{ "vercy": "1.0-draft", "publication": { "status": "research-draft", "adjudicationStatus": "unreviewed", "publishableCanonical": false, "generatedAt": "2026-09-12T08:35:14Z", "providers": [ "Codex" ], "breadth": "recalled by Codex without web access - no source was read", "missingProviders": [], "pass": 2, "cost": { "grok": { "seconds": 28.4, "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: 01a094c0-9483-7753-a9da-0d83f8e8c01d\n--------\nuser\nDescribe what is already known about one registered thing. Answer as JSON only, no prose around it.\n\nThing: chemical database\nSense to describe: (none recorded)\nDomain code: INF.MED\nAlso known as: (none)\n\n\nContext for this batch of 1001 things:\n# Batch 043: 10", "usd": 0.0, "recall": true }, "codex": { "seconds": 71.1, "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: 01a094c0-947b-7643-8918-0cce10838f01\n--------\nuser\nYou are drafting a Vercy meta-model for one registered thing. Answer as JSON only, no prose around it.\n\nThing: chemical database\nRegistry id: vr.tr.chemical-database\nPlane / domain: INF / INF.MED\nRegistry definition: (none recorded)\nNames folded into this entr" } }, "enrichment": { "pass": 3, "engine": "claude", "producedAt": "2026-10-06T12:00:00Z", "ingestedAt": "2026-10-06T08:42:05+00:00", "fields": [ "agent_conduct", "ethics", "failure_modes_and_hazards", "owners" ] }, "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-Q2881060", "registryId": "vr.tr.chemical-database", "name": "chemical database", "version": "0.1.0-research.1", "entryKind": "thing", "family": "Thing Registry", "domain": [ "INF.MED" ], "status": "research-draft" }, "canonicalUrl": "https://ver.cy/models/thing/q2881060/", "model": { "registry_id": "vr.tr.chemical-database", "name": "chemical database", "purpose": "Enable an agent to recognise a chemical database, assess whether its chemical records support an intended use, and determine which retrieval, comparison, reuse or update actions are appropriate.", "definition": "A chemical database is an organized collection of electronically retrievable records describing chemical entities, their structures, properties, reactions or associated evidence, with mechanisms for identifying and searching those records.", "scope_statement": "This model owns the chemical database as an organised information resource, including its chemical coverage, identity conventions, evidence practices, retrieval capabilities, releases and access conditions; it does not own the substances described or the software infrastructure hosting it.", "in_scope": [ "Database identity, stewardship, intended audience and chemical coverage", "Chemical record types and rules for distinguishing or grouping chemical entities", "Representation of chemical structures, properties and associated evidence", "Chemical search, record linking, export and retrieval capabilities", "Curation state, release history, access conditions and permitted reuse" ], "out_of_scope": [ "Physical chemical substances, mixtures, specimens and their intrinsic states", "Laboratory experiments and instruments that generate source measurements", "Database engines, hosting infrastructure and application source code", "Research articles and other source works as independently managed publications", "Chemical inventory holdings, procurement and physical stock movements", "Clinical, toxicological or regulatory decisions made using retrieved information" ], "distinguishing_features": [ "Its organising subjects are chemical entities or chemically characterised materials, rather than documents that merely mention chemistry.", "It exposes chemical records through explicit identifiers, names, structures or composition descriptions that support repeatable retrieval.", "It has an ascertainable convention for what a record denotes, such as a compound identity, depositor substance description or mixture.", "It associates chemical entities with structured information or links; a standalone molecular drawing or unindexed document collection does not meet this test.", "Its identity is distinguishable from both a particular downloaded release and the web interface or software used to access it." ], "characteristics": [ { "name": "Chemical coverage", "kind": "category", "unit_or_values": "Declared included and excluded chemical classes, material types and application domains", "why_it_matters": "An absent record is meaningful only relative to the database's intended coverage." }, { "name": "Record referent", "kind": "category", "unit_or_values": "Compound identity; depositor substance; mixture; material; other declared referent", "why_it_matters": "Determines what a record represents and whether records can validly be compared or combined." }, { "name": "Chemical identity policy", "kind": "category", "unit_or_values": "Declared handling of stereochemistry, isotopes, charge, protonation, tautomers, salts and components", "why_it_matters": "Controls when apparently similar chemical descriptions count as the same entity." }, { "name": "Structure representation support", "kind": "category", "unit_or_values": "Supported encodings and their treatment of connectivity, stereochemistry, coordinates and uncertain structure", "why_it_matters": "Determines what chemical distinctions can survive storage, search and export." }, { "name": "Chemical record count", "kind": "measurement", "unit_or_values": "Records, qualified by referent type, release and counting rule", "why_it_matters": "Makes coverage estimates interpretable without confusing submitted descriptions with distinct chemical identities." }, { "name": "Evidence traceability", "kind": "state", "unit_or_values": "Per-assertion provenance; record-level provenance only; mixed; undocumented", "why_it_matters": "Determines whether an agent can inspect the basis of a particular chemical claim." }, { "name": "Property evidence type", "kind": "category", "unit_or_values": "Measured; calculated; predicted; depositor-asserted; mixed; unspecified, recorded per assertion", "why_it_matters": "Prevents predictions and unsupported assertions from being treated as experimental measurements." }, { "name": "Chemical retrieval capabilities", "kind": "category", "unit_or_values": "Name; identifier; exact structure; substructure; similarity; formula; property filtering, as supported", "why_it_matters": "Determines which chemical questions the resource can answer and how results should be interpreted." }, { "name": "Release and maintenance state", "kind": "state", "unit_or_values": "Release identifier or retrieval timestamp, with active, frozen, archived, unavailable or unknown maintenance state", "why_it_matters": "Supports reproducibility and assessment of whether chemical records may have changed." }, { "name": "Chemical data reuse conditions", "kind": "relation", "unit_or_values": "Applicable terms linked to the database, contributed datasets and restricted record fields", "why_it_matters": "Determines whether retrieved chemical information may be cached, redistributed or incorporated into another resource." } ], "affordances": [ "Resolve a chemical name, identifier or structure to candidate records while preserving unresolved identity ambiguity.", "Retrieve chemical properties with units, conditions, evidence types and source attribution.", "Search for exact structures, substructures or similar structures where supported and retain the search semantics.", "Compare chemical records across resources using explicit equivalence criteria.", "Export or cite a reproducible set of chemical records subject to applicable access and reuse conditions.", "Flag suspected chemical identity errors, conflicting values or obsolete links through supported curation channels." ], "agent_conduct": { "may": [ "Search, cite and summarize records from chemical databases it is authorized to use, naming the source and version.", "Flag inconsistent or missing data, such as conflicting identifiers or properties." ], "must_not": [ "Use database records to help anyone make chemical weapons, explosives or illicit drugs.", "Present predicted or unverified values as measured data.", "Scrape or redistribute database content against its licence.", "Alter records in a shared database without authorization." ], "requires_human": [ "Publishing data on hazardous substances beyond its existing audience.", "Correcting or removing records in a shared database." ] }, "ethics": { "considerations": [ "Chemical databases support safety and research but can also aid misuse.", "Errors spread quickly into safety data sheets and models that people rely on." ], "affected_parties": [ "Laboratory workers", "Researchers", "The public exposed to chemicals" ] }, "owners": { "steward": "The organization that curates the database.", "master_systems": [] }, "failure_modes_and_hazards": [ "Wrong structures or identifiers lead to mistaken handling of hazardous substances.", "Data errors spread through copies and models that reuse the records." ], "what_it_is_for": [ "Chemical databases support retrieval and comparison of chemical structures, properties, reactions and supporting evidence.", "They are used in research, substance identification, laboratory informatics and regulatory information management." ], "standards_and_regulation": [ "The International Chemical Identifier standard, issued by the International Union of Pure and Applied Chemistry, supports chemical structure identification in databases that implement it.", "The SQL standard ISO/IEC 9075, issued by the International Organization for Standardization and the International Electrotechnical Commission, applies to relational database implementations using SQL." ], "facets_not_applicable": { "recognition": "A chemical database is an organized information collection whose identity and scope require examination of its records and schema rather than visual appearance." } }, "sources": [ { "id": "wikidata", "title": "Wikidata item Q2881060: chemical database", "url": "https://www.wikidata.org/wiki/Q2881060", "url_status": "live", "what_it_supports": "identity and sense of the item", "checked_by": "wikidata-api" }, { "id": "wikipedia-en", "title": "Wikipedia: Chemical database", "url": "https://en.wikipedia.org/wiki/Chemical_database", "url_status": "live", "what_it_supports": "general description of the item", "checked_by": "wikidata-api sitelink" } ], "structure": { "bundles": [ { "id": "chemical-coverage-and-record-boundaries", "name": "Chemical coverage and record boundaries", "description": "Establishes which chemical subjects the resource covers and what each kind of record denotes.", "rationale": "An agent must know whether a missing chemical is outside scope and whether a retrieved record denotes the intended kind of entity.", "layers": [ { "id": "chemical-collection-remit", "name": "Chemical collection remit", "description": "Captures the resource's inclusion rules and intended chemical uses.", "findings": [ { "id": "declared-chemical-coverage", "name": "Declared chemical coverage", "description": "Record the stated inclusion and exclusion criteria without interpreting catalogue size as completeness.", "questions": [ { "text": "Which chemical classes, material types and application domains does this database explicitly include or exclude?", "kind": "boundary", "id": "declared-chemical-coverage-q01" }, { "text": "What evidence supports any claim that its coverage is complete for a particular chemical population?", "kind": "provenance", "id": "declared-chemical-coverage-q02" } ] } ] }, { "id": "chemical-record-referents", "name": "Chemical record referents", "description": "Distinguishes chemical identities from submitted substance descriptions and multicomponent materials.", "findings": [ { "id": "record-denotation", "name": "Record denotation", "description": "Make explicit whether a record denotes a defined chemical identity, a submitted description, a mixture or another chemically described subject.", "questions": [ { "text": "What does each record type denote, and can several depositor records refer to one chemical identity?", "kind": "definition", "id": "record-denotation-q01" }, { "text": "How are mixtures, polymers and materials with incomplete or variable composition represented or excluded?", "kind": "boundary", "id": "record-denotation-q02" } ] } ] } ] }, { "id": "chemical-identity-and-representation", "name": "Chemical identity and representation", "description": "Describes how chemical distinctions are encoded, normalised and linked.", "rationale": "Chemical matching requires explicit rules for identity; shared names or similar structures alone do not establish equivalence.", "layers": [ { "id": "structure-identity-rules", "name": "Structure identity rules", "description": "Records which structural differences create separate identities and which are normalised.", "findings": [ { "id": "normalisation-and-distinction-policy", "name": "Normalisation and distinction policy", "description": "Capture the treatment of stereochemistry, isotopes, charge, protonation, tautomers and salt components, including information lost during normalisation.", "questions": [ { "text": "Which differences in stereochemistry, isotope specification, protonation, tautomerism or salt composition create separate records?", "kind": "boundary", "id": "normalisation-and-distinction-policy-q01" }, { "text": "Which transformations are applied to submitted structures, and is the original representation retained?", "kind": "provenance", "id": "normalisation-and-distinction-policy-q02" } ] } ] }, { "id": "chemical-names-and-cross-references", "name": "Chemical names and cross-references", "description": "Connects chemical records to names and external identifiers without assuming every link expresses exact identity.", "findings": [ { "id": "identifier-equivalence", "name": "Identifier equivalence", "description": "Record identifier authority, mapping provenance and whether a cross-reference means exact identity, a broader relationship or an unresolved candidate match.", "questions": [ { "text": "Which names and identifiers are preferred, supplied by depositors or mapped from external resources?", "kind": "provenance", "id": "identifier-equivalence-q01" }, { "text": "How can an agent distinguish exact chemical equivalence from parent-compound, component or ambiguous-name links?", "kind": "action", "id": "identifier-equivalence-q02" } ] } ] } ] }, { "id": "chemical-assertions-and-evidence", "name": "Chemical assertions and evidence", "description": "Qualifies chemical properties and associated claims by their origin, conditions and uncertainty.", "rationale": "A chemical value becomes usable only when its referent, evidence type and relevant conditions are understood.", "layers": [ { "id": "property-meaning-and-conditions", "name": "Property meaning and conditions", "description": "Preserves the meaning of chemical measurements and computed descriptors.", "findings": [ { "id": "qualified-property-values", "name": "Qualified property values", "description": "Associate values with units, methods and relevant conditions such as temperature, pressure, solvent, pH or material form.", "questions": [ { "text": "For a retrieved property, which units, experimental conditions and chemical or material form are recorded?", "kind": "measurement", "id": "qualified-property-values-q01" }, { "text": "Does the record distinguish measured values from calculations or predictions and identify the relevant method or model version?", "kind": "provenance", "id": "qualified-property-values-q02" } ] } ] }, { "id": "assertion-lineage-and-conflict", "name": "Assertion lineage and conflict", "description": "Makes supporting evidence and disagreements inspectable at the chemical assertion level.", "findings": [ { "id": "traceable-and-contested-claims", "name": "Traceable and contested claims", "description": "Retain source attribution, extraction or transformation history, and unresolved disagreement rather than silently treating one value as definitive.", "questions": [ { "text": "Can each chemical assertion be traced to an inspected source, depositor submission or documented computation?", "kind": "provenance", "id": "traceable-and-contested-claims-q01" }, { "text": "When values disagree, does the database preserve alternatives and explain any preferred-value selection?", "kind": "definition", "id": "traceable-and-contested-claims-q02" } ] } ] } ] }, { "id": "chemical-search-and-data-transfer", "name": "Chemical search and data transfer", "description": "Defines what chemical queries mean and what survives retrieval and export.", "rationale": "An agent must distinguish a search result from an identity determination and know whether transferred records retain necessary chemical detail.", "layers": [ { "id": "chemical-query-semantics", "name": "Chemical query semantics", "description": "Qualifies name, structure, substructure and similarity searches by their actual matching rules.", "findings": [ { "id": "interpretable-chemical-matches", "name": "Interpretable chemical matches", "description": "Record supported query modes and the parameters that determine inclusion, ranking and chemical equivalence.", "questions": [ { "text": "How do exact-structure and substructure searches handle unspecified stereochemistry, aromaticity, tautomers and disconnected components?", "kind": "definition", "id": "interpretable-chemical-matches-q01" }, { "text": "For similarity search, which representation, metric and threshold define a match, and are those settings exposed?", "kind": "measurement", "id": "interpretable-chemical-matches-q02" } ] } ] }, { "id": "chemical-export-fidelity", "name": "Chemical export fidelity", "description": "Assesses whether exported chemical records preserve identity and evidence needed for downstream use.", "findings": [ { "id": "transferable-chemical-context", "name": "Transferable chemical context", "description": "Identify whether exports preserve structural distinctions, property qualifications, provenance and stable references.", "questions": [ { "text": "Which export formats preserve stereochemistry, isotope labels, component relationships and uncertain structural information?", "kind": "boundary", "id": "transferable-chemical-context-q01" }, { "text": "How can an agent retrieve a complete result set with property conditions, evidence links and release information intact?", "kind": "action", "id": "transferable-chemical-context-q02" } ] } ] } ] }, { "id": "chemical-curation-and-permitted-use", "name": "Chemical curation and permitted use", "description": "Tracks chemical record changes and the conditions under which chemical content may be accessed or reused.", "rationale": "Chemical identities and claims can be corrected, while contributed content can carry distinct reuse conditions.", "layers": [ { "id": "chemical-record-lifecycle", "name": "Chemical record lifecycle", "description": "Preserves continuity when structures, identities or property assertions change.", "findings": [ { "id": "chemical-corrections-and-release-history", "name": "Chemical corrections and release history", "description": "Track record merges, splits, withdrawals and corrected structures or values with sufficient history to reproduce prior use.", "questions": [ { "text": "What happens to identifiers and incoming links when chemical records are merged, split or withdrawn?", "kind": "definition", "id": "chemical-corrections-and-release-history-q01" }, { "text": "How can an agent identify the exact chemical record version used and submit a suspected structure or property error?", "kind": "action", "id": "chemical-corrections-and-release-history-q02" } ] } ] }, { "id": "chemical-content-access-and-rights", "name": "Chemical content access and rights", "description": "Connects retrieval and reuse actions to terms covering the relevant chemical records and contributed data.", "findings": [ { "id": "permitted-chemical-data-operations", "name": "Permitted chemical data operations", "description": "Record access constraints and applicable terms for structure collections, property tables and contributed annotations.", "questions": [ { "text": "Do chemical structures, property values and third-party annotations share the same reuse terms, or are exceptions identified?", "kind": "boundary", "id": "permitted-chemical-data-operations-q01" }, { "text": "Which conditions apply to automated retrieval, local caching, bulk export and redistribution of the intended chemical dataset?", "kind": "action", "id": "permitted-chemical-data-operations-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": [ "No narrower sense is recorded; this description treats chemical database as an information resource rather than its software or hosting service.", "Identifier coverage and identity rules vary: compound, substance, mixture and reaction records are not interchangeable.", "This is recall-based; applicability of standards and provider-specific licensing should be checked before use." ], "questions": [ { "id": "evidence-confidence-notes-q01", "text": "Which of these check these first hold for the sense of chemical database 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": [ "Chemical structure and compound databases", "Substance and material databases", "Chemical reaction databases", "Spectral databases", "Physicochemical property databases", "Bioactivity and toxicology databases" ], "questions": [ { "id": "evidence-kinds-q01", "text": "Which of these kinds and varieties hold for the sense of chemical database 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": "Database accession identifiers", "value_or_pattern": "PubChem CID for compound records; PubChem SID for substance records", "note": "Identify records within a particular database and record class, not the database itself." }, { "scheme": "CAS Registry Number", "value_or_pattern": "Two to seven digits, a hyphen, two digits, a hyphen and one check digit", "note": "Identifies substances registered by CAS; coverage and reuse conditions depend on the data source." }, { "scheme": "IUPAC International Chemical Identifier (InChI)", "value_or_pattern": "Standard InChI strings begin with InChI=1S/", "note": "Encodes chemical structure under defined representation rules; it is not a database accession number." }, { "scheme": "InChIKey", "value_or_pattern": "27 characters arranged as 14 uppercase letters, a hyphen, 10 uppercase letters, a hyphen and one uppercase letter", "note": "A compact hash-derived representation of an InChI, useful for indexing but not reversible into a structure." } ], "questions": [ { "id": "evidence-identifiers-q01", "text": "Which of these identifiers and schemes hold for the sense of chemical database 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": [ "IUPAC chemical nomenclature recommendations provide systematic naming conventions.", "The IUPAC International Chemical Identifier (InChI), developed and maintained with the InChI Trust, supports standardized structure identification." ], "questions": [ { "id": "evidence-standards-and-regulation-q01", "text": "Which of these standards and regulation hold for the sense of chemical database 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": [ "Finding chemical records by name, identifier, exact structure, substructure or structural similarity.", "Supporting drug discovery through compound and bioactivity retrieval.", "Planning synthesis using recorded reactions and experimental conditions.", "Identifying substances by comparing measured spectra with reference records.", "Retrieving property, hazard and toxicology evidence for chemical assessment." ], "questions": [ { "id": "evidence-real-world-use-q01", "text": "Which of these real-world use hold for the sense of chemical database 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": [ "Incorrectly merging or separating records because of salts, mixtures, tautomers, stereochemistry or protonation states.", "Propagating incorrect structures, names or identifier mappings between databases.", "Treating predicted properties as experimental measurements or omitting conditions such as temperature, solvent and assay method.", "Using outdated or poorly documented records without checking provenance and supporting evidence.", "Interpreting missing hazard or bioactivity data as evidence of safety or inactivity." ], "questions": [ { "id": "evidence-failure-modes-and-hazards-q01", "text": "Which of these failure modes and hazards hold for the sense of chemical database 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": [ "Names, language coverage and links to national chemical inventories vary by database and jurisdiction.", "Database rights, licensing and permitted extraction or redistribution vary by jurisdiction and provider." ], "questions": [ { "id": "evidence-regional-variation-q01", "text": "Which of these regional variation hold for the sense of chemical database 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": "Chemical registry", "difference": "Primarily establishes substance identities and assigns identifiers; a chemical database may instead organize structures, properties, reactions or other evidence without acting as a registry." }, { "name": "Chemical inventory", "difference": "Tracks substances present in a location, organization or regulatory scope, often including quantities or eligibility; a chemical database need not track holdings or inventory status." }, { "name": "Chemical database management system", "difference": "The software that stores and queries chemical data, rather than the organized data collection it manages." }, { "name": "Chemical dataset", "difference": "A bounded collection of chemical data that may be distributed as files without the maintained retrieval facilities associated with a database." } ], "questions": [ { "id": "evidence-neighbours-q01", "text": "Which of these neighbouring kinds and how to tell them apart hold for the sense of chemical database this model covers, and on what evidence?", "kind": "provenance" } ] } ] } ] } ] }, "openQuestions": [ "Does the registry intend chemical database to include reaction-centred and spectral databases, or should those be neighbouring specialisations?", "Which existing Vercy information-resource or database model should supply inherited concepts without duplicating this chemical specialisation?", "What minimum chemical organisation distinguishes a chemical database from a searchable collection of chemistry documents?", "Which identity-policy and evidence fields can be established consistently across representative chemical databases, and which must remain explicitly unknown?", "Should archived chemical dataset releases instantiate this model directly or be modelled as manifestations of a continuing database resource?" ], "statistics": { "bundles": 6, "layers": 11, "findings": 18, "questions": 28 } }