chemical database
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.
Bundle → Layer → Finding → Questions Filled
6 bundles · 11 layers · 18 findings · 28 questions
Chemical coverage and record boundaries Establishes which chemical subjects the resource covers and what each kind of record denotes.
Chemical collection remit
Captures the resource's inclusion rules and intended chemical uses.
Declared chemical coverage
Record the stated inclusion and exclusion criteria without interpreting catalogue size as completeness.
- Which chemical classes, material types and application domains does this database explicitly include or exclude? boundary
- What evidence supports any claim that its coverage is complete for a particular chemical population? provenance
Chemical record referents
Distinguishes chemical identities from submitted substance descriptions and multicomponent materials.
Record denotation
Make explicit whether a record denotes a defined chemical identity, a submitted description, a mixture or another chemically described subject.
- What does each record type denote, and can several depositor records refer to one chemical identity? definition
- How are mixtures, polymers and materials with incomplete or variable composition represented or excluded? boundary
Chemical identity and representation Describes how chemical distinctions are encoded, normalised and linked.
Structure identity rules
Records which structural differences create separate identities and which are normalised.
Normalisation and distinction policy
Capture the treatment of stereochemistry, isotopes, charge, protonation, tautomers and salt components, including information lost during normalisation.
- Which differences in stereochemistry, isotope specification, protonation, tautomerism or salt composition create separate records? boundary
- Which transformations are applied to submitted structures, and is the original representation retained? provenance
Chemical names and cross-references
Connects chemical records to names and external identifiers without assuming every link expresses exact identity.
Identifier equivalence
Record identifier authority, mapping provenance and whether a cross-reference means exact identity, a broader relationship or an unresolved candidate match.
- Which names and identifiers are preferred, supplied by depositors or mapped from external resources? provenance
- How can an agent distinguish exact chemical equivalence from parent-compound, component or ambiguous-name links? action
Chemical assertions and evidence Qualifies chemical properties and associated claims by their origin, conditions and uncertainty.
Property meaning and conditions
Preserves the meaning of chemical measurements and computed descriptors.
Qualified property values
Associate values with units, methods and relevant conditions such as temperature, pressure, solvent, pH or material form.
- For a retrieved property, which units, experimental conditions and chemical or material form are recorded? measurement
- Does the record distinguish measured values from calculations or predictions and identify the relevant method or model version? provenance
Assertion lineage and conflict
Makes supporting evidence and disagreements inspectable at the chemical assertion level.
Traceable and contested claims
Retain source attribution, extraction or transformation history, and unresolved disagreement rather than silently treating one value as definitive.
- Can each chemical assertion be traced to an inspected source, depositor submission or documented computation? provenance
- When values disagree, does the database preserve alternatives and explain any preferred-value selection? definition
Chemical search and data transfer Defines what chemical queries mean and what survives retrieval and export.
Chemical query semantics
Qualifies name, structure, substructure and similarity searches by their actual matching rules.
Interpretable chemical matches
Record supported query modes and the parameters that determine inclusion, ranking and chemical equivalence.
- How do exact-structure and substructure searches handle unspecified stereochemistry, aromaticity, tautomers and disconnected components? definition
- For similarity search, which representation, metric and threshold define a match, and are those settings exposed? measurement
Chemical export fidelity
Assesses whether exported chemical records preserve identity and evidence needed for downstream use.
Transferable chemical context
Identify whether exports preserve structural distinctions, property qualifications, provenance and stable references.
- Which export formats preserve stereochemistry, isotope labels, component relationships and uncertain structural information? boundary
- How can an agent retrieve a complete result set with property conditions, evidence links and release information intact? action
Chemical curation and permitted use Tracks chemical record changes and the conditions under which chemical content may be accessed or reused.
Chemical record lifecycle
Preserves continuity when structures, identities or property assertions change.
Chemical corrections and release history
Track record merges, splits, withdrawals and corrected structures or values with sufficient history to reproduce prior use.
- What happens to identifiers and incoming links when chemical records are merged, split or withdrawn? definition
- How can an agent identify the exact chemical record version used and submit a suspected structure or property error? action
Chemical content access and rights
Connects retrieval and reuse actions to terms covering the relevant chemical records and contributed data.
Permitted chemical data operations
Record access constraints and applicable terms for structure collections, property tables and contributed annotations.
- Do chemical structures, property values and third-party annotations share the same reuse terms, or are exceptions identified? boundary
- Which conditions apply to automated retrieval, local caching, bulk export and redistribution of the intended chemical dataset? action
Evidence and external alignment What the world already says about this thing, gathered so the model can be checked against it.
Reported evidence
Findings from the breadth pass, kept separate from the structural claims.
Check these first
Recalled without web access and unsourced; every item is a lead to verify.
- Which of these check these first hold for the sense of chemical database this model covers, and on what evidence? provenance
Kinds and varieties
Recalled without web access and unsourced; every item is a lead to verify.
- Which of these kinds and varieties hold for the sense of chemical database this model covers, and on what evidence? provenance
Identifiers and schemes
Recalled without web access and unsourced; every item is a lead to verify.
- Which of these identifiers and schemes hold for the sense of chemical database this model covers, and on what evidence? provenance
Standards and regulation
Recalled without web access and unsourced; every item is a lead to verify.
- Which of these standards and regulation hold for the sense of chemical database this model covers, and on what evidence? provenance
Real-world use
Recalled without web access and unsourced; every item is a lead to verify.
- Which of these real-world use hold for the sense of chemical database this model covers, and on what evidence? provenance
Failure modes and hazards
Recalled without web access and unsourced; every item is a lead to verify.
- Which of these failure modes and hazards hold for the sense of chemical database this model covers, and on what evidence? provenance
Regional variation
Recalled without web access and unsourced; every item is a lead to verify.
- Which of these regional variation hold for the sense of chemical database this model covers, and on what evidence? provenance
Neighbouring kinds and how to tell them apart
Recalled without web access and unsourced; every item is a lead to verify.
- 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? provenance
Classifiers Filled
- Family
- Thing Registry
- Category
- Information and virtual systems
- Entry kind
- thing
- Plane
- INF
- Domain
- INF.MED
- Other names and narrower kinds
- biochemical database, crystallographic database, nucleic acid database
What it is Filled
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.
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
Why it exists Filled
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.
Distinguishing features Filled
- 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.
What robots and AI may and may not do Filled
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.
Only with a human decision
- Publishing data on hazardous substances beyond its existing audience.
- Correcting or removing records in a shared database.
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.
Moral aspects Filled
- Chemical databases support safety and research but can also aid misuse.
- Errors spread quickly into safety data sheets and models that people rely on.
Who is affected
- Laboratory workers
- Researchers
- The public exposed to chemicals
Owners Filled
Steward
The organization that curates the database.
Links to other meta-models Filled
parent
- Q1391125 - registry parent class
What else AI and robots need to interact with it Filled
Identity and identifiers required Filled
- Vercy registry: vr.tr.chemical-database
- Wikidata: Q2881060 (https://www.wikidata.org/wiki/Q2881060)
Direct properties not applicable Not applicable
- Chemical coverage: Declared included and excluded chemical classes, material types and application domains
- Record referent: Compound identity; depositor substance; mixture; material; other declared referent
- Chemical identity policy: Declared handling of stereochemistry, isotopes, charge, protonation, tautomers, salts and components
- Structure representation support: Supported encodings and their treatment of connectivity, stereochemistry, coordinates and uncertain structure
- Chemical record count: Records, qualified by referent type, release and counting rule
- Evidence traceability: Per-assertion provenance; record-level provenance only; mixed; undocumented
- Property evidence type: Measured; calculated; predicted; depositor-asserted; mixed; unspecified, recorded per assertion
- Chemical retrieval capabilities: Name; identifier; exact structure; substructure; similarity; formula; property filtering, as supported
- Release and maintenance state: Release identifier or retrieval timestamp, with active, frozen, archived, unavailable or unknown maintenance state
- Chemical data reuse conditions: Applicable terms linked to the database, contributed datasets and restricted record fields
Plane INF: no invented physical properties.
Recognition not applicable Not applicable
Not applicable
A chemical database is an organized information collection whose identity and scope require examination of its records and schema rather than visual appearance.
Capabilities and actions required Filled
- 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.
Hazards and failure modes required Filled
- Wrong structures or identifiers lead to mistaken handling of hazardous substances.
- Data errors spread through copies and models that reuse the records.
Standards and interfaces required Filled
- 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.
Context of use required Filled
- 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.
Sources Filled
- Wikidata item Q2881060: chemical database - identity and sense of the item
- Wikipedia: Chemical database - general description of the item
Open questions
- 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?
Machine files
Provenance
thing registry research (pass 2) · unreviewed
Built from: models/things/publications/thing-q2881060/spec.json