{ "model": { "rank": 6759, "code": "thing-q17153", "model_id": "vr.tr.amylase", "name": "amylase", "purpose": "Enable an AI agent to recognise an amylase enzyme or preparation, assess its starch-hydrolysing activity and condition, and select handling and uses supported by its identity and measured performance.", "family": "Thing Registry", "category": "Physical world and living systems", "status": "research-draft", "kind": "thing", "plane": "PHY", "domain": "PHY.MAT", "industry": "", "version": "", "url": "/models/thing/q17153/", "tier": 2, "score": 58, "payload": { "layer": "wikidata", "aliases": [ "alpha-amylase", "beta-amylase family", "Glucoamylase", "salivary amylase", "alpha amylase, subgroup", "Alpha-amylase, MalS type", "Alpha-amylase-like", "pancreatic alpha-amylases", "Alpha-amylase, domain of unknown function DUF1966, C-terminal domain, protein family", "Alpha-amylase, C-terminal beta-sheet, protein family", "Glycoside hydrolase, family 14A, bacterial", "Glycoside hydrolase, family 14B, plant", "amylase alpha 1C", "glucan 1,4-a-glucosidase" ], "aliasCount": 14, "merged": 14, "knownIn": 58, "facets": null, "markers": [], "lexicalClass": "", "senseRank": null, "alsoRegisteredAs": null, "source": { "dataset": "wikidata", "item": "Q17153", "url": "https://www.wikidata.org/wiki/Q17153", "license": "CC0 1.0" } }, "research": { "vercy": "1.0-draft", "publication": { "status": "research-draft", "adjudicationStatus": "unreviewed", "publishableCanonical": false, "generatedAt": "2026-09-09T23:26:53Z", "providers": [ "Codex" ], "breadth": "recalled by Codex without web access - no source was read", "missingProviders": [], "pass": 2, "cost": { "grok": { "seconds": 22.5, "error": "Reading additional input from stdin...\nOpenAI Codex v0.153.4\n--------\nworkdir: R:\\02_PROJECTS\\02_Meta_Models_Platforms\\Ver.cy\\current\\thing-registry-backlog\nmodel: gpt-6-astra\nprovider: openai\napproval: never\nsandbox: read-only\nreasoning effort: none\nreasoning summaries: none\nsession id: 01a0887d-e81d-7050-a29f-4b6d3833fd33\n--------\nuser\nDescribe what is already known about one registered thing. Answer as JSON only, no prose around it.\n\nThing: amylase\nSense to describe: (none recorded)\nDomain code: PHY.MAT\nAlso known as: (none)\n\n\nContext for this batch of 1001 things:\n# Batch 007: 1001 registe", "usd": 0, "recall": true }, "codex": { "seconds": 65.9, "error": "Reading additional input from stdin...\nOpenAI Codex v0.153.4\n--------\nworkdir: R:\\02_PROJECTS\\02_Meta_Models_Platforms\\Ver.cy\\current\\thing-registry-backlog\nmodel: gpt-6-astra\nprovider: openai\napproval: never\nsandbox: read-only\nreasoning effort: none\nreasoning summaries: none\nsession id: 01a0887d-e81b-7630-bfc6-4a384f631f28\n--------\nuser\nYou are drafting a Vercy meta-model for one registered thing. Answer as JSON only, no prose around it.\n\nThing: amylase\nRegistry id: vr.tr.amylase\nPlane / domain: PHY / PHY.MAT\nRegistry definition: (none recorded)\nNames folded into this entry: (none)\n\n\nContext " } } }, "metaModel": { "id": "THING-Q17153", "registryId": "vr.tr.amylase", "name": "amylase", "version": "0.1.0-research.1", "entryKind": "thing", "family": "Thing Registry", "domain": [ "PHY.MAT" ], "status": "research-draft" }, "canonicalUrl": "https://ver.cy/models/thing/q17153/", "model": { "registry_id": "vr.tr.amylase", "name": "amylase", "purpose": "Enable an AI agent to recognise an amylase enzyme or preparation, assess its starch-hydrolysing activity and condition, and select handling and uses supported by its identity and measured performance.", "definition": "Amylase is a collective name for enzymes that hydrolyse glycosidic bonds in starch and related polysaccharides, yielding shorter carbohydrate chains or sugars according to enzyme type.", "scope_statement": "This model owns the identity, catalytic specificity, biological origin, preparation quality, assay-dependent activity, stability and use constraints of amylase under registry entry vr.tr.amylase, distinguishing the enzyme family from individual variants and formulated products.", "in_scope": [ "Amylase class, molecular variant and substrate specificity", "Biological source and production provenance", "Enzyme preparation composition, purity and physical form", "Catalytic activity and performance under specified assay conditions", "Storage stability, handling hazards and suitability for a stated use" ], "out_of_scope": [ "Starch and other carbohydrate substrates as independently modelled materials", "Complete organisms or engineered production strains", "Manufacturing plants and complete starch-processing workflows", "Finished foods, detergents or medicines containing amylase", "Clinical diagnosis based on amylase measurements" ], "distinguishing_features": [ "Identify the starch-related substrate and glycosidic linkage acted upon; generic carbohydrate hydrolysis alone does not establish amylase identity.", "Use cleavage pattern and product profile to distinguish alpha-amylase, beta-amylase and activities described as gamma-amylase or glucoamylase.", "Distinguish an identified amylase protein from a preparation containing multiple starch-degrading enzymes.", "Separate enzyme amount from catalytic activity: protein concentration alone does not establish starch-hydrolysing capacity.", "Treat source-specific isoenzymes and engineered variants as differentiated instances within this entry unless registry policy requires a separate concept." ], "characteristics": [ { "name": "Catalytic class", "kind": "category", "unit_or_values": "Alpha-amylase; beta-amylase; gamma-amylase/glucoamylase where included by the adopted nomenclature; unresolved", "why_it_matters": "The class constrains expected cleavage behaviour and products; the adopted naming authority must be recorded." }, { "name": "Molecular identity", "kind": "relation", "unit_or_values": "Protein sequence or accession, isoenzyme designation and variant record", "why_it_matters": "A family name is insufficient to transfer performance claims between proteins." }, { "name": "Biological and production origin", "kind": "relation", "unit_or_values": "Source organism and tissue where applicable; expression host and production batch", "why_it_matters": "Distinguishes native origin from manufacturing provenance and supports traceability." }, { "name": "Substrate and cleavage specificity", "kind": "category", "unit_or_values": "Tested substrate, linkage acted upon, endo/exo behaviour and branching limitations", "why_it_matters": "Determines which starch structures the enzyme can transform." }, { "name": "Catalytic activity", "kind": "measurement", "unit_or_values": "U/mL, U/g or kat-based units, with complete assay and unit definition", "why_it_matters": "Enables dosing and comparison only when the measurement conditions and endpoint are compatible." }, { "name": "Specific activity", "kind": "measurement", "unit_or_values": "U/mg protein, with protein quantification method and activity assay", "why_it_matters": "Relates measured activity to protein content without equating it directly with purity." }, { "name": "Preparation composition", "kind": "measurement", "unit_or_values": "Enzyme or protein concentration, water content, component fractions and impurity levels with methods", "why_it_matters": "Carriers, stabilisers and contaminating enzymes can alter performance and suitability." }, { "name": "Physical presentation", "kind": "category", "unit_or_values": "Liquid solution; suspension; powder; granule; immobilised preparation; other documented form", "why_it_matters": "Affects dispensing, accessibility to substrate and exposure routes." }, { "name": "Activity response to conditions", "kind": "measurement", "unit_or_values": "Activity versus pH, temperature in °C, substrate concentration and specified medium composition", "why_it_matters": "An apparent optimum depends on the assay and does not establish long-term stability." }, { "name": "Ion and additive response", "kind": "measurement", "unit_or_values": "Relative activity or stability at stated concentrations of ions, chelators, inhibitors and formulation additives", "why_it_matters": "Requirements and sensitivities must be established for the actual enzyme variant." }, { "name": "Residual activity", "kind": "measurement", "unit_or_values": "% of initial activity after a specified time, storage condition or treatment", "why_it_matters": "Supports shelf-life assessment and decisions about continued use or inactivation." }, { "name": "Use eligibility", "kind": "state", "unit_or_values": "Supported; conditional; unsupported; unresolved, for a stated application and jurisdiction", "why_it_matters": "Suitability depends on the preparation, evidence and intended use rather than the name amylase alone." } ], "affordances": [ "Resolve a labelled amylase to its catalytic class, molecular variant and preparation.", "Choose an activity assay appropriate to its substrate specificity and expected products.", "Calculate an enzyme dose from measured activity when assay conditions support the intended application.", "Compare candidate preparations using compatible activity, stability and composition evidence.", "Select storage and handling conditions supported for the actual preparation.", "Verify whether a treatment has reduced amylase activity to a stated acceptance threshold." ] }, "sources": [], "structure": { "bundles": [ { "id": "amylase-identity-and-boundaries", "name": "Amylase identity and boundaries", "description": "Establish which catalytic entity the amylase name denotes.", "rationale": "Amylase is a family-level designation and cannot safely inherit the identity or constants of one substance record.", "layers": [ { "id": "catalytic-class", "name": "Catalytic class", "description": "Resolve the enzyme name through its reaction and accepted nomenclature.", "findings": [ { "id": "class-assignment", "name": "Class assignment", "description": "Record the evidence required to assign an amylase class without relying solely on a commercial label.", "questions": [ { "text": "Which amylase class and enzyme nomenclature identifier are supported, and by which authority?", "kind": "definition", "id": "class-assignment-q01" }, { "text": "Does this registry entry include gamma-amylase/glucoamylase, or does the catalogue assign that concept elsewhere?", "kind": "boundary", "id": "class-assignment-q02" } ] } ] }, { "id": "protein-and-preparation", "name": "Protein and preparation", "description": "Separate the molecular enzyme from its supplied mixture.", "findings": [ { "id": "identity-resolution", "name": "Identity resolution", "description": "Associate identifiers with the protein, enzyme class or preparation they actually describe.", "questions": [ { "text": "Which sequence, accession, isoenzyme or engineered variant identifies the active protein?", "kind": "definition", "id": "identity-resolution-q01" }, { "text": "Do any supplied CAS, chemical database or supplier identifiers denote this protein, a broad enzyme category or a mixture?", "kind": "boundary", "id": "identity-resolution-q02" } ] } ] } ] }, { "id": "starch-cleavage-and-products", "name": "Starch cleavage and products", "description": "Describe what the enzyme acts on and what transformations it supports.", "rationale": "Substrate structure and cleavage behaviour determine whether an amylase can deliver the intended conversion.", "layers": [ { "id": "substrate-access-and-specificity", "name": "Substrate access and specificity", "description": "Characterise activity against defined starch structures and physical presentations.", "findings": [ { "id": "supported-substrates", "name": "Supported substrates", "description": "Capture demonstrated substrate activity and limits caused by linkage, branching or accessibility.", "questions": [ { "text": "Which substrates and linkages have been tested, and is cleavage internal or terminal?", "kind": "measurement", "id": "supported-substrates-q01" }, { "text": "How do branching and raw versus gelatinised starch affect conversion under the intended conditions?", "kind": "measurement", "id": "supported-substrates-q02" } ] } ] }, { "id": "conversion-outcomes", "name": "Conversion outcomes", "description": "Connect enzyme action to products and application endpoints.", "findings": [ { "id": "product-and-endpoint-profile", "name": "Product and endpoint profile", "description": "Distinguish starch disappearance, viscosity reduction and sugar production as separate outcomes.", "questions": [ { "text": "Which sugars or oligosaccharides accumulate over time, and how were they identified?", "kind": "measurement", "id": "product-and-endpoint-profile-q01" }, { "text": "Does the intended endpoint require this amylase alone or complementary enzyme activities?", "kind": "action", "id": "product-and-endpoint-profile-q02" } ] } ] } ] }, { "id": "activity-and-operating-conditions", "name": "Activity and operating conditions", "description": "Make activity claims interpretable and connect them to the proposed use.", "rationale": "Amylase activity values depend on assay definitions, while useful operating conditions depend on both reaction rate and enzyme survival.", "layers": [ { "id": "assay-definition", "name": "Assay definition", "description": "Record the conditions that give an activity value its meaning.", "findings": [ { "id": "traceable-activity-value", "name": "Traceable activity value", "description": "Require a defined substrate, endpoint, unit and measurement procedure.", "questions": [ { "text": "What substrate, pH, temperature, reaction time and detection method define the reported activity unit?", "kind": "measurement", "id": "traceable-activity-value-q01" }, { "text": "What controls, calibration and uncertainty support comparisons between batches or suppliers?", "kind": "provenance", "id": "traceable-activity-value-q02" } ] } ] }, { "id": "reaction-environment", "name": "Reaction environment", "description": "Establish the usable reaction window for the specific preparation.", "findings": [ { "id": "condition-dependent-performance", "name": "Condition-dependent performance", "description": "Evaluate pH, temperature and medium effects without assuming family-wide requirements.", "questions": [ { "text": "How do activity and time-dependent activity loss change across the intended pH and temperature range?", "kind": "measurement", "id": "condition-dependent-performance-q01" }, { "text": "Which ions, chelators or process additives activate, inhibit or destabilise this variant at relevant concentrations?", "kind": "measurement", "id": "condition-dependent-performance-q02" }, { "text": "What evidence supports transferring the assay activity to a dose in the intended process medium?", "kind": "action", "id": "condition-dependent-performance-q03" } ] } ] } ] }, { "id": "origin-composition-and-quality", "name": "Origin, composition and quality", "description": "Track where the enzyme came from and what accompanies its activity.", "rationale": "Production origin and preparation composition affect reproducibility, contaminant risks and the interpretation of observed starch degradation.", "layers": [ { "id": "biological-provenance", "name": "Biological provenance", "description": "Link the enzyme variant to its source and production history.", "findings": [ { "id": "source-and-expression-history", "name": "Source and expression history", "description": "Distinguish the source of the enzyme sequence from the organism used to manufacture it.", "questions": [ { "text": "What source organism, tissue or sequence donor is documented, and what expression host was used if different?", "kind": "provenance", "id": "source-and-expression-history-q01" }, { "text": "Which batch records document variant modifications, recovery and purification relevant to the supplied enzyme?", "kind": "provenance", "id": "source-and-expression-history-q02" } ] } ] }, { "id": "preparation-quality", "name": "Preparation quality", "description": "Describe active protein, formulation components and unwanted activities.", "findings": [ { "id": "composition-and-coactivities", "name": "Composition and coactivities", "description": "Determine whether observed performance belongs to the identified amylase or other constituents.", "questions": [ { "text": "What enzyme concentration, purity, carriers, preservatives and stabilisers are measured or declared?", "kind": "measurement", "id": "composition-and-coactivities-q01" }, { "text": "Which additional starch-degrading activities, proteases or use-relevant contaminants were tested, and with what detection limits?", "kind": "measurement", "id": "composition-and-coactivities-q02" } ] } ] } ] }, { "id": "stability-handling-and-use", "name": "Stability, handling and use", "description": "Support decisions about storage, exposure control, application and termination of enzyme action.", "rationale": "A preparation can retain its label while losing useful activity, and permitted uses and handling requirements depend on its actual form and composition.", "layers": [ { "id": "activity-retention-and-inactivation", "name": "Activity retention and inactivation", "description": "Assess usable life and verify deliberate stopping of catalysis.", "findings": [ { "id": "activity-through-treatment", "name": "Activity through treatment", "description": "Connect storage and treatment history to measured residual activity.", "questions": [ { "text": "What residual activity is demonstrated after relevant storage, moisture exposure, freeze-thaw cycles or reconstitution?", "kind": "measurement", "id": "activity-through-treatment-q01" }, { "text": "Which treatment achieves the required residual-activity threshold in the intended material, and how is it verified?", "kind": "action", "id": "activity-through-treatment-q02" } ] } ] }, { "id": "handling-and-application-eligibility", "name": "Handling and application eligibility", "description": "Bind safety and use decisions to the supplied preparation and jurisdiction.", "findings": [ { "id": "preparation-specific-constraints", "name": "Preparation-specific constraints", "description": "Record documented exposure hazards and application requirements without assigning a universal classification to all amylases.", "questions": [ { "text": "What current safety documentation addresses sensitisation, dust or aerosol exposure and formulation-specific hazards?", "kind": "provenance", "id": "preparation-specific-constraints-q01" }, { "text": "What evidence establishes eligibility of this source, production route and grade for the stated food, industrial, laboratory or other use?", "kind": "action", "id": "preparation-specific-constraints-q02" }, { "text": "Which jurisdiction-specific classifications or exposure limits apply to this preparation, and which remain unresolved?", "kind": "boundary", "id": "preparation-specific-constraints-q03" } ] } ] } ] }, { "id": "evidence-and-external-alignment", "name": "Evidence and external alignment", "description": "What the world already says about this thing, gathered so the model can be checked against it.", "rationale": "A model that cannot be lined up against existing standards, identifiers and practice cannot be adopted by anyone who already uses them.", "layers": [ { "id": "reported-evidence", "name": "Reported evidence", "description": "Findings from the breadth pass, kept separate from the structural claims.", "findings": [ { "id": "evidence-confidence-notes", "name": "Check these first", "description": "Recalled without web access and unsourced; every item is a lead to verify.", "evidence": [ "Amylase denotes multiple enzymes rather than one chemically uniform substance; source organism, sequence and enzyme type must be established before assigning a substance identifier or molecular properties.", "Confirm whether the registry intends the broad enzyme grouping or specifically alpha-amylase; gamma-amylase terminology is less consistently used.", "Activity values, temperature and pH optima, clinical reference intervals and hazard classifications require a specified enzyme or preparation and documented methods." ], "questions": [ { "id": "evidence-confidence-notes-q01", "text": "Which of these check these first hold for the sense of amylase this model covers, and on what evidence?", "kind": "provenance" } ] }, { "id": "evidence-kinds", "name": "Kinds and varieties", "description": "Recalled without web access and unsourced; every item is a lead to verify.", "evidence": [ "Alpha-amylase", "Beta-amylase", "Gamma-amylase, commonly called glucoamylase" ], "questions": [ { "id": "evidence-kinds-q01", "text": "Which of these kinds and varieties hold for the sense of amylase this model covers, and on what evidence?", "kind": "provenance" } ] }, { "id": "evidence-identifiers", "name": "Identifiers and schemes", "description": "Recalled without web access and unsourced; every item is a lead to verify.", "evidence": [ { "scheme": "IUBMB Enzyme Commission number", "value_or_pattern": "EC 3.2.1.1", "note": "Alpha-amylase; hydrolyses internal alpha-1,4 linkages in suitable glucan chains." }, { "scheme": "IUBMB Enzyme Commission number", "value_or_pattern": "EC 3.2.1.2", "note": "Beta-amylase; releases maltose from non-reducing chain ends." }, { "scheme": "IUBMB Enzyme Commission number", "value_or_pattern": "EC 3.2.1.3", "note": "Glucan 1,4-alpha-glucosidase, commonly called glucoamylase or gamma-amylase; releases glucose from non-reducing chain ends." } ], "questions": [ { "id": "evidence-identifiers-q01", "text": "Which of these identifiers and schemes hold for the sense of amylase this model covers, and on what evidence?", "kind": "provenance" } ] }, { "id": "evidence-standards-and-regulation", "name": "Standards and regulation", "description": "Recalled without web access and unsourced; every item is a lead to verify.", "evidence": [ "International Union of Biochemistry and Molecular Biology enzyme nomenclature classifies these enzymes by their catalysed reactions." ], "questions": [ { "id": "evidence-standards-and-regulation-q01", "text": "Which of these standards and regulation hold for the sense of amylase this model covers, and on what evidence?", "kind": "provenance" } ] }, { "id": "evidence-real-world-use", "name": "Real-world use", "description": "Recalled without web access and unsourced; every item is a lead to verify.", "evidence": [ "Starch digestion, including the action of human salivary and pancreatic alpha-amylases.", "Starch processing to produce dextrins and, with appropriate enzymes, sugar syrups.", "Baking and brewing to modify starch breakdown and fermentable sugar availability.", "Removal of starch-based stains in detergents and starch sizing from textiles.", "Measurement of amylase activity in clinical laboratory testing." ], "questions": [ { "id": "evidence-real-world-use-q01", "text": "Which of these real-world use hold for the sense of amylase this model covers, and on what evidence?", "kind": "provenance" } ] }, { "id": "evidence-measurements", "name": "Typical measurements", "description": "Recalled without web access and unsourced; every item is a lead to verify.", "evidence": [ { "quantity": "Catalytic activity", "typical_range": "Preparation- and assay-dependent; no single range applies to amylases collectively.", "unit": "U, commonly defined as micromoles of substrate converted or product formed per minute under specified assay conditions" }, { "quantity": "Specific catalytic activity", "typical_range": "Depends on enzyme identity, purity and assay conditions.", "unit": "U/mg protein" } ], "questions": [ { "id": "evidence-measurements-q01", "text": "Which of these typical measurements hold for the sense of amylase this model covers, and on what evidence?", "kind": "provenance" } ] }, { "id": "evidence-failure-modes-and-hazards", "name": "Failure modes and hazards", "description": "Recalled without web access and unsourced; every item is a lead to verify.", "evidence": [ "Enzyme dust or aerosols can cause respiratory sensitisation and occupational asthma.", "Excessive heat or unsuitable pH can denature the enzyme and reduce activity.", "Storage conditions, proteolysis or incompatible formulation ingredients can reduce activity.", "An enzyme with unsuitable linkage specificity may leave substantial starch-derived material unhydrolysed.", "Excessive amylase activity can impair product quality, including bread crumb texture." ], "questions": [ { "id": "evidence-failure-modes-and-hazards-q01", "text": "Which of these failure modes and hazards hold for the sense of amylase this model covers, and on what evidence?", "kind": "provenance" } ] }, { "id": "evidence-regional-variation", "name": "Regional variation", "description": "Recalled without web access and unsourced; every item is a lead to verify.", "evidence": [ "Food and processing-aid requirements vary by jurisdiction and may depend on the production organism, manufacturing process and intended use.", "Clinical laboratories use assay-specific reference intervals and reporting conventions." ], "questions": [ { "id": "evidence-regional-variation-q01", "text": "Which of these regional variation hold for the sense of amylase this model covers, and on what evidence?", "kind": "provenance" } ] }, { "id": "evidence-neighbours", "name": "Neighbouring kinds and how to tell them apart", "description": "Recalled without web access and unsourced; every item is a lead to verify.", "evidence": [ { "name": "Starch", "difference": "Starch is a polysaccharide substrate; amylase is an enzyme that catalyses its breakdown." }, { "name": "Alpha-glucosidase", "difference": "Typically removes terminal glucose residues from alpha-linked substrates; it is classified separately from alpha-amylase, which cleaves internally." }, { "name": "Pullulanase", "difference": "Targets alpha-1,6 branch linkages in suitable substrates, whereas alpha-amylase primarily cleaves internal alpha-1,4 linkages." }, { "name": "Cellulase", "difference": "Acts on beta-1,4-linked cellulose rather than the alpha-linked glucans targeted by amylases." }, { "name": "Amylase preparation", "difference": "A commercial preparation contains enzyme plus possible carriers, stabilisers and other components; its composition and hazards are not those of a single purified enzyme." } ], "questions": [ { "id": "evidence-neighbours-q01", "text": "Which of these neighbouring kinds and how to tell them apart hold for the sense of amylase this model covers, and on what evidence?", "kind": "provenance" } ] } ] } ] } ] }, "openQuestions": [ "Does the existing Vercy catalogue already cover amylase, and how does its authoritative boundary treat glucoamylase and other starch-degrading enzymes?", "Which nomenclature and identifier sources distinguish the amylase family, individual proteins and commercial preparations without conflating them?", "Which reference assays allow meaningful comparison across amylase classes, and where must activities remain explicitly incomparable?", "Which source- and variant-specific measurements establish substrate range, ion dependence and operating stability?", "Which current preparation-specific documents substantiate handling requirements, shelf life and eligibility for each proposed application?" ], "statistics": { "bundles": 6, "layers": 11, "findings": 19, "questions": 31 } }, "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 amylase, record what state it is in, and decide what may be done with it.", "whatItIs": "Enable an AI agent to recognise an amylase enzyme or preparation, assess its starch-hydrolysing activity and condition, and select handling and uses supported by its identity and measured performance.", "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: alpha-amylase, beta-amylase family, Glucoamylase, salivary amylase, alpha amylase, subgroup, Alpha-amylase, MalS type, Alpha-amylase-like, pancreatic alpha-amylases, Alpha-amylase, domain of unknown function DUF1966, C-terminal domain, protein family, Alpha-amylase, C-terminal beta-sheet, protein family, Glycoside hydrolase, family 14A, bacterial, Glycoside hydrolase, family 14B, plant.", "14 finer distinctions are held as aliases rather than separate entries, because telling them apart needs a task that asks for it.", "Described in 58 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 amylase, 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": [ "alpha-amylase", "beta-amylase family", "Glucoamylase", "salivary amylase", "alpha amylase, subgroup", "Alpha-amylase, MalS type", "Alpha-amylase-like", "pancreatic alpha-amylases", "Alpha-amylase, domain of unknown function DUF1966, C-terminal domain, protein family", "Alpha-amylase, C-terminal beta-sheet, protein family", "Glycoside hydrolase, family 14A, bacterial", "Glycoside hydrolase, family 14B, plant" ] } ], "standing": "Described in 58 Wikipedia languages, which measures how widely it is written about rather than how important or how common it is. 14 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 amylase from another, and a amylase 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 amylase, 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 amylase, 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 amylase 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 amylase, 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 amylase, 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 amylase 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 amylase 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 amylase, 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 amylase, 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 amylase 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 amylase from the things most often confused with it.", "questions": [ { "id": "distinguishing-features-q01", "text": "What identifies and describes what distinguishes a amylase, 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 amylase, 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 amylase 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 amylase 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 amylase, 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 amylase, 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 amylase 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 amylase is built from and which parts are replaceable.", "questions": [ { "id": "parts-and-materials-q01", "text": "What identifies and describes the composition of a amylase, 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 amylase, 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 amylase 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 amylase is judged and by whom.", "questions": [ { "id": "condition-assessment-q01", "text": "What identifies and describes the condition of a amylase, 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 amylase, 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 amylase 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 amylase 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 amylase is, and what that position is measured against.", "questions": [ { "id": "position-and-frame-q01", "text": "What identifies and describes the location of a amylase, 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 amylase, 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 amylase 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 amylase 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 amylase, 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 amylase, 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 amylase 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 amylase 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 amylase between them.", "questions": [ { "id": "stages-and-transitions-q01", "text": "What identifies and describes the lifecycle of a amylase, 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 amylase, 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 amylase 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 amylase, how often and by whom.", "findings": [ { "id": "observation-record", "name": "Observation record", "description": "How an observation of a amylase 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 amylase, 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 amylase, 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 amylase 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 amylase 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 amylase is for, and what it is used for anyway.", "findings": [ { "id": "function-and-purpose", "name": "Function, purpose and misuse", "description": "The function a amylase performs and the uses that fall outside it.", "questions": [ { "id": "function-and-purpose-q01", "text": "What identifies and describes the use of a amylase, 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 amylase, 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 amylase 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 amylase.", "findings": [ { "id": "procedures-and-skills", "name": "Procedures, skills and required tools", "description": "What an agent needs before it can act on a amylase at all.", "questions": [ { "id": "procedures-and-skills-q01", "text": "What identifies and describes handling a amylase, 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 amylase, 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 amylase 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 amylase there is and how fast it goes.", "questions": [ { "id": "consumption-and-stock-q01", "text": "What identifies and describes the supply of a amylase, 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 amylase, 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 amylase 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 amylase 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 amylase 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 amylase 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 amylase 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 amylase, 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 amylase 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 amylase 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 amylase 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 amylase, 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 amylase 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 amylase and how confident it is.", "questions": [ { "id": "claim-provenance-q01", "text": "What identifies and describes a claim about a amylase, 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 amylase, 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 amylase 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 amylase is retired without being erased.", "questions": [ { "id": "validity-and-supersession-q01", "text": "What identifies and describes the validity of a claim about a amylase, 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 amylase, 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 amylase 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 } } } }