{ "model": { "rank": 14706, "code": "thing-q407727", "model_id": "vr.tr.lyase", "name": "lyase", "purpose": "Let an agent explain lyases and their classification, relay subclasses and examples from enzyme databases, describe roles in metabolism and biotechnology, and distinguish lyases 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/q407727/", "tier": 2, "score": 35, "payload": { "layer": "wikidata", "aliases": [ "Dihydroxy-acid/6-phosphogluconate dehydratase", "Holocytochrome-c synthase", "Peptidylamidoglycolate lyase", "1,4-Dihydroxy-2-naphthoyl-CoA synthase, MenB", "D-cysteine desulphhydrase, bacterial", "L-methionine gamma-lyase", "Cystathionine beta-lyase, eukaryotic", "Cystathionine beta-lyase, bacterial", "Aminodeoxychorismate lyase, class IV", "3-dehydroquinate synthase", "carbon-sulfur lyase", "phosphorus-oxygen lyase", "carbon-halide lyase", "carbon-nitrogen lyase", "Drimenol cyclase", "Ribonuclease T2", "Bacillus subtilis ribonuclease", "Ribonuclease U2", "Enterobacter ribonuclease", "TRNA-intron endonuclease", "Mesaconyl-CoA hydratase", "Isoprene synthase", "Indole-3-glycerol-phosphate lyase", "Mandelonitrile lyase", "4-(2-carboxyphenyl)-2-oxobut-3-enoate aldolase", "D-threonine aldolase", "3-hexulose-6-phosphate synthase", "Benzoyl-CoA-dihydrodiol lyase", "Trans-o-hydroxybenzylidenepyruvate hydratase-aldolase", "Aliphatic (R)-hydroxynitrile lyase", "(S)-hydroxynitrile lyase", "Low-specificity L-threonine aldolase", "6-carboxytetrahydropterin synthase", "N-acetylneuraminate lyase", "Naphthoate synthase", "3-hydroxy-D-aspartate aldolase", "(6-4)DNA photolyase", "Phosphomethylpyrimidine synthase", "Cyclic pyranopterin monophosphate synthase", "2-iminoacetate synthase" ], "aliasCount": 468, "merged": 475, "knownIn": 35, "facets": null, "markers": [], "lexicalClass": "", "senseRank": null, "alsoRegisteredAs": null, "source": { "dataset": "wikidata", "item": "Q407727", "url": "https://www.wikidata.org/wiki/Q407727", "license": "CC0 1.0" } }, "research": { "vercy": "1.0-draft", "publication": { "status": "research-draft", "adjudicationStatus": "unreviewed", "publishableCanonical": false, "generatedAt": "2026-09-13T00:40:15Z", "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-Q407727", "registryId": "vr.tr.lyase", "name": "lyase", "version": "0.2.0-wave.3", "entryKind": "thing", "family": "Thing Registry", "domain": [ "PHY.MAT" ], "status": "research-draft" }, "canonicalUrl": "https://ver.cy/models/thing/q407727/", "model": { "registry_id": "vr.tr.lyase", "name": "lyase", "purpose": "Let an agent explain lyases and their classification, relay subclasses and examples from enzyme databases, describe roles in metabolism and biotechnology, and distinguish lyases from other enzyme classes.", "definition": "A class of enzymes that catalyse the breaking of chemical bonds by means other than hydrolysis or oxidation, forming a double bond or ring, or the reverse addition of groups to double bonds, classified as EC 4 and including decarboxylases, aldolases, dehydratases such as dihydroxy-acid dehydratase, desulfhydrases such as D-cysteine desulfhydrase, methionine gamma-lyase, holocytochrome-c synthase and many others; lyases are central to metabolism and are used in biocatalysis.", "what_it_is_for": "Catalysing non-hydrolytic bond cleavage and addition.", "affordances": [ "explain the class and subclasses", "relay examples and nomenclature", "describe metabolic and industrial roles", "distinguish from other classes" ], "distinguishing_features": [ "Non-hydrolytic cleavage", "Double bond or ring formation", "Seven subclasses", "Reversible addition" ], "appearance": "Not visible; proteins shown as structural models.", "visual_identification": [ "EC 4 enzymes", "Carbon-carbon, carbon-oxygen, carbon-nitrogen and carbon-sulfur lyases", "Hydrolases use water; oxidoreductases transfer electrons; ligases join with ATP" ], "physical_properties": [], "families_and_kinds": [ "carbon-carbon lyases such as decarboxylases and aldolases", "carbon-oxygen lyases such as dehydratases", "carbon-nitrogen lyases", "carbon-sulfur lyases such as desulfhydrases and methionine gamma-lyase", "carbon-halide and phosphorus-oxygen lyases", "other lyases such as holocytochrome-c synthase" ], "related_models": [ { "relation": "is a kind of", "target": "enzyme", "why": "in registry terms" }, { "relation": "is classified as", "target": "EC 4", "why": "in the Enzyme Commission system" }, { "relation": "is contrasted with", "target": "hydrolase", "why": "EC 3" }, { "relation": "acts in", "target": "metabolic pathway", "why": "such as glycolysis" } ], "identifiers": [ { "scheme": "EC number", "value_or_pattern": "4.-.-.-", "note": "" }, { "scheme": "Gene Ontology", "value_or_pattern": "GO:0016829", "note": "lyase activity" } ], "standards_and_regulation": [ "IUBMB enzyme nomenclature", "Regulation of enzymes used in food and pharmaceuticals" ], "failure_modes_and_hazards": [ "Misclassifying enzymes", "Outdated nomenclature", "Confusing lyases with synthases in naming" ], "in_scope": [], "out_of_scope": [], "characteristics": [] }, "sources": [], "structure": { "bundles": [ { "id": "understand", "name": "Understand", "description": "What lyases are.", "rationale": "Science.", "layers": [ { "id": "definition", "name": "Definition", "description": "Definition and subclasses.", "findings": [ { "id": "definition-finding", "name": "Definition", "description": "Definition.", "questions": [ { "text": "What is a lyase, and what subclasses exist?", "kind": "definition" }, { "text": "Is the enzyme a lyase or another class?", "kind": "boundary" } ] } ] }, { "id": "mechanism", "name": "Mechanism", "description": "Mechanisms.", "findings": [ { "id": "mechanism-finding", "name": "Mechanism", "description": "Mechanism.", "questions": [ { "text": "How do lyases catalyse elimination and addition reactions?", "kind": "definition" }, { "text": "Which entry fits the specific enzyme?", "kind": "action" } ] } ] } ] }, { "id": "biology", "name": "Biology", "description": "Metabolic roles.", "rationale": "Science.", "layers": [ { "id": "metabolism", "name": "Metabolism", "description": "Metabolism.", "findings": [ { "id": "metabolism-finding", "name": "Metabolism", "description": "Metabolism.", "questions": [ { "text": "What roles do lyases play in glycolysis, amino acid metabolism and other pathways?", "kind": "provenance" }, { "text": "Which entry fits the specific pathway?", "kind": "action" } ] } ] }, { "id": "disease", "name": "Disease", "description": "Disease.", "findings": [ { "id": "disease-finding", "name": "Disease", "description": "Disease.", "questions": [ { "text": "Which lyase deficiencies cause disease, in general terms?", "kind": "provenance" }, { "text": "Is the user asking about a personal diagnosis, which needs a clinician?", "kind": "boundary" } ] } ] } ] }, { "id": "apply", "name": "Apply", "description": "Applications.", "rationale": "Application.", "layers": [ { "id": "biocatalysis", "name": "Biocatalysis", "description": "Biocatalysis.", "findings": [ { "id": "biocatalysis-finding", "name": "Biocatalysis", "description": "Biocatalysis.", "questions": [ { "text": "How are lyases used in industrial biocatalysis and synthesis?", "kind": "provenance" }, { "text": "Which references are standard?", "kind": "provenance" } ] } ] }, { "id": "therapy", "name": "Therapy", "description": "Therapeutic and diagnostic uses.", "findings": [ { "id": "therapy-finding", "name": "Therapy", "description": "Therapy.", "questions": [ { "text": "How are lyases such as methionine gamma-lyase studied for therapy, with findings attributed?", "kind": "provenance" }, { "text": "Which sources are cited?", "kind": "provenance" } ] } ] } ] }, { "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 lyases, and why are some named synthases?", "kind": "provenance" }, { "text": "Which entry fits enzyme nomenclature?", "kind": "action" } ] } ] }, { "id": "history", "name": "History", "description": "History.", "findings": [ { "id": "history-finding", "name": "History", "description": "History.", "questions": [ { "text": "How were lyases discovered and classified?", "kind": "provenance" }, { "text": "Which entry fits the history of enzymology?", "kind": "action" } ] } ] } ] } ] }, "openQuestions": [ "Should each subclass be a separate entry?", "How should enzyme databases be linked?", "The registry entry has merged aliases naming specific enzymes; 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 lyase, record what state it is in, and decide what may be done with it.", "whatItIs": "Let an agent explain lyases and their classification, relay subclasses and examples from enzyme databases, describe roles in metabolism and biotechnology, and distinguish lyases 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: Dihydroxy-acid/6-phosphogluconate dehydratase, Holocytochrome-c synthase, Peptidylamidoglycolate lyase, 1,4-Dihydroxy-2-naphthoyl-CoA synthase, MenB, D-cysteine desulphhydrase, bacterial, L-methionine gamma-lyase, Cystathionine beta-lyase, eukaryotic, Cystathionine beta-lyase, bacterial, Aminodeoxychorismate lyase, class IV, 3-dehydroquinate synthase, carbon-sulfur lyase, phosphorus-oxygen lyase.", "475 finer distinctions are held as aliases rather than separate entries, because telling them apart needs a task that asks for it.", "Described in 35 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 lyase, 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": [ "Dihydroxy-acid/6-phosphogluconate dehydratase", "Holocytochrome-c synthase", "Peptidylamidoglycolate lyase", "1,4-Dihydroxy-2-naphthoyl-CoA synthase, MenB", "D-cysteine desulphhydrase, bacterial", "L-methionine gamma-lyase", "Cystathionine beta-lyase, eukaryotic", "Cystathionine beta-lyase, bacterial", "Aminodeoxychorismate lyase, class IV", "3-dehydroquinate synthase", "carbon-sulfur lyase", "phosphorus-oxygen lyase" ] } ], "standing": "Described in 35 Wikipedia languages, which measures how widely it is written about rather than how important or how common it is. 475 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 lyase from another, and a lyase 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 lyase, 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 lyase, 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 lyase 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 lyase, 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 lyase, 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 lyase 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 lyase 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 lyase, 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 lyase, 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 lyase 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 lyase from the things most often confused with it.", "questions": [ { "id": "distinguishing-features-q01", "text": "What identifies and describes what distinguishes a lyase, 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 lyase, 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 lyase 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 lyase 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 lyase, 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 lyase, 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 lyase 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 lyase is built from and which parts are replaceable.", "questions": [ { "id": "parts-and-materials-q01", "text": "What identifies and describes the composition of a lyase, 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 lyase, 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 lyase 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 lyase is judged and by whom.", "questions": [ { "id": "condition-assessment-q01", "text": "What identifies and describes the condition of a lyase, 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 lyase, 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 lyase 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 lyase 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 lyase is, and what that position is measured against.", "questions": [ { "id": "position-and-frame-q01", "text": "What identifies and describes the location of a lyase, 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 lyase, 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 lyase 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 lyase 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 lyase, 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 lyase, 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 lyase 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 lyase 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 lyase between them.", "questions": [ { "id": "stages-and-transitions-q01", "text": "What identifies and describes the lifecycle of a lyase, 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 lyase, 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 lyase 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 lyase, how often and by whom.", "findings": [ { "id": "observation-record", "name": "Observation record", "description": "How an observation of a lyase 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 lyase, 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 lyase, 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 lyase 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 lyase 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 lyase is for, and what it is used for anyway.", "findings": [ { "id": "function-and-purpose", "name": "Function, purpose and misuse", "description": "The function a lyase performs and the uses that fall outside it.", "questions": [ { "id": "function-and-purpose-q01", "text": "What identifies and describes the use of a lyase, 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 lyase, 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 lyase 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 lyase.", "findings": [ { "id": "procedures-and-skills", "name": "Procedures, skills and required tools", "description": "What an agent needs before it can act on a lyase at all.", "questions": [ { "id": "procedures-and-skills-q01", "text": "What identifies and describes handling a lyase, 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 lyase, 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 lyase 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 lyase there is and how fast it goes.", "questions": [ { "id": "consumption-and-stock-q01", "text": "What identifies and describes the supply of a lyase, 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 lyase, 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 lyase 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 lyase 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 lyase 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 lyase 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 lyase 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 lyase, 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 lyase 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 lyase 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 lyase 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 lyase, 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 lyase 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 lyase and how confident it is.", "questions": [ { "id": "claim-provenance-q01", "text": "What identifies and describes a claim about a lyase, 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 lyase, 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 lyase 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 lyase is retired without being erased.", "questions": [ { "id": "validity-and-supersession-q01", "text": "What identifies and describes the validity of a claim about a lyase, 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 lyase, 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 lyase 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 } } } }