{ "model": { "rank": 13588, "code": "thing-q118026", "model_id": "vr.tr.isomerase", "name": "isomerase", "purpose": "Let an agent explain isomerases and their classification, relay examples and mechanisms from biochemistry references, describe roles in metabolism and DNA, and distinguish isomerases from other enzyme classes.", "family": "Thing Registry", "category": "Physical world and living systems", "status": "research-draft", "kind": "thing", "plane": "PHY", "domain": "PHY.MAT", "industry": "", "version": "", "url": "/models/thing/q118026/", "tier": 2, "score": 37, "payload": { "layer": "wikidata", "aliases": [ "2,3-bisphosphoglycerate-independent phosphoglycerate mutase", "Fumarate lyase", "Tartrate epimerase", "Microtubule-severing ATPase", "topoisomerase", "Racemase Bsr/Lyr", "UDP-N-acetyl-alpha-D-muramoyl-L-alanyl-L-glutamate epimerase MurL", "intramolecular lyase", "3-hydroxybutyryl-CoA epimerase", "lactate racemase", "epimerase and racemase", "mutase", "microfilament motor", "microtubule motor", "plus-end-directed kinesin ATPase", "Minus-end-directed kinesin ATPase", "chaperonin ATPase", "UDP-N-acetylglucosamine 2-epimerase", "UDP-2,3-diacetamido-2,3-dideoxyglucuronic acid 2-epimerase", "N-acetylneuraminate epimerase", "dTDP-L-rhamnose 4-epimerase", "Hydantoin racemase", "NAD(P)H-hydrate epimerase", "1-(5-phosphoribosyl)-5-((5-phosphoribosylamino)methylideneamino)imidazole-4-carboxamide isomerase", "6-phospho-3-hexuloisomerase", "TDP-4-oxo-6-deoxy-alpha-D-glucose-3,4-oxoisomerase (dTDP-3-dehydro-6-deoxy-alpha-D-galactopyranose-forming)", "TDP-4-oxo-6-deoxy-alpha-D-glucose-3,4-oxoisomerase (dTDP-3-dehydro-6-deoxy-alpha-D-glucopyranose-forming)", "2-hydroxymuconate tautomerase", "Methylitaconate Delta-isomerase", "Isopiperitenone Delta-isomerase", "4-oxalomesaconate tautomerase", "Trans-2,3-dihydro-3-hydroxyanthranilate isomerase", "2-(1,2-epoxy-1,2-dihydrophenyl)acetyl-CoA isomerase", "Capsanthin/capsorubin synthase", "Neoxanthin synthase", "Thiazole tautomerase", "Glutamate 2,3-aminomutase", "Geraniol isomerase", "9,12-octadecadienoate 8-hydroperoxide 8R-isomerase", "9,12-octadecadienoate 8-hydroperoxide 8S-isomerase" ], "aliasCount": 373, "merged": 384, "knownIn": 37, "facets": null, "markers": [], "lexicalClass": "", "senseRank": null, "alsoRegisteredAs": null, "source": { "dataset": "wikidata", "item": "Q118026", "url": "https://www.wikidata.org/wiki/Q118026", "license": "CC0 1.0" } }, "research": { "vercy": "1.0-draft", "publication": { "status": "research-draft", "adjudicationStatus": "unreviewed", "publishableCanonical": false, "generatedAt": "2026-09-13T03:05:08Z", "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-Q118026", "registryId": "vr.tr.isomerase", "name": "isomerase", "version": "0.2.0-wave.3", "entryKind": "thing", "family": "Thing Registry", "domain": [ "PHY.MAT" ], "status": "research-draft" }, "canonicalUrl": "https://ver.cy/models/thing/q118026/", "model": { "registry_id": "vr.tr.isomerase", "name": "isomerase", "purpose": "Let an agent explain isomerases and their classification, relay examples and mechanisms from biochemistry references, describe roles in metabolism and DNA, and distinguish isomerases from other enzyme classes.", "definition": "An enzyme that catalyses the conversion of a molecule into one of its isomers by rearranging bonds without changing the molecular formula, classified as EC 5 in enzyme nomenclature and including racemases and epimerases such as tartrate epimerase, intramolecular oxidoreductases, intramolecular transferases or mutases such as phosphoglycerate mutase, intramolecular lyases, and topoisomerases that change DNA topology; isomerases act in glycolysis, DNA replication and many metabolic pathways.", "what_it_is_for": "Not applicable; an enzyme class.", "affordances": [ "explain the class and subclasses", "relay examples and mechanisms", "describe biological roles", "distinguish from other classes" ], "distinguishing_features": [ "Intramolecular rearrangement", "Same molecular formula", "Six subclasses", "Metabolic and DNA roles" ], "appearance": "Not a visible object; proteins in cells.", "visual_identification": [ "EC 5 enzymes converting isomers", "Racemases, epimerases, mutases, cis-trans isomerases, topoisomerases", "Lyases break bonds without hydrolysis; transferases move groups between molecules; some registry aliases such as fumarate lyase and microtubule-severing ATPase belong to other classes" ], "physical_properties": [ { "quantity": "EC class", "typical_range": "5", "unit": "number", "note": "" }, { "quantity": "subclasses", "typical_range": "6", "unit": "count", "note": "EC 5.1 to 5.6" } ], "families_and_kinds": [ "racemases and epimerases, EC 5.1", "cis-trans isomerases, EC 5.2", "intramolecular oxidoreductases such as triosephosphate isomerase, EC 5.3", "intramolecular transferases or mutases such as phosphoglycerate mutase, EC 5.4", "intramolecular lyases, EC 5.5", "isomerases altering macromolecular conformation including topoisomerases, EC 5.6" ], "related_models": [ { "relation": "is a kind of", "target": "enzyme", "why": "in registry terms" }, { "relation": "is classified under", "target": "Enzyme Commission number", "why": "as EC 5" }, { "relation": "includes", "target": "topoisomerase", "why": "acting on DNA" }, { "relation": "acts in", "target": "glycolysis", "why": "through several steps" } ], "identifiers": [ { "scheme": "EC", "value_or_pattern": "5", "note": "isomerases" }, { "scheme": "GO", "value_or_pattern": "GO:0016853", "note": "isomerase activity" } ], "standards_and_regulation": [ "IUBMB enzyme nomenclature", "No regulation of the concept" ], "failure_modes_and_hazards": [ "Misclassifying enzymes across EC classes", "Confusing isomerases with lyases and transferases", "Registry aliases that belong to other classes" ], "in_scope": [], "out_of_scope": [], "characteristics": [] }, "sources": [], "structure": { "bundles": [ { "id": "understand", "name": "Understand", "description": "What isomerases are.", "rationale": "Science.", "layers": [ { "id": "definition", "name": "Definition", "description": "Definition and classification.", "findings": [ { "id": "definition-finding", "name": "Definition", "description": "Definition.", "questions": [ { "text": "What is an isomerase, and how are the six subclasses defined?", "kind": "definition" }, { "text": "Is the enzyme an isomerase or a member of another EC class?", "kind": "boundary" } ] } ] }, { "id": "examples", "name": "Examples", "description": "Examples.", "findings": [ { "id": "examples-finding", "name": "Examples", "description": "Examples.", "questions": [ { "text": "What do phosphoglycerate mutase, tartrate epimerase, triosephosphate isomerase and topoisomerases do?", "kind": "definition" }, { "text": "Which entry fits the specific enzyme?", "kind": "action" } ] } ] } ] }, { "id": "mechanism", "name": "Mechanism", "description": "Mechanisms.", "rationale": "Science.", "layers": [ { "id": "catalysis", "name": "Catalysis", "description": "Catalytic mechanisms.", "findings": [ { "id": "catalysis-finding", "name": "Catalysis", "description": "Catalysis.", "questions": [ { "text": "How do isomerases rearrange bonds, and what cofactors do they use?", "kind": "provenance" }, { "text": "Which references are standard?", "kind": "provenance" } ] } ] }, { "id": "topology", "name": "Topology", "description": "DNA topology.", "findings": [ { "id": "topology-finding", "name": "Topology", "description": "Topology.", "questions": [ { "text": "How do topoisomerases change DNA supercoiling, and why are they drug targets?", "kind": "provenance" }, { "text": "Which entry fits topoisomerase?", "kind": "action" } ] } ] } ] }, { "id": "biology", "name": "Biology", "description": "Biological roles.", "rationale": "Science.", "layers": [ { "id": "metabolism", "name": "Metabolism", "description": "Metabolism.", "findings": [ { "id": "metabolism-finding", "name": "Metabolism", "description": "Metabolism.", "questions": [ { "text": "Where do isomerases act in glycolysis, the pentose phosphate pathway and other metabolism?", "kind": "provenance" }, { "text": "Which sources are cited?", "kind": "provenance" } ] } ] }, { "id": "medicine", "name": "Medicine", "description": "Medicine and industry.", "findings": [ { "id": "medicine-finding", "name": "Medicine", "description": "Medicine.", "questions": [ { "text": "How are isomerases targeted by drugs and used in industry such as glucose isomerase for high-fructose syrup?", "kind": "provenance" }, { "text": "Which entry fits glucose isomerase?", "kind": "action" } ] } ] } ] }, { "id": "context", "name": "Context", "description": "Nomenclature and history.", "rationale": "Context.", "layers": [ { "id": "nomenclature", "name": "Nomenclature", "description": "Nomenclature.", "findings": [ { "id": "nomenclature-finding", "name": "Nomenclature", "description": "Nomenclature.", "questions": [ { "text": "How does the EC system classify enzymes, and why is EC 5.6 a recent addition?", "kind": "provenance" }, { "text": "Which entry fits Enzyme Commission number?", "kind": "action" } ] } ] }, { "id": "history", "name": "History", "description": "History.", "findings": [ { "id": "history-finding", "name": "History", "description": "History.", "questions": [ { "text": "How were isomerases discovered and characterised?", "kind": "provenance" }, { "text": "Which entry fits the history of enzymology?", "kind": "action" } ] } ] } ] } ] }, "openQuestions": [ "Should topoisomerase be a separate primary entry?", "How should enzyme databases be linked?", "The registry entry has merged aliases including non-isomerase enzymes; should they be corrected?" ], "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 isomerase, record what state it is in, and decide what may be done with it.", "whatItIs": "Let an agent explain isomerases and their classification, relay examples and mechanisms from biochemistry references, describe roles in metabolism and DNA, and distinguish isomerases from other enzyme classes.", "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: 2,3-bisphosphoglycerate-independent phosphoglycerate mutase, Fumarate lyase, Tartrate epimerase, Microtubule-severing ATPase, topoisomerase, Racemase Bsr/Lyr, UDP-N-acetyl-alpha-D-muramoyl-L-alanyl-L-glutamate epimerase MurL, intramolecular lyase, 3-hydroxybutyryl-CoA epimerase, lactate racemase, epimerase and racemase, mutase.", "384 finer distinctions are held as aliases rather than separate entries, because telling them apart needs a task that asks for it.", "Described in 37 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 isomerase, 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": [ "2,3-bisphosphoglycerate-independent phosphoglycerate mutase", "Fumarate lyase", "Tartrate epimerase", "Microtubule-severing ATPase", "topoisomerase", "Racemase Bsr/Lyr", "UDP-N-acetyl-alpha-D-muramoyl-L-alanyl-L-glutamate epimerase MurL", "intramolecular lyase", "3-hydroxybutyryl-CoA epimerase", "lactate racemase", "epimerase and racemase", "mutase" ] } ], "standing": "Described in 37 Wikipedia languages, which measures how widely it is written about rather than how important or how common it is. 384 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 isomerase from another, and a isomerase 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 isomerase, 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 isomerase, 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 isomerase 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 isomerase, 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 isomerase, 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 isomerase 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 isomerase 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 isomerase, 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 isomerase, 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 isomerase 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 isomerase from the things most often confused with it.", "questions": [ { "id": "distinguishing-features-q01", "text": "What identifies and describes what distinguishes a isomerase, 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 isomerase, 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 isomerase 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 isomerase 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 isomerase, 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 isomerase, 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 isomerase 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 isomerase is built from and which parts are replaceable.", "questions": [ { "id": "parts-and-materials-q01", "text": "What identifies and describes the composition of a isomerase, 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 isomerase, 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 isomerase 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 isomerase is judged and by whom.", "questions": [ { "id": "condition-assessment-q01", "text": "What identifies and describes the condition of a isomerase, 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 isomerase, 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 isomerase 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 isomerase 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 isomerase is, and what that position is measured against.", "questions": [ { "id": "position-and-frame-q01", "text": "What identifies and describes the location of a isomerase, 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 isomerase, 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 isomerase 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 isomerase 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 isomerase, 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 isomerase, 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 isomerase 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 isomerase 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 isomerase between them.", "questions": [ { "id": "stages-and-transitions-q01", "text": "What identifies and describes the lifecycle of a isomerase, 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 isomerase, 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 isomerase 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 isomerase, how often and by whom.", "findings": [ { "id": "observation-record", "name": "Observation record", "description": "How an observation of a isomerase 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 isomerase, 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 isomerase, 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 isomerase 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 isomerase 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 isomerase is for, and what it is used for anyway.", "findings": [ { "id": "function-and-purpose", "name": "Function, purpose and misuse", "description": "The function a isomerase performs and the uses that fall outside it.", "questions": [ { "id": "function-and-purpose-q01", "text": "What identifies and describes the use of a isomerase, 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 isomerase, 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 isomerase 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 isomerase.", "findings": [ { "id": "procedures-and-skills", "name": "Procedures, skills and required tools", "description": "What an agent needs before it can act on a isomerase at all.", "questions": [ { "id": "procedures-and-skills-q01", "text": "What identifies and describes handling a isomerase, 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 isomerase, 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 isomerase 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 isomerase there is and how fast it goes.", "questions": [ { "id": "consumption-and-stock-q01", "text": "What identifies and describes the supply of a isomerase, 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 isomerase, 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 isomerase 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 isomerase 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 isomerase 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 isomerase 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 isomerase 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 isomerase, 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 isomerase 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 isomerase 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 isomerase 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 isomerase, 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 isomerase 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 isomerase and how confident it is.", "questions": [ { "id": "claim-provenance-q01", "text": "What identifies and describes a claim about a isomerase, 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 isomerase, 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 isomerase 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 isomerase is retired without being erased.", "questions": [ { "id": "validity-and-supersession-q01", "text": "What identifies and describes the validity of a claim about a isomerase, 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 isomerase, 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 isomerase 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 } } } }