a protein domain 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 protein domain, 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 protein domain, 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 protein domain 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 protein domain 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 protein domain 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 protein domain 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 protein domain 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 protein domain?", "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 protein domain?", "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 protein domain 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 protein domain and how confident it is.", "questions": [ { "id": "claim-provenance-q01", "text": "What identifies and describes a claim about a protein domain, 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 protein domain, 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 protein domain 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 protein domain is retired without being erased.", "questions": [ { "id": "validity-and-supersession-q01", "text": "What identifies and describes the validity of a claim about a protein domain, 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 protein domain, 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 protein domain 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 } } } }