{ "model": { "rank": 11955, "code": "thing-q407384", "model_id": "vr.tr.transcription-factor", "name": "transcription factor", "purpose": "Let an agent explain transcription factors and their families, relay mechanisms, classification and examples from molecular biology references, describe roles in development and disease, and route to entries for specific factors.", "family": "Thing Registry", "category": "Physical world and living systems", "status": "research-draft", "kind": "thing", "plane": "PHY", "domain": "PHY.MAT", "industry": "", "version": "", "url": "/models/thing/q407384/", "tier": 2, "score": 41, "payload": { "layer": "wikidata", "aliases": [ "Zinc finger protein WIP", "PR domain zinc finger protein 1", "Plant bZIP transcription factors", "Zinc finger CCCH-type with G patch domain-containing protein", "Transcription factor LHW-like", "Myb-related protein A", "GATA transcription factor 18/19/20", "WUSCHEL-related homeobox 13-like", "Protein WUSCHEL-like", "Transcription factor PIF3-like", "WUSCHEL-related homeobox 8/9-like", "C2H2-type zinc-finger protein AZF1/2/3-like", "Transcription factor FAMA/SPEECHLESS/MUTE", "Transcription factor RKD-like", "Transcription factor bHLH11/121", "MYB-like transcription factor EOBI/EOBII-like, plant", "WUSCHEL-related homeobox 4", "Zinc finger protein GIS/GIS2/ZFP8", "Transcription factor RADIALIS-like", "Transcription factor BIM1/2/3", "WUSCHEL-related homeobox 11-like", "bZIP transcription factor RISBZ3/4/5", "Transcription factor BHLH95-like", "CRC domain-containing protein TSO1-like", "Class III homeodomain-leucine zipper family", "NAC domain-containing protein SOG1-like", "PHR1-like", "B3 domain-containing transcription factor LEC2-like", "Ethylene-responsive transcription factor", "Myb family transcription factor HRS1-like", "Transcription factor ILR3-like", "Transcription activator GLK1/2-like", "Transcription factor LUX/BOA-like", "G-box-binding factor-like", "WRKY transcription factor, plant", "ETS family", "Transcription factor AIB/MYC-like", "Dof zinc finger protein", "Zinc finger protein JAGGED/KNUCKLES-like", "Dehydration-responsive element-binding protein 1A-I" ], "aliasCount": 332, "merged": 332, "knownIn": 41, "facets": null, "markers": [], "lexicalClass": "", "senseRank": null, "alsoRegisteredAs": null, "source": { "dataset": "wikidata", "item": "Q407384", "url": "https://www.wikidata.org/wiki/Q407384", "license": "CC0 1.0" } }, "research": { "vercy": "1.0-draft", "publication": { "status": "research-draft", "adjudicationStatus": "unreviewed", "publishableCanonical": false, "generatedAt": "2026-09-13T02:31:45Z", "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-Q407384", "registryId": "vr.tr.transcription-factor", "name": "transcription factor", "version": "0.2.0-wave.3", "entryKind": "thing", "family": "Thing Registry", "domain": [ "PHY.MAT" ], "status": "research-draft" }, "canonicalUrl": "https://ver.cy/models/thing/q407384/", "model": { "registry_id": "vr.tr.transcription-factor", "name": "transcription factor", "purpose": "Let an agent explain transcription factors and their families, relay mechanisms, classification and examples from molecular biology references, describe roles in development and disease, and route to entries for specific factors.", "definition": "A protein that binds specific DNA sequences to regulate the transcription of genes, activating or repressing RNA polymerase, classified by DNA-binding domains such as zinc fingers, homeodomains, basic helix-loop-helix, bZIP and Myb domains, with thousands of family members across organisms including plant bZIP factors, PR domain zinc finger proteins and Myb-related proteins; transcription factors control development, cell identity and responses to signals, and their mutations underlie many diseases.", "what_it_is_for": "Not applicable; a class of proteins.", "affordances": [ "explain mechanism and families", "relay classification", "describe roles in development and disease", "route to specific factors" ], "distinguishing_features": [ "Sequence-specific binding", "Domain-based families", "Regulatory networks", "Disease relevance" ], "appearance": "Not a visible object; proteins with DNA-binding and regulatory domains.", "visual_identification": [ "Sequence-specific DNA-binding regulators of transcription", "Zinc finger, homeodomain, bHLH, bZIP, Myb and other families", "General transcription factors form the polymerase complex; cofactors do not bind DNA directly" ], "physical_properties": [ { "quantity": "human transcription factors", "typical_range": "about 1600", "unit": "count", "note": "Lambert et al. 2018" }, { "quantity": "largest human family", "typical_range": "C2H2 zinc fingers", "unit": "family", "note": "about 700 members" } ], "families_and_kinds": [ "zinc finger transcription factors including C2H2, CCCH and PR domain zinc finger proteins", "homeodomain factors", "basic helix-loop-helix factors", "bZIP factors including plant bZIP families", "Myb and Myb-related proteins", "nuclear receptors", "general transcription factors" ], "related_models": [ { "relation": "is a kind of", "target": "DNA-binding protein", "why": "in registry terms" }, { "relation": "regulates", "target": "transcription", "why": "of genes" }, { "relation": "binds", "target": "DNA", "why": "at specific motifs" }, { "relation": "is classified by", "target": "protein domain", "why": "of DNA binding" } ], "identifiers": [ { "scheme": "GO", "value_or_pattern": "GO:0003700", "note": "DNA-binding transcription factor activity" }, { "scheme": "MeSH", "value_or_pattern": "D014157", "note": "transcription factors" } ], "standards_and_regulation": [ "Gene Ontology and nomenclature standards", "Databases such as JASPAR and TFClass", "No regulation of the concept" ], "failure_modes_and_hazards": [ "Confusing sequence-specific and general transcription factors", "Overstating single-factor causation", "Stale family counts" ], "in_scope": [], "out_of_scope": [], "characteristics": [] }, "sources": [], "structure": { "bundles": [ { "id": "understand", "name": "Understand", "description": "What transcription factors are.", "rationale": "Science.", "layers": [ { "id": "definition", "name": "Definition", "description": "Definition and mechanism.", "findings": [ { "id": "definition-finding", "name": "Definition", "description": "Definition.", "questions": [ { "text": "What is a transcription factor, and how does it activate or repress genes?", "kind": "definition" }, { "text": "Is the question about sequence-specific factors, general factors or cofactors?", "kind": "boundary" } ] } ] }, { "id": "families", "name": "Families", "description": "Families.", "findings": [ { "id": "families-finding", "name": "Families", "description": "Families.", "questions": [ { "text": "What are the main families by DNA-binding domain, such as zinc finger, bZIP and Myb?", "kind": "definition" }, { "text": "Which entry fits the specific family or protein?", "kind": "action" } ] } ] } ] }, { "id": "biology", "name": "Biology", "description": "Roles.", "rationale": "Science.", "layers": [ { "id": "development", "name": "Development", "description": "Development and identity.", "findings": [ { "id": "development-finding", "name": "Development", "description": "Development.", "questions": [ { "text": "How do transcription factors control development, cell identity and reprogramming?", "kind": "provenance" }, { "text": "Which references are standard?", "kind": "provenance" } ] } ] }, { "id": "signals", "name": "Signals", "description": "Signal responses.", "findings": [ { "id": "signals-finding", "name": "Signals", "description": "Signals.", "questions": [ { "text": "How do factors respond to hormones, stress and signals in animals and plants?", "kind": "provenance" }, { "text": "Which entry fits signal transduction?", "kind": "action" } ] } ] } ] }, { "id": "disease", "name": "Disease", "description": "Disease and therapy.", "rationale": "Clinical.", "layers": [ { "id": "disease", "name": "Disease", "description": "Disease.", "findings": [ { "id": "disease-finding", "name": "Disease", "description": "Disease.", "questions": [ { "text": "What diseases arise from transcription factor mutations or dysregulation, in general terms?", "kind": "provenance" }, { "text": "Which sources are cited?", "kind": "provenance" } ] } ] }, { "id": "therapy", "name": "Therapy", "description": "Therapeutic targeting.", "findings": [ { "id": "therapy-finding", "name": "Therapy", "description": "Therapy.", "questions": [ { "text": "How are transcription factors targeted or used in therapy and research?", "kind": "provenance" }, { "text": "Which entry fits drug target?", "kind": "action" } ] } ] } ] }, { "id": "context", "name": "Context", "description": "Methods and history.", "rationale": "Context.", "layers": [ { "id": "methods", "name": "Methods", "description": "Methods.", "findings": [ { "id": "methods-finding", "name": "Methods", "description": "Methods.", "questions": [ { "text": "How are transcription factors and their binding sites studied, from ChIP-seq to motif databases?", "kind": "provenance" }, { "text": "Which entry fits ChIP sequencing?", "kind": "action" } ] } ] }, { "id": "history", "name": "History", "description": "History.", "findings": [ { "id": "history-finding", "name": "History", "description": "History.", "questions": [ { "text": "How were transcription factors discovered, from the lac repressor onward?", "kind": "provenance" }, { "text": "Which entry fits the history of molecular biology?", "kind": "action" } ] } ] } ] } ] }, "openQuestions": [ "Should zinc finger protein and bZIP be separate primary entries?", "How should databases be linked?", "The registry entry has merged aliases naming individual proteins; 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": "chemical substance or material", "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 transcription factor, record what state it is in, and decide what may be done with it.", "whatItIs": "Let an agent explain transcription factors and their families, relay mechanisms, classification and examples from molecular biology references, describe roles in development and disease, and route to entries for specific factors.", "characteristics": { "substance": "material", "origin": "natural", "agency": "inert", "mobility": "varies" }, "whatYouCanDoWithIt": [ "observed and measured", "consumed or used up" ], "distinguishingFeatures": [ "Names folded into this entry, which a task may need to split apart again: Zinc finger protein WIP, PR domain zinc finger protein 1, Plant bZIP transcription factors, Zinc finger CCCH-type with G patch domain-containing protein, Transcription factor LHW-like, Myb-related protein A, GATA transcription factor 18/19/20, WUSCHEL-related homeobox 13-like, Protein WUSCHEL-like, Transcription factor PIF3-like, WUSCHEL-related homeobox 8/9-like, C2H2-type zinc-finger protein AZF1/2/3-like.", "332 finer distinctions are held as aliases rather than separate entries, because telling them apart needs a task that asks for it.", "Described in 41 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 transcription factor, and on what evidence are they told apart?" ], "whatItIsMadeOf": "matter you can touch", "physicalCharacter": [ "Mobility varies between examples.", "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", "use it up, and then need more of it" ], "howItIsRecognised": [ "Not recognisable by sight in any reliable way. Appearance varies with grade, form and additives; identification is by label, by documentation, or by assay." ], "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": [ "Zinc finger protein WIP", "PR domain zinc finger protein 1", "Plant bZIP transcription factors", "Zinc finger CCCH-type with G patch domain-containing protein", "Transcription factor LHW-like", "Myb-related protein A", "GATA transcription factor 18/19/20", "WUSCHEL-related homeobox 13-like", "Protein WUSCHEL-like", "Transcription factor PIF3-like", "WUSCHEL-related homeobox 8/9-like", "C2H2-type zinc-finger protein AZF1/2/3-like" ] } ], "standing": "Described in 41 Wikipedia languages, which measures how widely it is written about rather than how important or how common it is. 332 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 transcription factor from another, and a transcription factor 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 transcription factor, 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 transcription factor, 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 transcription factor 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 transcription factor, 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 transcription factor, 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 transcription factor 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 transcription factor 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 transcription factor, 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 transcription factor, 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 transcription factor 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 transcription factor from the things most often confused with it.", "questions": [ { "id": "distinguishing-features-q01", "text": "What identifies and describes what distinguishes a transcription factor, 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 transcription factor, 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 transcription factor is known, and what must it refuse?", "kind": "action", "answer_data": [ "permitted actions", "preconditions", "refusals", "escalation" ] } ] } ] } ] }, { "id": "form-and-composition", "name": "Form, composition and condition", "description": "What a transcription factor is made of, what shape and size it takes, and what state it is in.", "rationale": "A physical thing can be measured, and a model that cannot record its measurements cannot support any decision that depends on them.", "layers": [ { "id": "form-and-dimensions", "name": "Form and dimensions", "description": "Shape, size, mass and the ranges these take across examples.", "findings": [ { "id": "measurable-dimensions", "name": "Measurable dimensions and their units", "description": "The quantities worth recording and the units they are recorded in.", "questions": [ { "id": "measurable-dimensions-q01", "text": "What identifies and describes the dimensions of a transcription factor, and in what units or vocabulary?", "kind": "definition", "answer_data": [ "identifiers", "types and classes", "values with units", "explicit unknowns" ] }, { "id": "measurable-dimensions-q02", "text": "Who or what asserted this about the dimensions of a transcription factor, by which method, and when was it true?", "kind": "provenance", "answer_data": [ "authority", "method", "evidence", "event time", "knowledge time" ] }, { "id": "measurable-dimensions-q03", "text": "What may an agent decide or do once the dimensions of a transcription factor is known, and what must it refuse?", "kind": "action", "answer_data": [ "permitted actions", "preconditions", "refusals", "escalation" ] } ] } ] }, { "id": "material-and-composition", "name": "Material and composition", "description": "Materials, parts and how they are put together.", "findings": [ { "id": "parts-and-materials", "name": "Parts and materials", "description": "What a transcription factor is built from and which parts are replaceable.", "questions": [ { "id": "parts-and-materials-q01", "text": "What identifies and describes the composition of a transcription factor, and in what units or vocabulary?", "kind": "definition", "answer_data": [ "identifiers", "types and classes", "values with units", "explicit unknowns" ] }, { "id": "parts-and-materials-q02", "text": "Who or what asserted this about the composition of a transcription factor, by which method, and when was it true?", "kind": "provenance", "answer_data": [ "authority", "method", "evidence", "event time", "knowledge time" ] }, { "id": "parts-and-materials-q03", "text": "What may an agent decide or do once the composition of a transcription factor is known, and what must it refuse?", "kind": "action", "answer_data": [ "permitted actions", "preconditions", "refusals", "escalation" ] } ] } ] }, { "id": "condition-and-integrity", "name": "Condition and integrity", "description": "Wear, damage, health and the difference between working and broken.", "findings": [ { "id": "condition-assessment", "name": "Condition, damage and health", "description": "How the condition of a transcription factor is judged and by whom.", "questions": [ { "id": "condition-assessment-q01", "text": "What identifies and describes the condition of a transcription factor, and in what units or vocabulary?", "kind": "definition", "answer_data": [ "identifiers", "types and classes", "values with units", "explicit unknowns" ] }, { "id": "condition-assessment-q02", "text": "Who or what asserted this about the condition of a transcription factor, by which method, and when was it true?", "kind": "provenance", "answer_data": [ "authority", "method", "evidence", "event time", "knowledge time" ] }, { "id": "condition-assessment-q03", "text": "What may an agent decide or do once the condition of a transcription factor is known, and what must it refuse?", "kind": "action", "answer_data": [ "permitted actions", "preconditions", "refusals", "escalation" ] } ] } ] } ] }, { "id": "place-and-movement", "name": "Place and movement", "description": "Where a transcription factor is, how it got there and where it may go (varies).", "rationale": "A thing that can move needs its position recorded with a time, or every later claim about it is about a place it has left.", "layers": [ { "id": "location-and-placement", "name": "Location and placement", "description": "Position, containment and the reference frame the position is given in.", "findings": [ { "id": "position-and-frame", "name": "Position, container and reference frame", "description": "Where a transcription factor is, and what that position is measured against.", "questions": [ { "id": "position-and-frame-q01", "text": "What identifies and describes the location of a transcription factor, and in what units or vocabulary?", "kind": "definition", "answer_data": [ "identifiers", "types and classes", "values with units", "explicit unknowns" ] }, { "id": "position-and-frame-q02", "text": "Who or what asserted this about the location of a transcription factor, by which method, and when was it true?", "kind": "provenance", "answer_data": [ "authority", "method", "evidence", "event time", "knowledge time" ] }, { "id": "position-and-frame-q03", "text": "What may an agent decide or do once the location of a transcription factor is known, and what must it refuse?", "kind": "action", "answer_data": [ "permitted actions", "preconditions", "refusals", "escalation" ] } ] } ] }, { "id": "movement-and-transfer", "name": "Movement and transfer", "description": "How a transcription factor is carried, installed or relocated.", "findings": [ { "id": "movement-events", "name": "Movement events and constraints", "description": "What counts as a movement, what records it and what limits it.", "questions": [ { "id": "movement-events-q01", "text": "What identifies and describes the movement of a transcription factor, and in what units or vocabulary?", "kind": "definition", "answer_data": [ "identifiers", "types and classes", "values with units", "explicit unknowns" ] }, { "id": "movement-events-q02", "text": "Who or what asserted this about the movement of a transcription factor, by which method, and when was it true?", "kind": "provenance", "answer_data": [ "authority", "method", "evidence", "event time", "knowledge time" ] }, { "id": "movement-events-q03", "text": "What may an agent decide or do once the movement of a transcription factor 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 transcription factor 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 transcription factor between them.", "questions": [ { "id": "stages-and-transitions-q01", "text": "What identifies and describes the lifecycle of a transcription factor, 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 transcription factor, 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 transcription factor 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 transcription factor, how often and by whom.", "findings": [ { "id": "observation-record", "name": "Observation record", "description": "How an observation of a transcription factor 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 transcription factor, 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 transcription factor, 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 transcription factor is known, and what must it refuse?", "kind": "action", "answer_data": [ "permitted actions", "preconditions", "refusals", "escalation" ] } ] } ] } ] }, { "id": "use-and-operation", "name": "Use and operation", "description": "What can be done with a transcription factor and what it takes to do it.", "rationale": "An agent that can recognise a thing but not act on it has only half a model.", "layers": [ { "id": "intended-use", "name": "Intended use and function", "description": "What a transcription factor is for, and what it is used for anyway.", "findings": [ { "id": "function-and-purpose", "name": "Function, purpose and misuse", "description": "The function a transcription factor performs and the uses that fall outside it.", "questions": [ { "id": "function-and-purpose-q01", "text": "What identifies and describes the use of a transcription factor, and in what units or vocabulary?", "kind": "definition", "answer_data": [ "identifiers", "types and classes", "values with units", "explicit unknowns" ] }, { "id": "function-and-purpose-q02", "text": "Who or what asserted this about the use of a transcription factor, by which method, and when was it true?", "kind": "provenance", "answer_data": [ "authority", "method", "evidence", "event time", "knowledge time" ] }, { "id": "function-and-purpose-q03", "text": "What may an agent decide or do once the use of a transcription factor is known, and what must it refuse?", "kind": "action", "answer_data": [ "permitted actions", "preconditions", "refusals", "escalation" ] } ] } ] }, { "id": "handling-and-procedure", "name": "Handling and procedure", "description": "The steps, skills and tools involved in using a transcription factor.", "findings": [ { "id": "procedures-and-skills", "name": "Procedures, skills and required tools", "description": "What an agent needs before it can act on a transcription factor at all.", "questions": [ { "id": "procedures-and-skills-q01", "text": "What identifies and describes handling a transcription factor, and in what units or vocabulary?", "kind": "definition", "answer_data": [ "identifiers", "types and classes", "values with units", "explicit unknowns" ] }, { "id": "procedures-and-skills-q02", "text": "Who or what asserted this about handling a transcription factor, by which method, and when was it true?", "kind": "provenance", "answer_data": [ "authority", "method", "evidence", "event time", "knowledge time" ] }, { "id": "procedures-and-skills-q03", "text": "What may an agent decide or do once handling a transcription factor is known, and what must it refuse?", "kind": "action", "answer_data": [ "permitted actions", "preconditions", "refusals", "escalation" ] } ] } ] }, { "id": "supply-and-consumption", "name": "Supply and consumption", "description": "Quantities, rates and what running out means.", "findings": [ { "id": "consumption-and-stock", "name": "Consumption, stock and replenishment", "description": "How much of a transcription factor there is and how fast it goes.", "questions": [ { "id": "consumption-and-stock-q01", "text": "What identifies and describes the supply of a transcription factor, and in what units or vocabulary?", "kind": "definition", "answer_data": [ "identifiers", "types and classes", "values with units", "explicit unknowns" ] }, { "id": "consumption-and-stock-q02", "text": "Who or what asserted this about the supply of a transcription factor, by which method, and when was it true?", "kind": "provenance", "answer_data": [ "authority", "method", "evidence", "event time", "knowledge time" ] }, { "id": "consumption-and-stock-q03", "text": "What may an agent decide or do once the supply of a transcription factor is known, and what must it refuse?", "kind": "action", "answer_data": [ "permitted actions", "preconditions", "refusals", "escalation" ] } ] } ] } ] }, { "id": "composition-and-identity", "name": "Composition, grade and chemical identity", "description": "What transcription factor is made of and how pure the thing in hand is.", "rationale": "Grade decides what a substance may be used for, so a model that records only the name cannot support any decision about use.", "layers": [ { "id": "chemical-identity", "name": "Chemical identity", "description": "Formula, structure and the registry numbers that name it unambiguously.", "findings": [ { "id": "identity-record", "name": "Identity and registry numbers", "description": "What identifies this substance across suppliers and regulators.", "questions": [ { "id": "identity-record-q01", "text": "What formula, structure and registry identifiers name transcription factor unambiguously?", "kind": "definition" }, { "id": "identity-record-q02", "text": "Which related substances share a name in common use but not an identifier?", "kind": "boundary" } ] } ] }, { "id": "grade-and-impurities", "name": "Grade, purity and impurities", "description": "The specification a batch meets and what else is in it.", "findings": [ { "id": "specification", "name": "Specification and assay", "description": "How purity is stated and measured, and which impurities matter.", "questions": [ { "id": "specification-q01", "text": "What grades of transcription factor exist, how is purity assayed, and which impurities are limited?", "kind": "measurement" }, { "id": "specification-q02", "text": "Which use requires which grade, and what happens when a lower grade is substituted?", "kind": "action" } ] } ] } ] }, { "id": "properties-and-behaviour", "name": "Properties and behaviour", "description": "How transcription factor behaves under conditions an agent can measure or change.", "rationale": "Physical constants are the part of a substance model that transfers between contexts, and each needs its unit and its conditions.", "layers": [ { "id": "physical-constants", "name": "Physical constants", "description": "Values that hold for the pure substance, with their conditions.", "findings": [ { "id": "constants-record", "name": "Constants and conditions", "description": "The quantities worth recording and the state they apply in.", "questions": [ { "id": "constants-record-q01", "text": "What are the defining physical constants of transcription factor, in what units and under what conditions?", "kind": "measurement" }, { "id": "constants-record-q02", "text": "Which of these values change with grade or form rather than being fixed?", "kind": "boundary" } ] } ] }, { "id": "stability-and-reactivity", "name": "Stability and reactivity", "description": "What it reacts with, degrades into, and how it is stored.", "findings": [ { "id": "incompatibilities", "name": "Incompatibilities and degradation", "description": "What must not meet it, and what it becomes over time.", "questions": [ { "id": "incompatibilities-q01", "text": "What is transcription factor incompatible with, and what does it degrade into under storage?", "kind": "definition" }, { "id": "incompatibilities-q02", "text": "What storage and handling does that require, and who is competent to do it?", "kind": "action" } ] } ] } ] }, { "id": "hazard-and-regulation", "name": "Hazard classification and regulation", "description": "How transcription factor can harm, and what the law says about holding and moving it.", "rationale": "A substance model without its hazard class and its regulatory identity is unusable in exactly the situations that matter.", "layers": [ { "id": "hazard-class", "name": "Hazard classification", "description": "Classified hazards, exposure limits and protective measures.", "findings": [ { "id": "classified-hazards", "name": "Classified hazards and limits", "description": "The classification, the scheme it belongs to, and the limits set.", "questions": [ { "id": "classified-hazards-q01", "text": "How is transcription factor classified for hazard, under which scheme, and what exposure limits apply?", "kind": "definition" }, { "id": "classified-hazards-q02", "text": "What protection does handling require, and what must an agent refuse to do without it?", "kind": "action" } ] } ] }, { "id": "regulatory-identity", "name": "Regulatory identity and control", "description": "Registration, restriction and transport rules by jurisdiction.", "findings": [ { "id": "controls", "name": "Controls and jurisdiction", "description": "Where it is restricted and what the restriction attaches to.", "questions": [ { "id": "controls-q01", "text": "Which registrations, restrictions or transport rules cover transcription factor, and where?", "kind": "provenance" }, { "id": "controls-q02", "text": "Does the control attach to the substance, its concentration, or its intended use?", "kind": "boundary" } ] } ] } ] }, { "id": "provenance-and-evidence", "name": "Provenance, evidence and time", "description": "Where every claim about a transcription factor 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 transcription factor and how confident it is.", "questions": [ { "id": "claim-provenance-q01", "text": "What identifies and describes a claim about a transcription factor, 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 transcription factor, 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 transcription factor 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 transcription factor is retired without being erased.", "questions": [ { "id": "validity-and-supersession-q01", "text": "What identifies and describes the validity of a claim about a transcription factor, 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 transcription factor, 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 transcription factor is known, and what must it refuse?", "kind": "action", "answer_data": [ "permitted actions", "preconditions", "refusals", "escalation" ] } ] } ] } ] } ] }, "statistics": { "bundles": 9, "layers": 20, "findings": 22, "questions": 60 } } } }