{ "vercy": "1.0-draft", "publication": { "status": "research-draft", "adjudicationStatus": "unreviewed", "publishableCanonical": false, "generatedAt": "2026-09-12T08:55:11Z", "providers": [ "Codex" ], "breadth": "recalled by Codex without web access - no source was read", "missingProviders": [], "pass": 2, "cost": { "grok": { "seconds": 21.7, "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: 01a094d2-bbc4-7bf3-9e07-8b3ec4a69ab6\n--------\nuser\nDescribe what is already known about one registered thing. Answer as JSON only, no prose around it.\n\nThing: crotonoyl-CoA\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 r", "usd": 0.0, "recall": true }, "codex": { "seconds": 78.3, "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: 01a094d2-bbb4-76a0-8a50-9ba25e28171a\n--------\nuser\nYou are drafting a Vercy meta-model for one registered thing. Answer as JSON only, no prose around it.\n\nThing: crotonoyl-CoA\nRegistry id: vr.tr.crotonoyl-coa\nPlane / domain: PHY / PHY.MAT\nRegistry definition: (none recorded)\nNames folded into this entry: (none" } }, "enrichment": { "pass": 3, "engine": "claude", "producedAt": "2026-10-06T12:00:00Z", "ingestedAt": "2026-10-06T08:53:40+00:00", "fields": [ "agent_conduct", "ethics", "failure_modes_and_hazards", "owners", "visual_identification" ] }, "gate": { "passed": true, "version": "1.0", "at": "2026-10-07T10:10:29+00:00", "evidence": [ "completeness 1.00", "sense: Wikidata description", "2 live sources", "review by codex: pass" ] } }, "metaModel": { "id": "THING-Q303169", "registryId": "vr.tr.crotonoyl-coa", "name": "crotonoyl-CoA", "version": "0.1.0-research.1", "entryKind": "thing", "family": "Thing Registry", "domain": [ "PHY.MAT" ], "status": "research-draft" }, "canonicalUrl": "https://ver.cy/models/thing/q303169/", "model": { "registry_id": "vr.tr.crotonoyl-coa", "name": "crotonoyl-CoA", "purpose": "Enable an AI agent to identify crotonoyl-CoA, assess the identity and condition of a preparation, and judge its suitability for a specified biochemical use.", "definition": "Crotonoyl-CoA, usually called crotonyl-CoA, is the coenzyme A thioester of crotonic acid, ordinarily referring to the trans (E) but-2-enoyl compound that participates in intermediary metabolism and supplies crotonyl groups for protein lysine crotonylation.", "scope_statement": "This model owns the registered crotonoyl-CoA concept and the evidence needed to distinguish its molecular identity, chemical form, preparation quality, biochemical participation and handling requirements; the intended relationship to the name crotonyl-CoA remains to be verified.", "in_scope": [ "Resolution of the registry name to a verified molecular structure and chemical identifiers", "Acyl-chain connectivity, double-bond geometry and linkage to coenzyme A", "Protonation, counterions, hydration and preparation composition", "Identity, concentration, purity and degradation measurements", "Evidence for participation in specified enzyme reactions", "Preparation-specific storage, handling and hazard information" ], "out_of_scope": [ "Coenzyme A and other acyl-CoA compounds as independently modelled substances", "Enzymes that produce or consume the compound", "Complete metabolic pathways and their regulation", "Protein crotonylation as a biological process", "Commercial reagent products, packaging and supplier organisations", "Organism-level effects inferred solely from detection of the metabolite" ], "distinguishing_features": [ "Require structural evidence that the registry name denotes the intended unsaturated four-carbon acyl-CoA rather than treating spelling similarity to crotonyl-CoA as sufficient identification.", "Distinguish a covalent acyl-CoA thioester from free crotonic acid, free coenzyme A or a mixture of those substances.", "Record double-bond position and geometry explicitly; a cis or differently positioned unsaturated acyl group must not be silently equated with a trans-2 assignment.", "Distinguish the unsaturated acyl group from the saturated acyl group of butyryl-CoA using evidence appropriate to the analytical method.", "Separate the molecular entity from its salt or hydrated preparation so that counterion and water content do not silently alter mass-based concentration calculations." ], "characteristics": [ { "name": "Verified molecular identity", "kind": "category", "unit_or_values": "Source-supported preferred name, structure representation and identifiers; unresolved where unverified", "why_it_matters": "The registry spelling alone does not establish a unique chemical identity." }, { "name": "Acyl-chain structure", "kind": "category", "unit_or_values": "Carbon connectivity, double-bond position and E/Z assignment, each with evidence", "why_it_matters": "Closely related acyl-CoA structures can differ in analytical identity and enzyme compatibility." }, { "name": "Coenzyme A linkage and stereochemistry", "kind": "category", "unit_or_values": "Acyl attachment site, linkage type and assigned stereochemistry", "why_it_matters": "An acyl-CoA assignment requires more than detecting an acyl fragment and a coenzyme A fragment." }, { "name": "Preparation chemical form", "kind": "category", "unit_or_values": "Protonation convention, counterion identity and stoichiometry, hydration and solvation", "why_it_matters": "Formula, formula mass and weighed amounts must refer to the same preparation form." }, { "name": "Intact compound concentration", "kind": "measurement", "unit_or_values": "mol/L or mmol/L, with method, calibration and uncertainty", "why_it_matters": "Reaction stoichiometry depends on intact compound rather than total dissolved material." }, { "name": "Purity and impurity profile", "kind": "measurement", "unit_or_values": "Mass fraction, mole fraction or chromatographic area percentage, with method and identified impurities", "why_it_matters": "Free coenzyme A, related acyl-CoAs and other components may affect assay interpretation." }, { "name": "Preparation condition", "kind": "state", "unit_or_values": "Physical form, solvent, pH, temperature, elapsed storage time and freeze-thaw history", "why_it_matters": "Suitability must be judged for the preparation under its actual conditions." }, { "name": "Reaction-specific biochemical role", "kind": "relation", "unit_or_values": "Named reaction, enzyme, role, direction, organism or experimental system, and supporting evidence", "why_it_matters": "A reported role in one system does not establish equivalent activity in every system." }, { "name": "Handling evidence status", "kind": "state", "unit_or_values": "Applicable safety documentation, assessed hazards, unassessed hazards and jurisdiction", "why_it_matters": "Missing hazard information must remain distinguishable from evidence of low hazard." } ], "affordances": [ "Resolve a label or registry reference to a source-supported structure and flag unresolved naming or isomer ambiguity.", "Compare a preparation with an authenticated reference using complementary analytical evidence.", "Calculate an assay amount from verified chemical form, purity and intact-compound concentration.", "Assess whether a preparation meets the identity and impurity requirements of a specified enzyme assay.", "Track storage history and analytical change to determine whether requalification is needed.", "Link measured consumption or formation to a specified reaction while preserving uncertainty about biological interpretation." ], "agent_conduct": { "may": [ "Describe crotonyl-CoA and its place in metabolism and histone modification from biochemical sources.", "Annotate metabolic pathways with it using recognized databases." ], "must_not": [ "Present research findings on crotonylation as established medical fact.", "Promote supplements or diets as raising or lowering it without evidence.", "Confuse the trans and cis forms or related acyl-CoA species in reports." ], "requires_human": [ "Publishing claims about it that inform clinical decisions." ] }, "ethics": { "considerations": [ "Early research on its role in gene regulation can be overstated to sell products.", "Accurate pathway data matters for diagnosis of metabolic disorders." ], "affected_parties": [ "Researchers", "Patients with metabolic disorders" ] }, "owners": { "steward": "Nobody owns the molecule; curated metabolic databases maintain records of it.", "master_systems": [ "Metabolic pathway and compound databases" ] }, "visual_identification": [ "Not visible; detected by laboratory methods such as mass spectrometry." ], "failure_modes_and_hazards": [ "Misannotation can mislead metabolic research and diagnosis." ], "what_it_is_for": [ "Crotonyl-CoA occurs in intermediary metabolism and is studied as a substrate or intermediate in enzyme reactions involving short-chain acyl groups.", "Biochemical research uses it as a crotonyl-group donor to investigate protein lysine crotonylation.", "Suitability for an experiment depends on the preparation's chemical identity, purity, concentration and stability." ], "standards_and_regulation": [ "The Globally Harmonized System of Classification and Labelling of Chemicals, issued by the United Nations, provides the framework for assessing and communicating preparation-specific chemical hazards where adopted." ] }, "sources": [ { "id": "wikidata", "title": "Wikidata item Q303169: crotonoyl-CoA", "url": "https://www.wikidata.org/wiki/Q303169", "url_status": "live", "what_it_supports": "identity and sense of the item", "checked_by": "wikidata-api" }, { "id": "wikipedia-en", "title": "Wikipedia: Crotonyl-CoA", "url": "https://en.wikipedia.org/wiki/Crotonyl-CoA", "url_status": "live", "what_it_supports": "general description of the item", "checked_by": "wikidata-api sitelink" } ], "structure": { "bundles": [ { "id": "molecular-identity", "name": "Molecular identity", "description": "Resolve what crotonoyl-CoA denotes before assigning properties or biochemical roles.", "rationale": "A naming or isomer error would propagate into every subsequent measurement and action.", "layers": [ { "id": "registry-name-resolution", "name": "Registry name resolution", "description": "Connect the supplied name to independently documented chemical identity.", "findings": [ { "id": "crotonoyl-crotonyl-equivalence", "name": "Crotonoyl and crotonyl equivalence", "description": "Treat the apparent relationship between these names as an identity question requiring verification.", "questions": [ { "text": "Which authoritative chemical record establishes what the registry name crotonoyl-CoA denotes?", "kind": "definition", "id": "crotonoyl-crotonyl-equivalence-q01" }, { "text": "Does that record explicitly support equivalence to crotonyl-CoA, and which structure-specific identifiers does it assign?", "kind": "provenance", "id": "crotonoyl-crotonyl-equivalence-q02" } ] } ] }, { "id": "structural-boundaries", "name": "Structural boundaries", "description": "Specify the acyl group, its geometry and its attachment to coenzyme A.", "findings": [ { "id": "acyl-coa-structure-assignment", "name": "Acyl-CoA structure assignment", "description": "Make structural assignments explicit enough to exclude neighbouring acyl-CoA entities.", "questions": [ { "text": "What evidence establishes the four-carbon acyl connectivity, double-bond position and E/Z geometry?", "kind": "definition", "id": "acyl-coa-structure-assignment-q01" }, { "text": "What evidence distinguishes the intended coenzyme A thioester from butyryl-CoA, positional or geometric isomers, and free-acid mixtures?", "kind": "boundary", "id": "acyl-coa-structure-assignment-q02" } ] } ] } ] }, { "id": "chemical-form-and-amount", "name": "Chemical form and amount", "description": "Relate the molecular entity to the material weighed, dissolved and delivered.", "rationale": "Counterions, water and purity can change the relationship between reagent mass and available acyl-CoA.", "layers": [ { "id": "salt-and-solvation", "name": "Salt and solvation", "description": "Identify the form to which formula and mass statements apply.", "findings": [ { "id": "preparation-formula-basis", "name": "Preparation formula basis", "description": "Keep molecular identity distinct from the composition of a supplied preparation.", "questions": [ { "text": "Which protonation state, counterions and hydration or solvation levels are documented for this preparation?", "kind": "definition", "id": "preparation-formula-basis-q01" }, { "text": "Does the stated formula mass describe the parent entity, a specified salt or a preparation with variable water content?", "kind": "boundary", "id": "preparation-formula-basis-q02" } ] } ] }, { "id": "assay-available-amount", "name": "Assay-available amount", "description": "Establish the concentration of intact compound under intended assay conditions.", "findings": [ { "id": "intact-acyl-coa-quantitation", "name": "Intact acyl-CoA quantitation", "description": "Require a concentration basis that accounts for preparation composition and analytical selectivity.", "questions": [ { "text": "How was intact crotonoyl-CoA concentration measured, and what calibration and uncertainty accompany the result?", "kind": "measurement", "id": "intact-acyl-coa-quantitation-q01" }, { "text": "How should the required assay volume be calculated after accounting for chemical form, purity and dilution?", "kind": "action", "id": "intact-acyl-coa-quantitation-q02" } ] } ] } ] }, { "id": "analytical-identity-and-integrity", "name": "Analytical identity and integrity", "description": "Evaluate whether a preparation contains the intended intact species at acceptable quality.", "rationale": "A plausible label or mass signal cannot by itself establish isomer identity, purity and biochemical usability.", "layers": [ { "id": "identity-evidence", "name": "Identity evidence", "description": "Combine measurements that resolve the specific identity claims being made.", "findings": [ { "id": "orthogonal-structure-confirmation", "name": "Complementary structure confirmation", "description": "Record what chromatography, mass spectrometry, spectroscopy or reference comparison actually establishes.", "questions": [ { "text": "Which observations support intact acyl-CoA identity, and which independently resolve double-bond position or geometry?", "kind": "measurement", "id": "orthogonal-structure-confirmation-q01" }, { "text": "Was the comparison standard authenticated for the same isomer and chemical form?", "kind": "provenance", "id": "orthogonal-structure-confirmation-q02" } ] } ] }, { "id": "impurities-and-transformation", "name": "Impurities and transformation", "description": "Track components and changes that could compromise an acyl-CoA preparation.", "findings": [ { "id": "impurity-specific-acceptance", "name": "Impurity-specific acceptance", "description": "Assess free coenzyme A, free acid, related acyl-CoAs and unidentified components without assuming their origin.", "questions": [ { "text": "Which impurities are detected, at what levels, and with what detection limits and response-factor assumptions?", "kind": "measurement", "id": "impurity-specific-acceptance-q01" }, { "text": "What evidence distinguishes components present initially from products formed during storage or assay preparation?", "kind": "provenance", "id": "impurity-specific-acceptance-q02" }, { "text": "Which impurity limits are necessary for the intended enzyme assay or analytical calibration?", "kind": "action", "id": "impurity-specific-acceptance-q03" } ] } ] } ] }, { "id": "biochemical-participation", "name": "Biochemical participation", "description": "Connect the verified compound to experimentally supported transformations and uses.", "rationale": "Substrate compatibility and reaction interpretation depend on the exact chemical species and experimental context.", "layers": [ { "id": "reaction-specific-role", "name": "Reaction-specific role", "description": "Describe documented production and consumption without treating pathway labels as sufficient evidence.", "findings": [ { "id": "enzyme-transformation-evidence", "name": "Enzyme transformation evidence", "description": "Resolve reported hydration, reduction or other transformations into explicit, supported reactions.", "questions": [ { "text": "Which reactions directly demonstrate consumption or formation of the verified species, with what products and stoichiometry?", "kind": "provenance", "id": "enzyme-transformation-evidence-q01" }, { "text": "Which enzyme, cofactors, pH and substrate geometry were used to establish each reaction?", "kind": "boundary", "id": "enzyme-transformation-evidence-q02" } ] } ] }, { "id": "assay-and-biological-interpretation", "name": "Assay and biological interpretation", "description": "Separate demonstrated reagent function from broader claims about metabolism or acyl transfer.", "findings": [ { "id": "use-specific-evidence", "name": "Use-specific evidence", "description": "Qualify intended uses through direct measurements and appropriate controls.", "questions": [ { "text": "What evidence supports use of this species as the intended enzyme substrate, analytical standard or crotonyl-group donor?", "kind": "provenance", "id": "use-specific-evidence-q01" }, { "text": "Which controls distinguish the intended reaction from spontaneous change, impurity activity or assay interference?", "kind": "action", "id": "use-specific-evidence-q02" }, { "text": "What additional evidence is required before a measured pool or reaction rate supports a claim about cellular flux or protein crotonylation?", "kind": "boundary", "id": "use-specific-evidence-q03" } ] } ] } ] }, { "id": "storage-and-handling", "name": "Storage and handling", "description": "Define evidence-based conditions for retaining and using a qualified preparation.", "rationale": "Handling decisions require preparation-specific stability and safety evidence rather than assumptions based on metabolite status.", "layers": [ { "id": "stability-window", "name": "Stability window", "description": "Relate retained integrity to solvent, pH, temperature and storage history.", "findings": [ { "id": "condition-dependent-requalification", "name": "Condition-dependent requalification", "description": "Use measured retention of intact compound to establish storage and reuse limits.", "questions": [ { "text": "How much intact compound remains after defined storage intervals, temperatures, solution conditions and freeze-thaw cycles?", "kind": "measurement", "id": "condition-dependent-requalification-q01" }, { "text": "Which documented conditions and acceptance thresholds determine whether a stored aliquot can be used or requires requalification?", "kind": "action", "id": "condition-dependent-requalification-q02" } ] } ] }, { "id": "preparation-specific-safety", "name": "Preparation-specific safety", "description": "Attach handling requirements to the actual substance form and formulation.", "findings": [ { "id": "applicable-hazard-record", "name": "Applicable hazard record", "description": "Distinguish documented hazards from missing assessments and formulation-dependent requirements.", "questions": [ { "text": "Which current safety data and regulatory identifiers apply to this exact chemical form and preparation?", "kind": "provenance", "id": "applicable-hazard-record-q01" }, { "text": "What handling and disposal measures follow from those records and from any solvent or additive present?", "kind": "action", "id": "applicable-hazard-record-q02" } ] } ] } ] }, { "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": [ "Confirm that the registry spelling 'crotonoyl-CoA' denotes the usual trans-crotonyl-CoA rather than an unspecified geometric isomer.", "Exact database identifiers and physicochemical values should be checked against the intended protonation state and salt form.", "This description is recalled knowledge; no sources or substance-specific hazard classifications were checked." ], "questions": [ { "id": "evidence-confidence-notes-q01", "text": "Which of these check these first hold for the sense of crotonoyl-CoA 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": "Biochemical nomenclature", "value_or_pattern": "(2E)-but-2-enoyl-CoA", "note": "Describes the usual trans compound; crotonyl-CoA is the more common name." } ], "questions": [ { "id": "evidence-identifiers-q01", "text": "Which of these identifiers and schemes hold for the sense of crotonoyl-CoA 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": [ "Metabolic intermediate in pathways involving short-chain acyl-CoA compounds, including fatty-acid degradation.", "Intermediate in microbial pathways producing butyrate or butanol.", "Crotonyl-group donor for enzyme-catalysed protein lysine crotonylation.", "Substrate or analytical reference material in biochemical research." ], "questions": [ { "id": "evidence-real-world-use-q01", "text": "Which of these real-world use hold for the sense of crotonoyl-CoA 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": [ "Thioester hydrolysis can reduce intact compound concentration and compromise biochemical assays.", "Confusing the usual trans compound with a cis isomer can lead to incorrect assumptions about enzyme specificity.", "Salt form, water content and purity can affect conversion between weighed mass and molar concentration." ], "questions": [ { "id": "evidence-failure-modes-and-hazards-q01", "text": "Which of these failure modes and hazards hold for the sense of crotonoyl-CoA 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": "Crotonic acid", "difference": "The free carboxylic acid; crotonoyl-CoA carries the corresponding acyl group linked to coenzyme A through a thioester." }, { "name": "Butyryl-CoA", "difference": "Has a saturated four-carbon acyl chain; crotonoyl-CoA has a double bond between acyl carbons 2 and 3." }, { "name": "Acetoacetyl-CoA", "difference": "Has a ketone at acyl carbon 3 rather than the carbon-carbon double bond of crotonoyl-CoA." }, { "name": "3-Hydroxybutyryl-CoA", "difference": "Has a hydroxyl group at acyl carbon 3 and a saturated chain; its stereochemistry matters in enzymatic interconversion." } ], "questions": [ { "id": "evidence-neighbours-q01", "text": "Which of these neighbouring kinds and how to tell them apart hold for the sense of crotonoyl-CoA this model covers, and on what evidence?", "kind": "provenance" } ] } ] } ] } ] }, "openQuestions": [ "Does crotonoyl-CoA denote the same entity as crotonyl-CoA, and does this registry entry specify trans-2 geometry or leave geometry unresolved?", "Which authoritative structure record, CAS number, PubChem CID or other identifiers match the intended entity rather than a particular salt or broader isomer class?", "Which analytical methods and authenticated standards can distinguish relevant isomers and quantify intact compound separately from free coenzyme A and related acyl-CoAs?", "What preparation-specific solubility and stability data support stock preparation, storage duration and freeze-thaw limits?", "Which biochemical uses, hazard classifications and exposure guidance are directly supported for the verified entity and its supplied forms?" ], "statistics": { "bundles": 6, "layers": 11, "findings": 15, "questions": 27 } }