{ "vercy": "1.0-draft", "publication": { "status": "research-draft", "adjudicationStatus": "unreviewed", "publishableCanonical": false, "generatedAt": "2026-09-12T09:08:48Z", "providers": [ "Codex" ], "breadth": "recalled by Codex without web access - no source was read", "missingProviders": [], "pass": 2, "cost": { "grok": { "seconds": 26.8, "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: 01a094df-2106-7930-8577-cde5b84c192b\n--------\nuser\nDescribe what is already known about one registered thing. Answer as JSON only, no prose around it.\n\nThing: diamine oxidase\nSense to describe: (none recorded)\nDomain code: PHY.MAT\nAlso known as: (none)\n\n\nContext for this batch of 1001 things:\n# Batch 043: 1001", "usd": 0.0, "recall": true }, "codex": { "seconds": 82.9, "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: 01a094df-20ed-7e62-bb37-ccb02cb04090\n--------\nuser\nYou are drafting a Vercy meta-model for one registered thing. Answer as JSON only, no prose around it.\n\nThing: diamine oxidase\nRegistry id: vr.tr.diamine-oxidase\nPlane / domain: PHY / PHY.MAT\nRegistry definition: (none recorded)\nNames folded into this entry: (" } }, "enrichment": { "pass": 3, "engine": "claude", "producedAt": "2026-10-06T12:00:00Z", "ingestedAt": "2026-10-06T08:43:02+00:00", "fields": [ "agent_conduct", "ethics", "failure_modes_and_hazards", "owners", "visual_identification" ] }, "gate": { "passed": true, "version": "1.0", "at": "2026-10-07T10:10:30+00:00", "evidence": [ "completeness 1.00", "sense: Wikidata description", "2 live sources", "review by codex: pass" ] } }, "metaModel": { "id": "THING-Q414006", "registryId": "vr.tr.diamine-oxidase", "name": "diamine oxidase", "version": "0.1.0-research.1", "entryKind": "thing", "family": "Thing Registry", "domain": [ "PHY.MAT" ], "status": "research-draft" }, "canonicalUrl": "https://ver.cy/models/thing/q414006/", "model": { "registry_id": "vr.tr.diamine-oxidase", "name": "diamine oxidase", "purpose": "Enable an agent to identify diamine oxidase, assess the catalytic competence of a specified enzyme preparation, and select evidence-supported conditions for its handling and use.", "definition": "Diamine oxidase is a copper-containing enzyme with a topaquinone cofactor that catalyses the oxidative deamination of diamines, including histamine and putrescine, producing an aldehyde, ammonia and hydrogen peroxide.", "scope_statement": "This model owns vr.tr.diamine-oxidase in PHY / PHY.MAT as an enzyme category and its identifiable protein forms and preparations, provisionally using EC 1.4.3.22 as the functional boundary rather than restricting the entry to human AOC1.", "in_scope": [ "Functional enzyme identity, organism of origin, protein accession and sequence variant", "Copper and topaquinone cofactor status and protein integrity", "Substrate-dependent oxidative deamination and its measured kinetics", "Preparation purity, formulation, storage history and retained activity", "Assay validity and evidence supporting a proposed catalytic use" ], "out_of_scope": [ "The AOC1 gene as a genomic entity and its regulation", "Histamine, other substrates and reaction products as independently modelled substances", "Histamine intolerance, patient diagnosis and treatment decisions", "Complete supplement products, delivery systems and their commercial claims", "Other amine oxidases and histamine-metabolising enzymes as independent enzyme categories" ], "distinguishing_features": [ "Require evidence of the diamine-oxidising activity classified under EC 1.4.3.22; an unspecified amine-oxidase label is insufficient. [IUBMB nomenclature](https://iubmb.qmul.ac.uk/enzyme/EC1/4/3/22.html)", "Check copper/topaquinone enzyme identity alongside catalytic evidence; human AOC1 is one identified protein representative. [UniProt AOC1](https://www.uniprot.org/uniprotkb/P19801)", "Distinguish oxidative deamination of histamine from other histamine transformations by measuring substrate loss and appropriate products. [IUBMB reaction](https://iubmb.qmul.ac.uk/enzyme/EC1/4/3/22.html)", "Resolve the abbreviation DAO against a full enzyme name, accession and reaction so that D-amino-acid oxidase is not admitted through abbreviation alone.", "Separate enzyme protein or preparation identity from a product label: a stated mass of DAO-containing material does not establish its catalytic activity." ], "characteristics": [ { "name": "Functional identity", "kind": "category", "unit_or_values": "EC 1.4.3.22 assignment: experimentally supported, annotated or unresolved", "why_it_matters": "Separates demonstrated catalytic identity from a supplier name or inferred annotation." }, { "name": "Biological and sequence identity", "kind": "relation", "unit_or_values": "Source taxon, protein accession and version, sequence variant, native tissue or expression host", "why_it_matters": "Prevents properties of one organism or construct from being attributed to every diamine oxidase." }, { "name": "Cofactor competence", "kind": "state", "unit_or_values": "Copper occupancy and topaquinone maturation: measured value, supported qualitative state or unknown", "why_it_matters": "Protein abundance alone cannot establish a catalytically competent enzyme population." }, { "name": "Protein integrity", "kind": "state", "unit_or_values": "Intact, fragmented, aggregated or unresolved; method and measurement date", "why_it_matters": "Supports interpretation of activity loss and preparation suitability." }, { "name": "Substrate activity profile", "kind": "measurement", "unit_or_values": "Reaction rate for each named substrate in µmol/min, with enzyme quantity and assay conditions", "why_it_matters": "Tests whether the preparation performs the intended diamine conversion." }, { "name": "Specific catalytic activity", "kind": "measurement", "unit_or_values": "U/mg protein, with the definition of U, substrate, pH, temperature and method", "why_it_matters": "Enables qualified comparison between preparations whose protein concentrations differ." }, { "name": "Apparent kinetic parameters", "kind": "measurement", "unit_or_values": "Km in mol/L; Vmax with explicit rate basis; kcat in s^-1 where active enzyme concentration is established", "why_it_matters": "Supports reaction design without treating condition-dependent measurements as universal constants." }, { "name": "Preparation composition", "kind": "measurement", "unit_or_values": "Protein concentration in mg/mL, purity percentage with method, and concentrations of carriers or additives", "why_it_matters": "Distinguishes enzyme content from total preparation mass and identifies possible assay interference." }, { "name": "Operating environment", "kind": "measurement", "unit_or_values": "pH, temperature in °C, dissolved oxygen in µmol/L, buffer composition and substrate concentration", "why_it_matters": "Defines the conditions under which a rate or stability claim applies." }, { "name": "Retained activity", "kind": "measurement", "unit_or_values": "Percentage of baseline activity after a specified storage or exposure interval", "why_it_matters": "Provides a functional basis for accepting, retesting or rejecting stored material." } ], "affordances": [ "Resolve a DAO-labelled material to a supported enzyme identity and source-specific protein record.", "Compare preparations after reconciling substrates, activity-unit definitions and assay conditions.", "Design a controlled assay for diamine conversion with checks for background and detection interference.", "Select substrate loading and operating conditions from measurements on the relevant enzyme form.", "Accept, retest or reject a preparation against predefined identity, purity and retained-activity requirements." ], "agent_conduct": { "may": [ "Explain the function of diamine oxidase in histamine breakdown from cited sources.", "Report the regulatory status of diamine oxidase supplements in a stated jurisdiction." ], "must_not": [ "Diagnose histamine intolerance or any condition in a person.", "Present supplements as proven treatment where evidence is weak.", "Advise stopping prescribed medicines in favour of enzyme supplements." ], "requires_human": [ "Any dietary or treatment decision for a person with suspected intolerance." ] }, "ethics": { "considerations": [ "Supplements are marketed with health claims that may outrun evidence.", "People with allergies or intolerance need accurate information to stay safe." ], "affected_parties": [ "People with food intolerances", "Consumers", "Researchers" ] }, "owners": { "steward": "Nobody owns the enzyme; the maker answers for each supplement or reagent product.", "master_systems": [ "Protein and enzyme databases" ] }, "visual_identification": [ "Not visible to the eye; as a reagent or supplement it is a powder or capsule identified only by its label.", "In databases it is recorded by its enzyme classification number." ], "failure_modes_and_hazards": [ "Unsupported health claims can delay proper diagnosis.", "Assay results vary by method, risking misinterpretation." ], "what_it_is_for": [ "Diamine oxidase is encountered in biochemical research on histamine metabolism and the breakdown of other diamines.", "Enzyme preparations are used in activity assays and analytical systems that detect substrates or reaction products.", "Preparation origin, purity and measured activity determine suitability for a particular laboratory application." ], "standards_and_regulation": [ "The enzyme nomenclature maintained by the International Union of Biochemistry and Molecular Biology classifies diamine oxidase as EC 1.4.3.22." ] }, "sources": [ { "id": "wikidata", "title": "Wikidata item Q414006: diamine oxidase", "url": "https://www.wikidata.org/wiki/Q414006", "url_status": "live", "what_it_supports": "identity and sense of the item", "checked_by": "wikidata-api" }, { "id": "wikipedia-en", "title": "Wikipedia: Diamine oxidase", "url": "https://en.wikipedia.org/wiki/Diamine_oxidase", "url_status": "live", "what_it_supports": "general description of the item", "checked_by": "wikidata-api sitelink" } ], "structure": { "bundles": [ { "id": "enzyme-identity-and-boundary", "name": "Enzyme identity and boundary", "description": "Establish what a diamine oxidase label denotes at functional, protein and preparation levels.", "rationale": "A catalytic category, human AOC1 and a commercial enzyme mixture require linked but distinct identity records.", "layers": [ { "id": "reaction-classification", "name": "Reaction classification", "description": "Anchor recognition in an enzyme classification and demonstrated chemistry.", "findings": [ { "id": "diamine-oxidation-boundary", "name": "Diamine oxidation boundary", "description": "EC 1.4.3.22 covers copper quinoproteins acting on diamines and some primary monoamines; substrate specificity must therefore be established rather than inferred from the name. [IUBMB classification](https://iubmb.qmul.ac.uk/enzyme/EC1/4/3/22.html)", "questions": [ { "text": "What reaction evidence or curated annotation supports assigning this material to EC 1.4.3.22?", "kind": "definition", "id": "diamine-oxidation-boundary-q01" }, { "text": "What evidence distinguishes it from primary-amine oxidase, monoamine oxidase and D-amino-acid oxidase?", "kind": "boundary", "id": "diamine-oxidation-boundary-q02" } ] } ] }, { "id": "source-specific-protein", "name": "Source-specific protein", "description": "Identify the molecular representative without making one organism authoritative for the whole category.", "findings": [ { "id": "protein-origin-and-construct", "name": "Protein origin and construct", "description": "Human AOC1 has a specific protein record; other source organisms and engineered constructs need their own identity evidence. [UniProt human AOC1](https://www.uniprot.org/uniprotkb/P19801)", "questions": [ { "text": "Which source organism, accession, sequence version and native or recombinant origin identify this enzyme?", "kind": "provenance", "id": "protein-origin-and-construct-q01" }, { "text": "Which sequence changes, tags or processing differences limit transfer of measurements from the reference protein?", "kind": "boundary", "id": "protein-origin-and-construct-q02" } ] } ] } ] }, { "id": "catalytic-material-state", "name": "Catalytic material state", "description": "Represent the difference between enzyme protein being present and that protein being active.", "rationale": "Cofactor competence, protein integrity and preparation composition affect the usable catalytic amount.", "layers": [ { "id": "cofactor-and-integrity", "name": "Cofactor and integrity", "description": "Track evidence that the protein retains its required catalytic machinery.", "findings": [ { "id": "active-enzyme-fraction", "name": "Active enzyme fraction", "description": "Record cofactor and integrity measurements separately from total protein concentration, retaining uncertainty when the active fraction is unknown.", "questions": [ { "text": "What measurements establish copper occupancy, topaquinone maturation and protein integrity in this preparation?", "kind": "measurement", "id": "active-enzyme-fraction-q01" }, { "text": "Is the active enzyme concentration measured, estimated or unknown, and how does that affect reported turnover?", "kind": "measurement", "id": "active-enzyme-fraction-q02" } ] } ] }, { "id": "preparation-composition", "name": "Preparation composition", "description": "Describe the enzyme-bearing material at the level needed to interpret activity.", "findings": [ { "id": "enzyme-versus-mixture", "name": "Enzyme versus mixture", "description": "Keep enzyme quantity, total protein, carriers and co-purifying activities distinguishable within each preparation record.", "questions": [ { "text": "How were enzyme concentration and purity established, and what substances contribute to the reported preparation mass?", "kind": "measurement", "id": "enzyme-versus-mixture-q01" }, { "text": "Could another enzyme or additive account for part of the observed substrate loss or assay signal?", "kind": "boundary", "id": "enzyme-versus-mixture-q02" } ] } ] } ] }, { "id": "substrate-conversion-and-assay", "name": "Substrate conversion and assay", "description": "Connect substrate specificity and quantitative activity to interpretable measurements.", "rationale": "A DAO activity number is useful only when its substrate, conditions and detection limitations are known.", "layers": [ { "id": "substrate-dependent-performance", "name": "Substrate-dependent performance", "description": "Record reaction performance separately for each substrate and environment.", "findings": [ { "id": "kinetic-context", "name": "Kinetic context", "description": "Treat kinetic constants and activity rankings as measurements of a specified enzyme form under stated conditions.", "questions": [ { "text": "What rates are measured for histamine, putrescine and relevant competing amines under comparable conditions?", "kind": "measurement", "id": "kinetic-context-q01" }, { "text": "What substrate range, oxygen availability, pH and temperature support the reported kinetic fit?", "kind": "measurement", "id": "kinetic-context-q02" } ] } ] }, { "id": "signal-attribution", "name": "Signal attribution", "description": "Establish that the detection signal represents the intended enzyme reaction.", "findings": [ { "id": "reaction-and-readout-controls", "name": "Reaction and readout controls", "description": "Histamine oxidation produces an aldehyde, ammonia and hydrogen peroxide; an indirect readout requires controls against unrelated signal generation or loss. [IUBMB reaction](https://iubmb.qmul.ac.uk/enzyme/EC1/4/3/22.html)", "questions": [ { "text": "Does the assay measure substrate depletion, a reaction product or a coupled signal, and how is it calibrated?", "kind": "measurement", "id": "reaction-and-readout-controls-q01" }, { "text": "Which blanks, recovery checks and independent measurements rule out background oxidation or interference with product detection?", "kind": "action", "id": "reaction-and-readout-controls-q02" } ] } ] } ] }, { "id": "stability-and-use-decisions", "name": "Stability and use decisions", "description": "Translate preparation-specific evidence into handling and catalytic-use decisions.", "rationale": "An identified enzyme can lose useful activity, and activity in one assay does not establish performance in another matrix.", "layers": [ { "id": "activity-retention", "name": "Activity retention", "description": "Track storage and exposure history against repeatable functional measurements.", "findings": [ { "id": "handling-dependent-acceptance", "name": "Handling-dependent acceptance", "description": "Base storage limits and acceptance decisions on retained activity for the relevant formulation and intended reaction.", "questions": [ { "text": "What activity remains after the recorded temperature, storage duration, freeze-thaw cycles and matrix exposure?", "kind": "measurement", "id": "handling-dependent-acceptance-q01" }, { "text": "What predefined retained-activity threshold triggers use, retesting or rejection of this preparation?", "kind": "action", "id": "handling-dependent-acceptance-q02" } ] } ] }, { "id": "intended-reaction-suitability", "name": "Intended reaction suitability", "description": "Bound a proposed use by demonstrated matrix performance and reaction-product management.", "findings": [ { "id": "application-evidence-boundary", "name": "Application evidence boundary", "description": "Record evidence for the intended catalytic task separately from product approvals or clinical claims.", "questions": [ { "text": "What tests establish the required amine conversion within the intended matrix, concentration range and contact time?", "kind": "action", "id": "application-evidence-boundary-q01" }, { "text": "How will oxygen supply and aldehyde, ammonia and hydrogen peroxide production be accounted for in the intended reaction?", "kind": "action", "id": "application-evidence-boundary-q02" }, { "text": "Which proposed claims require evidence beyond this enzyme model, such as finished-product performance or patient outcomes?", "kind": "boundary", "id": "application-evidence-boundary-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": [ "The registry name does not specify organism, molecular form or preparation; these must be resolved before assigning substance identifiers or physical constants.", "Activity values require explicit assay conditions and should not be compared across methods without validation.", "Clinical diagnostic performance, supplement efficacy and jurisdiction-specific product rules require research; no sources were consulted for this recall." ], "questions": [ { "id": "evidence-confidence-notes-q01", "text": "Which of these check these first hold for the sense of diamine oxidase 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": [ "Mammalian diamine oxidases", "Plant diamine oxidases" ], "questions": [ { "id": "evidence-kinds-q01", "text": "Which of these kinds and varieties hold for the sense of diamine oxidase 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 1.4.3.22", "note": "Diamine oxidase; an activity classification rather than an identifier for one molecular preparation." }, { "scheme": "HGNC gene symbol", "value_or_pattern": "AOC1", "note": "The human gene encoding diamine oxidase; identifies the gene rather than the enzyme substance." }, { "scheme": "Common biochemical names", "value_or_pattern": "DAO; histaminase", "note": "DAO is ambiguous because it is also used for D-amino-acid oxidase." } ], "questions": [ { "id": "evidence-identifiers-q01", "text": "Which of these identifiers and schemes hold for the sense of diamine oxidase 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": [ "Physiological degradation of histamine and other diamines, including a role in the intestinal barrier to dietary histamine.", "Polyamine metabolism and hydrogen-peroxide production in plants.", "Enzymatic assays for histamine and other susceptible amines.", "Measurement of enzyme activity in research and some clinical investigations.", "Ingredient in supplements marketed to support degradation of dietary histamine." ], "questions": [ { "id": "evidence-real-world-use-q01", "text": "Which of these real-world use hold for the sense of diamine oxidase 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; one enzyme unit conventionally represents conversion of one micromole of substrate per minute under specified conditions.", "unit": "U" }, { "quantity": "Specific catalytic activity", "typical_range": "Depends on enzyme source, purity, substrate, pH and temperature.", "unit": "U/mg protein" } ], "questions": [ { "id": "evidence-measurements-q01", "text": "Which of these typical measurements hold for the sense of diamine oxidase 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": [ "Denaturation or unsuitable storage conditions can reduce catalytic activity.", "Activity depends on copper and maturation of the topaquinone cofactor.", "Assays can be misleading when substrate specificity, interfering substances or assay conditions are not controlled.", "Hydrogen peroxide generated by the reaction can cause oxidative damage unless removed or controlled.", "A circulating DAO activity result alone does not establish intestinal enzyme function or diagnose adverse reactions to dietary histamine." ], "questions": [ { "id": "evidence-failure-modes-and-hazards-q01", "text": "Which of these failure modes and hazards hold for the sense of diamine oxidase 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": "Monoamine oxidase", "difference": "Monoamine oxidases are flavin-dependent enzymes with different substrate preferences and cellular locations; diamine oxidase uses copper and topaquinone." }, { "name": "Histamine N-methyltransferase", "difference": "Degrades histamine through methyl transfer rather than oxidative deamination." }, { "name": "D-amino-acid oxidase", "difference": "Oxidises D-amino acids and uses FAD; its shared abbreviation DAO does not indicate the same enzyme." }, { "name": "AOC1", "difference": "AOC1 is the human encoding gene; diamine oxidase is its protein product or, more broadly, the enzyme activity found across organisms." }, { "name": "Diamine oxidase supplement", "difference": "A formulated product containing an enzyme preparation, with source, activity and excipients that are not properties of the enzyme class itself." } ], "questions": [ { "id": "evidence-neighbours-q01", "text": "Which of these neighbouring kinds and how to tell them apart hold for the sense of diamine oxidase this model covers, and on what evidence?", "kind": "provenance" } ] } ] } ] } ] }, "openQuestions": [ "Does the registry intend the full EC 1.4.3.22 enzyme category or specifically the AOC1 protein, and is either already covered by an existing world model?", "Which native sources, recombinant constructs and preparation grades should receive explicit profiles within this entry?", "Which identifiers reliably denote the enzyme category versus a particular protein or commercial preparation, including any applicable CAS records?", "Which assay protocols and activity-unit definitions permit defensible comparison across sources and lots?", "What source-specific evidence establishes storage limits, matrix compatibility, inhibition and preparation-specific handling requirements?" ], "statistics": { "bundles": 5, "layers": 9, "findings": 15, "questions": 24 } }