{ "model": { "rank": 18146, "code": "thing-q424288", "model_id": "vr.tr.transaminase", "name": "transaminase", "purpose": "Let an agent explain transaminases, relay mechanism, metabolic roles, clinical testing and biocatalysis from biochemistry and clinical sources, describe the named enzymes, explain that abnormal liver enzyme results need interpretation by a clinician, and distinguish transaminases from deaminases, other transferases and liver function as a whole.", "family": "Thing Registry", "category": "Physical world and living systems", "status": "research-draft", "kind": "thing", "plane": "PHY", "domain": "PHY.MAT", "industry": "", "version": "", "url": "/models/thing/q424288/", "tier": 2, "score": 30, "payload": { "layer": "wikidata", "aliases": [ "D-amino acid aminotransferase", "Branched-chain aminotransferase", "(R)-3-amino-2-methylpropionate-pyruvate transaminase", "(S)-3-amino-2-methylpropionate transaminase", "Lysine-pyruvate 6-transaminase", "Methionine-glyoxylate transaminase", "N6-acetyl-beta-lysine transaminase", "Phenylalanine(histidine) transaminase", "Nicotianamine aminotransferase", "(S)-8-amino-7-oxononanoate synthase BioU-like", "Aminotransferase ALAT1/2-like", "Succinyldiaminopimelate transaminase, DapC, beta/gammaproteobacteria", "Diaminopimelate aminotransferase, DapL, Desulfovibrio-type", "Phosphoserine aminotransferase", "Tyrosine/nicotianamine aminotransferase", "Aminotransferase class-III", "Aspartate/other aminotransferase", "LL-diaminopimelate aminotransferase/aminotransferase ALD1", "Branched-chain amino acid aminotransferase II", "Branched-chain amino acid aminotransferase I", "Histidinol-phosphate aminotransferase family", "Putrescine aminotransferase", "2-aminoethylphosphonate-pyruvate transaminase", "UDP-4-amino-4-deoxy-L-arabinose-oxoglutarate aminotransferase, ArnB", "glucosamine-fructose-6-phosphate aminotransferase, isomerising", "Succinylornithine transaminase", "1D-1-guanidino-3-amino-1,3-dideoxy-scyllo-inositol transaminase", "2,5-diaminovalerate transaminase", "2-aminoadipate transaminase", "2-aminohexanoate transaminase", "4-aminobutyrate transaminase", "4-hydroxyglutamate transaminase", "5-aminovalerate transaminase", "Acetylornithine transaminase", "Adenosylmethionine-8-amino-7-oxononanoate transaminase", "Alanine-glyoxylate transaminase", "Alanine-oxo-acid transaminase", "Alanine-oxomalonate transaminase", "4-amino-4-deoxychorismate synthase", "Aminolevulinate transaminase" ], "aliasCount": 112, "merged": 114, "knownIn": 30, "facets": null, "markers": [], "lexicalClass": "", "senseRank": null, "alsoRegisteredAs": null, "source": { "dataset": "wikidata", "item": "Q424288", "url": "https://www.wikidata.org/wiki/Q424288", "license": "CC0 1.0" } }, "research": { "vercy": "1.0-draft", "publication": { "status": "research-draft", "adjudicationStatus": "unreviewed", "publishableCanonical": false, "generatedAt": "2026-09-13T20:08:43Z", "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": 4, "engine": "claude" }, "metaModel": { "id": "THING-Q424288", "registryId": "vr.tr.transaminase", "name": "transaminase", "version": "0.2.0-wave.4", "entryKind": "thing", "family": "Thing Registry", "domain": [ "PHY.MAT" ], "status": "research-draft" }, "canonicalUrl": "https://ver.cy/models/thing/q424288/", "model": { "registry_id": "vr.tr.transaminase", "name": "transaminase", "purpose": "Let an agent explain transaminases, relay mechanism, metabolic roles, clinical testing and biocatalysis from biochemistry and clinical sources, describe the named enzymes, explain that abnormal liver enzyme results need interpretation by a clinician, and distinguish transaminases from deaminases, other transferases and liver function as a whole.", "definition": "An enzyme, also called an aminotransferase, that catalyses the transfer of an amino group from an amino acid to a keto acid using the cofactor pyridoxal phosphate, central to amino acid synthesis and breakdown, with many specific enzymes such as D-amino acid aminotransferase, branched-chain aminotransferase, lysine-pyruvate 6-transaminase, methionine-glyoxylate transaminase and 3-amino-2-methylpropionate transaminases; alanine aminotransferase ALT and aspartate aminotransferase AST are measured in blood as liver function tests, and engineered transaminases are used to make chiral amines for drugs.", "what_it_is_for": "Transferring amino groups in metabolism.", "affordances": [ "explain mechanism", "relay metabolic and clinical roles", "describe named enzymes", "route abnormal results to clinicians" ], "distinguishing_features": [ "PLP dependent", "Amino group transfer", "Clinical biomarkers", "Industrial biocatalysts" ], "appearance": "Not a visible object; proteins.", "visual_identification": [ "Aminotransferase enzyme", "D-amino acid aminotransferase, branched-chain aminotransferase, lysine-pyruvate 6-transaminase, methionine-glyoxylate transaminase, 3-amino-2-methylpropionate transaminases", "Deaminases remove amino groups; other transferases move other groups; liver function tests include more than ALT and AST" ], "physical_properties": [ { "quantity": "cofactor", "typical_range": "pyridoxal 5-phosphate", "unit": "note", "note": "vitamin B6 derivative" }, { "quantity": "EC subclass", "typical_range": "2.6.1", "unit": "code", "note": "" }, { "quantity": "clinical markers", "typical_range": "ALT and AST", "unit": "list", "note": "" } ], "families_and_kinds": [ "alanine and aspartate aminotransferases", "branched-chain aminotransferases", "D-amino acid aminotransferases", "omega-transaminases for biocatalysis", "specialised pathway transaminases" ], "related_models": [ { "relation": "is a kind of", "target": "transferase", "why": "in registry terms" }, { "relation": "uses", "target": "pyridoxal phosphate", "why": "" }, { "relation": "includes", "target": "alanine transaminase", "why": "" }, { "relation": "is used in", "target": "liver function tests", "why": "" } ], "identifiers": [ { "scheme": "EC", "value_or_pattern": "2.6.1", "note": "transaminases" } ], "standards_and_regulation": [ "IUBMB enzyme nomenclature", "Clinical laboratory reference ranges" ], "failure_modes_and_hazards": [ "Interpreting individual liver test results without a clinician", "Treating named enzymes as synonyms", "Confusing transaminases and deaminases" ], "in_scope": [], "out_of_scope": [], "characteristics": [] }, "sources": [], "structure": { "bundles": [ { "id": "understand", "name": "Understand", "description": "What a transaminase is.", "rationale": "Science.", "layers": [ { "id": "definition", "name": "Definition", "description": "Definition.", "findings": [ { "id": "definition-finding", "name": "Definition", "description": "Definition.", "questions": [ { "text": "What is a transaminase, and how does it differ from deaminases, other transferases and liver function as a whole?", "kind": "definition" }, { "text": "Is the question about a blood test result, which a clinician should interpret, especially with jaundice or abdominal pain needing prompt care?", "kind": "boundary" } ] } ] }, { "id": "named", "name": "Named enzymes", "description": "Named enzymes.", "findings": [ { "id": "named-finding", "name": "Named enzymes", "description": "Named enzymes.", "questions": [ { "text": "What do the named D-amino acid, branched-chain, lysine-pyruvate, methionine-glyoxylate and aminomethylpropionate transaminases do?", "kind": "definition" }, { "text": "Which entry fits the specific enzyme?", "kind": "action" } ] } ] } ] }, { "id": "biochemistry", "name": "Biochemistry", "description": "Biochemistry.", "rationale": "Science.", "layers": [ { "id": "mechanism", "name": "Mechanism", "description": "Mechanism.", "findings": [ { "id": "mechanism-finding", "name": "Mechanism", "description": "Mechanism.", "questions": [ { "text": "How does the ping-pong mechanism with PLP work?", "kind": "provenance" }, { "text": "Which references are standard?", "kind": "provenance" } ] } ] }, { "id": "metabolism", "name": "Metabolism", "description": "Metabolic roles.", "findings": [ { "id": "metabolism-finding", "name": "Metabolism", "description": "Metabolism.", "questions": [ { "text": "How do transaminases link amino acid and carbohydrate metabolism?", "kind": "provenance" }, { "text": "Which sources are cited?", "kind": "provenance" } ] } ] } ] }, { "id": "clinical", "name": "Clinical", "description": "Clinical use.", "rationale": "Attribution.", "layers": [ { "id": "tests", "name": "Tests", "description": "Liver tests.", "findings": [ { "id": "tests-finding", "name": "Tests", "description": "Tests.", "questions": [ { "text": "What do ALT and AST tests measure, and what can raise them, in general terms?", "kind": "provenance" }, { "text": "Which entry fits liver function tests?", "kind": "action" } ] } ] }, { "id": "disorders", "name": "Disorders", "description": "Enzyme disorders.", "findings": [ { "id": "disorders-finding", "name": "Disorders", "description": "Disorders.", "questions": [ { "text": "Which inherited disorders involve transaminase deficiencies?", "kind": "provenance" }, { "text": "Which entry fits inborn error of amino acid metabolism?", "kind": "action" } ] } ] } ] }, { "id": "context", "name": "Context", "description": "Biocatalysis.", "rationale": "Context.", "layers": [ { "id": "industry", "name": "Industry", "description": "Biocatalysis.", "findings": [ { "id": "industry-finding", "name": "Industry", "description": "Industry.", "questions": [ { "text": "How are engineered transaminases used to make drugs such as sitagliptin?", "kind": "provenance" }, { "text": "Which entry fits biocatalysis?", "kind": "action" } ] } ] }, { "id": "history", "name": "History", "description": "History.", "findings": [ { "id": "history-finding", "name": "History", "description": "History.", "questions": [ { "text": "How was transamination discovered by Braunstein and Kritzmann?", "kind": "provenance" }, { "text": "Which entry fits Alexander Braunstein?", "kind": "action" } ] } ] } ] } ] }, "openQuestions": [ "Should ALT and AST be separate primary entries?", "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 transaminase, record what state it is in, and decide what may be done with it.", "whatItIs": "Let an agent explain transaminases, relay mechanism, metabolic roles, clinical testing and biocatalysis from biochemistry and clinical sources, describe the named enzymes, explain that abnormal liver enzyme results need interpretation by a clinician, and distinguish transaminases from deaminases, other transferases and liver function as a whole.", "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: D-amino acid aminotransferase, Branched-chain aminotransferase, (R)-3-amino-2-methylpropionate-pyruvate transaminase, (S)-3-amino-2-methylpropionate transaminase, Lysine-pyruvate 6-transaminase, Methionine-glyoxylate transaminase, N6-acetyl-beta-lysine transaminase, Phenylalanine(histidine) transaminase, Nicotianamine aminotransferase, (S)-8-amino-7-oxononanoate synthase BioU-like, Aminotransferase ALAT1/2-like, Succinyldiaminopimelate transaminase, DapC, beta/gammaproteobacteria.", "114 finer distinctions are held as aliases rather than separate entries, because telling them apart needs a task that asks for it.", "Described in 30 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 transaminase, 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": [ "D-amino acid aminotransferase", "Branched-chain aminotransferase", "(R)-3-amino-2-methylpropionate-pyruvate transaminase", "(S)-3-amino-2-methylpropionate transaminase", "Lysine-pyruvate 6-transaminase", "Methionine-glyoxylate transaminase", "N6-acetyl-beta-lysine transaminase", "Phenylalanine(histidine) transaminase", "Nicotianamine aminotransferase", "(S)-8-amino-7-oxononanoate synthase BioU-like", "Aminotransferase ALAT1/2-like", "Succinyldiaminopimelate transaminase, DapC, beta/gammaproteobacteria" ] } ], "standing": "Described in 30 Wikipedia languages, which measures how widely it is written about rather than how important or how common it is. 114 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 transaminase from another, and a transaminase 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 transaminase, 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 transaminase, 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 transaminase 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 transaminase, 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 transaminase, 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 transaminase 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 transaminase 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 transaminase, 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 transaminase, 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 transaminase 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 transaminase from the things most often confused with it.", "questions": [ { "id": "distinguishing-features-q01", "text": "What identifies and describes what distinguishes a transaminase, 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 transaminase, 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 transaminase 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 transaminase 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 transaminase, 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 transaminase, 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 transaminase 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 transaminase is built from and which parts are replaceable.", "questions": [ { "id": "parts-and-materials-q01", "text": "What identifies and describes the composition of a transaminase, 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 transaminase, 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 transaminase 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 transaminase is judged and by whom.", "questions": [ { "id": "condition-assessment-q01", "text": "What identifies and describes the condition of a transaminase, 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 transaminase, 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 transaminase 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 transaminase 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 transaminase is, and what that position is measured against.", "questions": [ { "id": "position-and-frame-q01", "text": "What identifies and describes the location of a transaminase, 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 transaminase, 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 transaminase 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 transaminase 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 transaminase, 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 transaminase, 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 transaminase 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 transaminase 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 transaminase between them.", "questions": [ { "id": "stages-and-transitions-q01", "text": "What identifies and describes the lifecycle of a transaminase, 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 transaminase, 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 transaminase 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 transaminase, how often and by whom.", "findings": [ { "id": "observation-record", "name": "Observation record", "description": "How an observation of a transaminase 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 transaminase, 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 transaminase, 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 transaminase 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 transaminase 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 transaminase is for, and what it is used for anyway.", "findings": [ { "id": "function-and-purpose", "name": "Function, purpose and misuse", "description": "The function a transaminase performs and the uses that fall outside it.", "questions": [ { "id": "function-and-purpose-q01", "text": "What identifies and describes the use of a transaminase, 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 transaminase, 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 transaminase 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 transaminase.", "findings": [ { "id": "procedures-and-skills", "name": "Procedures, skills and required tools", "description": "What an agent needs before it can act on a transaminase at all.", "questions": [ { "id": "procedures-and-skills-q01", "text": "What identifies and describes handling a transaminase, 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 transaminase, 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 transaminase 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 transaminase there is and how fast it goes.", "questions": [ { "id": "consumption-and-stock-q01", "text": "What identifies and describes the supply of a transaminase, 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 transaminase, 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 transaminase 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 transaminase 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 transaminase 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 transaminase 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 transaminase 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 transaminase, 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 transaminase 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 transaminase 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 transaminase 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 transaminase, 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 transaminase 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 transaminase and how confident it is.", "questions": [ { "id": "claim-provenance-q01", "text": "What identifies and describes a claim about a transaminase, 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 transaminase, 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 transaminase 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 transaminase is retired without being erased.", "questions": [ { "id": "validity-and-supersession-q01", "text": "What identifies and describes the validity of a claim about a transaminase, 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 transaminase, 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 transaminase 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 } } } }