# Vercy AI instruction - YAML 1.2 (JSON-compatible) { "vercy": "1.0-draft", "publication": { "status": "published", "adjudicationStatus": "reviewable-draft", "publishableCanonical": false, "generatedAt": "2026-09-06T00:35:00Z", "synthesisSha256": "1cbb676ccd2efe5bbcac05991d6c83c7c30bf56cdc3884ceb7d0d67f9c171864", "providerMode": "single-provider-waiver", "providers": [ "Codex" ], "waivedProviders": [ "Claude", "Grok" ] }, "metaModel": { "id": "WM-LIV-001", "registryId": "vr.wm-liv-001", "name": "Taxon", "version": "0.3.0-research.1", "previousVersions": [], "entryKind": "entity", "family": "World Models", "category": "Physical world and living systems", "industry": [ "Cross-industry" ], "domain": [ "PHY.LIV.TAX" ], "tags": [ "taxon", "phy.liv.tax" ], "status": "published" }, "canonicalUrl": "https://ver.cy/models/wm-liv-001-taxon/", "sourceUrl": "https://github.com/ver-cy/world-models/tree/feat/mega-model-registry/research/runs/wm-liv-001", "model": { "registry_id": "vr.wm-liv-001", "model_id": "WM-LIV-001", "name": "Taxon", "entry_kind": "entity", "purpose": "Represent a governed, source-qualified taxon concept so agents can identify, compare, cite, revise and exchange biological classifications without confusing concepts with names or organisms.", "scope_statement": "Owns taxon-concept identity, according-to authority, circumscription, source-relative name usages, placement, concept relations, mappings, diagnosis, evidence references, uncertainty, version history, stewardship and projections while external systems own nomenclatural codes and acts, publications, names, specimens, organisms, occurrences, sequences, habitats, distributions and conservation assessments.", "in_scope": [ "Taxon concept identity, source, release, circumscription, scope, code applicability, name usages, rank or rankless placement and hierarchy", "Concept succession and cross-classification relations, diagnosis, evidence references, confidence, disputes, stewardship, access, retention and provenance", "TCS, Darwin Core, Catalogue of Life, GBIF, NCBI and machine or human projections with version and loss controls" ], "out_of_scope": [ "Organism, population, specimen, material sample, occurrence, observation, sequence, trait, distribution, habitat or conservation-assessment master lifecycle", "Nomenclatural code, act, publication, scientific-name master, type-specimen custody or registry-service implementation", "Universal acceptance, placement or equivalence inferred from a name string, rank, matching label or one preferred backbone" ], "boundary_notes": [ { "neighbor": "Taxon Name and Nomenclatural Act", "distinction": "A taxon concept is a circumscribed grouping according to a source; names, typification and code-governed acts have separate identity and lifecycle and are attached as usages or evidence.", "source_refs": [ "SRC-001", "SRC-002", "SRC-004", "SRC-005" ] }, { "neighbor": "Organism, Population, Specimen and Occurrence", "distinction": "Physical or observed biological entities may support or instantiate identification, but their properties, location, custody and event history do not become properties of the concept.", "source_refs": [ "SRC-003", "SRC-004" ] }, { "neighbor": "Classification Scheme", "distinction": "A classification owns the ordered system and release; this model owns one source-qualified concept and its placement assertions within that system.", "source_refs": [ "SRC-001", "SRC-006" ] }, { "neighbor": "Distribution, Habitat, Trait and Conservation Assessment", "distinction": "These are time- and evidence-dependent assertions about members or populations and remain external references rather than defining taxon-concept identity by default.", "source_refs": [ "SRC-003", "SRC-006" ] }, { "neighbor": "Checklist and Taxonomy Registry", "distinction": "Catalogue of Life, GBIF and NCBI own service releases and local identifiers; Vercy preserves mappings and scope instead of declaring their records universally equivalent.", "source_refs": [ "SRC-006", "SRC-007", "SRC-008" ] } ] }, "sources": [ { "id": "SRC-001", "title": "Taxon Concept Standard", "organization": "Biodiversity Information Standards (TDWG)", "url": "https://tcs.tdwg.org/", "version_or_date": "Current vocabulary standard accessed 2026-09-06", "source_type": "standard", "primary_source": true, "authority_tier": 1, "accessed_at": "2026-09-06T00:31:00Z", "relevance": "Defines Taxon Concept, Taxon Name, Taxon Concept Mapping and Nomenclatural Type classes for format-independent exchange." }, { "id": "SRC-002", "title": "Taxon Concept Standard examples", "organization": "Biodiversity Information Standards (TDWG)", "url": "https://tcs.tdwg.org/examples/", "version_or_date": "Current examples accessed 2026-09-06", "source_type": "first-party-doc", "primary_source": true, "authority_tier": 1, "accessed_at": "2026-09-06T00:31:00Z", "relevance": "Demonstrates according-to, synonym, vernacular name, parent and child, congruence, inclusion, overlap, disjointness and typification semantics." }, { "id": "SRC-003", "title": "Darwin Core Quick Reference Guide", "organization": "Biodiversity Information Standards (TDWG)", "url": "https://dwc.tdwg.org/terms/", "version_or_date": "Current recommended terms accessed 2026-09-06", "source_type": "standard", "primary_source": true, "authority_tier": 1, "accessed_at": "2026-09-06T00:31:00Z", "relevance": "Defines the Taxon class and identifiers, name usage, parentage, rank, status, provenance, access and record-level terms used by biodiversity systems." }, { "id": "SRC-004", "title": "International Code of Zoological Nomenclature", "organization": "International Commission on Zoological Nomenclature", "url": "https://code.iczn.org/introduction/", "version_or_date": "Online Code accessed 2026-09-06", "source_type": "standard", "primary_source": true, "authority_tier": 1, "accessed_at": "2026-09-06T00:31:00Z", "relevance": "Establishes zoological nomenclatural scope and distinguishes taxonomic judgment from governed names and name-bearing types." }, { "id": "SRC-005", "title": "International Code of Nomenclature for algae, fungi, and plants", "organization": "International Association for Plant Taxonomy", "url": "https://www.iapt-taxon.org/nomen/main.php", "version_or_date": "Madrid Code notice and prior electronic Code accessed 2026-09-06", "source_type": "standard", "primary_source": true, "authority_tier": 1, "accessed_at": "2026-09-06T00:31:00Z", "relevance": "Establishes code-governed botanical, fungal and algal naming and shows that applicable code editions must be versioned." }, { "id": "SRC-006", "title": "ChecklistBank", "organization": "Catalogue of Life", "url": "https://www.catalogueoflife.org/about/checklistbank", "version_or_date": "Service documentation accessed 2026-09-06", "source_type": "registry", "primary_source": true, "authority_tier": 1, "accessed_at": "2026-09-06T00:31:00Z", "relevance": "Provides governed checklist, dataset, release, source, identifier and reconciliation context for taxonomic concepts." }, { "id": "SRC-007", "title": "Species API", "organization": "Global Biodiversity Information Facility", "url": "https://techdocs.gbif.org/en/openapi/v1/species", "version_or_date": "Current API reference accessed 2026-09-06", "source_type": "first-party-doc", "primary_source": true, "authority_tier": 1, "accessed_at": "2026-09-06T00:31:00Z", "relevance": "Provides operational lookup, matching, hierarchy, name usage and backbone-taxonomy projections with GBIF identifiers." }, { "id": "SRC-008", "title": "NCBI Taxonomy", "organization": "National Center for Biotechnology Information", "url": "https://www.ncbi.nlm.nih.gov/taxonomy", "version_or_date": "Current database page accessed 2026-09-06", "source_type": "registry", "primary_source": true, "authority_tier": 1, "accessed_at": "2026-09-06T00:31:00Z", "relevance": "Defines a curated classification and nomenclature for organisms represented in public sequence databases." }, { "id": "SRC-009", "title": "PROV-O: The PROV Ontology", "organization": "World Wide Web Consortium", "url": "https://www.w3.org/TR/prov-o/", "version_or_date": "W3C Recommendation, 30 April 2013", "source_type": "ontology", "primary_source": true, "authority_tier": 1, "accessed_at": "2026-09-06T00:31:00Z", "relevance": "Defines entity, activity, agent, attribution, source, derivation, revision and invalidation provenance for concept assertions and mappings." }, { "id": "SRC-010", "title": "RFC 3339: Date and Time on the Internet: Timestamps", "organization": "Internet Engineering Task Force", "url": "https://www.rfc-editor.org/rfc/rfc3339", "version_or_date": "RFC 3339, July 2002", "source_type": "standard", "primary_source": true, "authority_tier": 1, "accessed_at": "2026-09-06T00:31:00Z", "relevance": "Defines interoperable event timestamps with seconds and an explicit UTC offset for revision, review, ingestion and publication events." } ], "structure": { "bundles": [ { "id": "concept-identity-authority-and-scope", "name": "Concept identity, authority and scope", "description": "Establishes which taxon concept is asserted, by whom, in which classification and with which circumscription.", "rationale": "A name string cannot uniquely identify a taxon concept because the same name may denote different circumscriptions and competing classifications.", "source_refs": [ "SRC-001", "SRC-002", "SRC-003", "SRC-009" ], "layers": [ { "id": "concept-identity-and-source", "name": "Concept identity and source", "description": "Stable identity and according-to authority for a concept assertion.", "source_refs": [ "SRC-001", "SRC-002", "SRC-003", "SRC-006" ], "findings": [ { "id": "taxon-concept-master-identity", "name": "Taxon concept master identity", "description": "Records the authoritative concept identifier, governed namespace, alternate identifiers, source release and collision history independently of names.", "source_refs": [ "SRC-001", "SRC-003", "SRC-006", "SRC-007", "SRC-008" ], "questions": [ { "id": "taxon-concept-master-identity-q01", "text": "What exact values and source-qualified meaning must be recorded for taxon concept master identity?", "kind": "identity", "answer_data": [ "Taxon concept master identity", "Authoritative identifier or controlled value", "Source classification and version", "Explicit unknown or not-applicable reason" ] }, { "id": "taxon-concept-master-identity-q02", "text": "Which authority, source, method and evidence establish taxon concept master identity, with what confidence, effective time and limitations?", "kind": "evidence", "answer_data": [ "Authority or steward reference", "Source and method reference", "Evidence and confidence", "Effective and recorded timestamps" ] }, { "id": "taxon-concept-master-identity-q03", "text": "How must taxon concept master identity be related, validated and preserved when classifications disagree or change?", "kind": "validation", "answer_data": [ "Typed related concept or external reference", "Validation and conflict result", "Predecessor or successor link", "Provenance and retention decision" ] } ], "data_elements": [ { "id": "taxon-concept-master-identity-record", "name": "Taxon concept master identity record", "description": "Structured source-qualified values for taxon concept master identity, including authority, version, provenance, uncertainty and applicable time.", "value_kind": "object", "cardinality": "1", "required": true, "source_refs": [ "SRC-001", "SRC-003", "SRC-006", "SRC-007", "SRC-008" ] } ], "artifacts": [ { "id": "taxon-concept-master-identity-artifact", "name": "Concept identity record", "description": "Versioned evidence or exchange artifact supporting taxon concept master identity without replacing the authoritative master record.", "media_or_form": [ "JSON", "YAML", "RDF or CSV when mapped", "Human-readable record" ], "serial": true, "identity_strategy": "Use the authoritative taxon-concept ID plus immutable assertion or event ID; never use a scientific name, date, filename or hash alone as semantic identity.", "source_refs": [ "SRC-001", "SRC-003", "SRC-006", "SRC-007", "SRC-008" ] } ], "inline_only_rationale": null }, { "id": "according-to-source-and-circumscription", "name": "According-to source and circumscription", "description": "Binds the concept to the classification, checklist, revision, publication or database that asserts its included and excluded biological scope.", "source_refs": [ "SRC-001", "SRC-002", "SRC-003", "SRC-006" ], "questions": [ { "id": "according-to-source-and-circumscription-q01", "text": "What exact values and source-qualified meaning must be recorded for according-to source and circumscription?", "kind": "definition", "answer_data": [ "According-to source and circumscription", "Authoritative identifier or controlled value", "Source classification and version", "Explicit unknown or not-applicable reason" ] }, { "id": "according-to-source-and-circumscription-q02", "text": "Which authority, source, method and evidence establish according-to source and circumscription, with what confidence, effective time and limitations?", "kind": "evidence", "answer_data": [ "Authority or steward reference", "Source and method reference", "Evidence and confidence", "Effective and recorded timestamps" ] }, { "id": "according-to-source-and-circumscription-q03", "text": "How must according-to source and circumscription be related, validated and preserved when classifications disagree or change?", "kind": "validation", "answer_data": [ "Typed related concept or external reference", "Validation and conflict result", "Predecessor or successor link", "Provenance and retention decision" ] } ], "data_elements": [ { "id": "according-to-source-and-circumscription-record", "name": "According-to source and circumscription record", "description": "Structured source-qualified values for according-to source and circumscription, including authority, version, provenance, uncertainty and applicable time.", "value_kind": "collection", "cardinality": "1", "required": true, "source_refs": [ "SRC-001", "SRC-002", "SRC-003", "SRC-006" ] } ], "artifacts": [ { "id": "according-to-source-and-circumscription-artifact", "name": "Circumscription assertion", "description": "Versioned evidence or exchange artifact supporting according-to source and circumscription without replacing the authoritative master record.", "media_or_form": [ "JSON", "YAML", "RDF or CSV when mapped", "Human-readable record" ], "serial": true, "identity_strategy": "Use the authoritative taxon-concept ID plus immutable assertion or event ID; never use a scientific name, date, filename or hash alone as semantic identity.", "source_refs": [ "SRC-001", "SRC-002", "SRC-003", "SRC-006" ] } ], "inline_only_rationale": null } ] }, { "id": "scope-applicability-and-boundary", "name": "Scope, applicability and boundary", "description": "Domain applicability and separation from neighboring biological records.", "source_refs": [ "SRC-001", "SRC-003", "SRC-004", "SRC-005" ], "findings": [ { "id": "taxonomic-scope-and-code-applicability", "name": "Taxonomic scope and code applicability", "description": "Records kingdom or organismal domain, extant or fossil scope, hybrid or operational treatment, applicable nomenclatural code and explicit exceptions.", "source_refs": [ "SRC-001", "SRC-004", "SRC-005", "SRC-008" ], "questions": [ { "id": "taxonomic-scope-and-code-applicability-q01", "text": "What exact values and source-qualified meaning must be recorded for taxonomic scope and code applicability?", "kind": "classification", "answer_data": [ "Taxonomic scope and code applicability", "Authoritative identifier or controlled value", "Source classification and version", "Explicit unknown or not-applicable reason" ] }, { "id": "taxonomic-scope-and-code-applicability-q02", "text": "Which authority, source, method and evidence establish taxonomic scope and code applicability, with what confidence, effective time and limitations?", "kind": "evidence", "answer_data": [ "Authority or steward reference", "Source and method reference", "Evidence and confidence", "Effective and recorded timestamps" ] }, { "id": "taxonomic-scope-and-code-applicability-q03", "text": "How must taxonomic scope and code applicability be related, validated and preserved when classifications disagree or change?", "kind": "validation", "answer_data": [ "Typed related concept or external reference", "Validation and conflict result", "Predecessor or successor link", "Provenance and retention decision" ] } ], "data_elements": [ { "id": "taxonomic-scope-and-code-applicability-record", "name": "Taxonomic scope and code applicability record", "description": "Structured source-qualified values for taxonomic scope and code applicability, including authority, version, provenance, uncertainty and applicable time.", "value_kind": "collection", "cardinality": "1", "required": true, "source_refs": [ "SRC-001", "SRC-004", "SRC-005", "SRC-008" ] } ], "artifacts": [ { "id": "taxonomic-scope-and-code-applicability-artifact", "name": "Applicability profile", "description": "Versioned evidence or exchange artifact supporting taxonomic scope and code applicability without replacing the authoritative master record.", "media_or_form": [ "JSON", "YAML", "RDF or CSV when mapped", "Human-readable record" ], "serial": true, "identity_strategy": "Use the authoritative taxon-concept ID plus immutable assertion or event ID; never use a scientific name, date, filename or hash alone as semantic identity.", "source_refs": [ "SRC-001", "SRC-004", "SRC-005", "SRC-008" ] } ], "inline_only_rationale": null }, { "id": "concept-name-organism-and-specimen-boundary", "name": "Concept, name, organism and specimen boundary", "description": "States why the concept is distinct from its name usages, organisms, populations, specimens, occurrences and observations, with typed references only.", "source_refs": [ "SRC-001", "SRC-003", "SRC-004" ], "questions": [ { "id": "concept-name-organism-and-specimen-boundary-q01", "text": "What exact values and source-qualified meaning must be recorded for concept, name, organism and specimen boundary?", "kind": "relationship", "answer_data": [ "Concept, name, organism and specimen boundary", "Authoritative identifier or controlled value", "Source classification and version", "Explicit unknown or not-applicable reason" ] }, { "id": "concept-name-organism-and-specimen-boundary-q02", "text": "Which authority, source, method and evidence establish concept, name, organism and specimen boundary, with what confidence, effective time and limitations?", "kind": "evidence", "answer_data": [ "Authority or steward reference", "Source and method reference", "Evidence and confidence", "Effective and recorded timestamps" ] }, { "id": "concept-name-organism-and-specimen-boundary-q03", "text": "How must concept, name, organism and specimen boundary be related, validated and preserved when classifications disagree or change?", "kind": "validation", "answer_data": [ "Typed related concept or external reference", "Validation and conflict result", "Predecessor or successor link", "Provenance and retention decision" ] } ], "data_elements": [ { "id": "concept-name-organism-and-specimen-boundary-record", "name": "Concept, name, organism and specimen boundary record", "description": "Structured source-qualified values for concept, name, organism and specimen boundary, including authority, version, provenance, uncertainty and applicable time.", "value_kind": "collection", "cardinality": "1", "required": true, "source_refs": [ "SRC-001", "SRC-003", "SRC-004" ] } ], "artifacts": [ { "id": "concept-name-organism-and-specimen-boundary-artifact", "name": "Boundary decision record", "description": "Versioned evidence or exchange artifact supporting concept, name, organism and specimen boundary without replacing the authoritative master record.", "media_or_form": [ "JSON", "YAML", "RDF or CSV when mapped", "Human-readable record" ], "serial": true, "identity_strategy": "Use the authoritative taxon-concept ID plus immutable assertion or event ID; never use a scientific name, date, filename or hash alone as semantic identity.", "source_refs": [ "SRC-001", "SRC-003", "SRC-004" ] } ], "inline_only_rationale": null } ] } ] }, { "id": "name-usage-and-nomenclature", "name": "Name usage and nomenclature", "description": "Represents scientific and vernacular name usages attached to a taxon concept without collapsing names into concepts.", "rationale": "Taxonomic acceptance is source-relative, while nomenclatural availability, validity or legitimacy follows an applicable code and edition.", "source_refs": [ "SRC-001", "SRC-002", "SRC-003", "SRC-004", "SRC-005" ], "layers": [ { "id": "scientific-name-usage", "name": "Scientific name usage", "description": "Scientific name forms and source-relative usage status.", "source_refs": [ "SRC-001", "SRC-002", "SRC-003" ], "findings": [ { "id": "scientific-name-and-canonical-form", "name": "Scientific name and canonical form", "description": "Records the full scientific name, canonical form, rank context, spelling, identifier, language or script and exact source usage.", "source_refs": [ "SRC-001", "SRC-003", "SRC-004", "SRC-005" ], "questions": [ { "id": "scientific-name-and-canonical-form-q01", "text": "What exact values and source-qualified meaning must be recorded for scientific name and canonical form?", "kind": "definition", "answer_data": [ "Scientific name and canonical form", "Authoritative identifier or controlled value", "Source classification and version", "Explicit unknown or not-applicable reason" ] }, { "id": "scientific-name-and-canonical-form-q02", "text": "Which authority, source, method and evidence establish scientific name and canonical form, with what confidence, effective time and limitations?", "kind": "evidence", "answer_data": [ "Authority or steward reference", "Source and method reference", "Evidence and confidence", "Effective and recorded timestamps" ] }, { "id": "scientific-name-and-canonical-form-q03", "text": "How must scientific name and canonical form be related, validated and preserved when classifications disagree or change?", "kind": "validation", "answer_data": [ "Typed related concept or external reference", "Validation and conflict result", "Predecessor or successor link", "Provenance and retention decision" ] } ], "data_elements": [ { "id": "scientific-name-and-canonical-form-record", "name": "Scientific name and canonical form record", "description": "Structured source-qualified values for scientific name and canonical form, including authority, version, provenance, uncertainty and applicable time.", "value_kind": "collection", "cardinality": "1", "required": true, "source_refs": [ "SRC-001", "SRC-003", "SRC-004", "SRC-005" ] } ], "artifacts": [ { "id": "scientific-name-and-canonical-form-artifact", "name": "Scientific name usage record", "description": "Versioned evidence or exchange artifact supporting scientific name and canonical form without replacing the authoritative master record.", "media_or_form": [ "JSON", "YAML", "RDF or CSV when mapped", "Human-readable record" ], "serial": true, "identity_strategy": "Use the authoritative taxon-concept ID plus immutable assertion or event ID; never use a scientific name, date, filename or hash alone as semantic identity.", "source_refs": [ "SRC-001", "SRC-003", "SRC-004", "SRC-005" ] } ], "inline_only_rationale": null }, { "id": "accepted-synonym-and-misapplied-usage", "name": "Accepted, synonym and misapplied usage", "description": "Classifies a name usage as accepted, synonym, misapplied, doubtful, unavailable, invalid or another governed source-relative status.", "source_refs": [ "SRC-001", "SRC-002", "SRC-003" ], "questions": [ { "id": "accepted-synonym-and-misapplied-usage-q01", "text": "What exact values and source-qualified meaning must be recorded for accepted, synonym and misapplied usage?", "kind": "state", "answer_data": [ "Accepted, synonym and misapplied usage", "Authoritative identifier or controlled value", "Source classification and version", "Explicit unknown or not-applicable reason" ] }, { "id": "accepted-synonym-and-misapplied-usage-q02", "text": "Which authority, source, method and evidence establish accepted, synonym and misapplied usage, with what confidence, effective time and limitations?", "kind": "evidence", "answer_data": [ "Authority or steward reference", "Source and method reference", "Evidence and confidence", "Effective and recorded timestamps" ] }, { "id": "accepted-synonym-and-misapplied-usage-q03", "text": "How must accepted, synonym and misapplied usage be related, validated and preserved when classifications disagree or change?", "kind": "validation", "answer_data": [ "Typed related concept or external reference", "Validation and conflict result", "Predecessor or successor link", "Provenance and retention decision" ] } ], "data_elements": [ { "id": "accepted-synonym-and-misapplied-usage-record", "name": "Accepted, synonym and misapplied usage record", "description": "Structured source-qualified values for accepted, synonym and misapplied usage, including authority, version, provenance, uncertainty and applicable time.", "value_kind": "collection", "cardinality": "1", "required": true, "source_refs": [ "SRC-001", "SRC-002", "SRC-003" ] } ], "artifacts": [ { "id": "accepted-synonym-and-misapplied-usage-artifact", "name": "Name usage status assertion", "description": "Versioned evidence or exchange artifact supporting accepted, synonym and misapplied usage without replacing the authoritative master record.", "media_or_form": [ "JSON", "YAML", "RDF or CSV when mapped", "Human-readable record" ], "serial": true, "identity_strategy": "Use the authoritative taxon-concept ID plus immutable assertion or event ID; never use a scientific name, date, filename or hash alone as semantic identity.", "source_refs": [ "SRC-001", "SRC-002", "SRC-003" ] } ], "inline_only_rationale": null } ] }, { "id": "authorship-publication-and-type", "name": "Authorship, publication and type", "description": "Nomenclatural evidence referenced from authoritative masters.", "source_refs": [ "SRC-001", "SRC-002", "SRC-003", "SRC-004", "SRC-005" ], "findings": [ { "id": "authorship-and-original-publication", "name": "Authorship and original publication", "description": "Records parsed and verbatim authorship, basionym or original combination references, publication citation and source-specific interpretation.", "source_refs": [ "SRC-001", "SRC-003", "SRC-004", "SRC-005" ], "questions": [ { "id": "authorship-and-original-publication-q01", "text": "What exact values and source-qualified meaning must be recorded for authorship and original publication?", "kind": "provenance", "answer_data": [ "Authorship and original publication", "Authoritative identifier or controlled value", "Source classification and version", "Explicit unknown or not-applicable reason" ] }, { "id": "authorship-and-original-publication-q02", "text": "Which authority, source, method and evidence establish authorship and original publication, with what confidence, effective time and limitations?", "kind": "evidence", "answer_data": [ "Authority or steward reference", "Source and method reference", "Evidence and confidence", "Effective and recorded timestamps" ] }, { "id": "authorship-and-original-publication-q03", "text": "How must authorship and original publication be related, validated and preserved when classifications disagree or change?", "kind": "validation", "answer_data": [ "Typed related concept or external reference", "Validation and conflict result", "Predecessor or successor link", "Provenance and retention decision" ] } ], "data_elements": [ { "id": "authorship-and-original-publication-record", "name": "Authorship and original publication record", "description": "Structured source-qualified values for authorship and original publication, including authority, version, provenance, uncertainty and applicable time.", "value_kind": "collection", "cardinality": "1", "required": true, "source_refs": [ "SRC-001", "SRC-003", "SRC-004", "SRC-005" ] } ], "artifacts": [ { "id": "authorship-and-original-publication-artifact", "name": "Authorship and publication reference", "description": "Versioned evidence or exchange artifact supporting authorship and original publication without replacing the authoritative master record.", "media_or_form": [ "JSON", "YAML", "RDF or CSV when mapped", "Human-readable record" ], "serial": true, "identity_strategy": "Use the authoritative taxon-concept ID plus immutable assertion or event ID; never use a scientific name, date, filename or hash alone as semantic identity.", "source_refs": [ "SRC-001", "SRC-003", "SRC-004", "SRC-005" ] } ], "inline_only_rationale": null }, { "id": "type-and-nomenclatural-act-reference", "name": "Type and nomenclatural act reference", "description": "References name-bearing type material, typification, proposal, conservation, rejection, ruling or other act without importing specimen or act lifecycle.", "source_refs": [ "SRC-001", "SRC-002", "SRC-004", "SRC-005" ], "questions": [ { "id": "type-and-nomenclatural-act-reference-q01", "text": "What exact values and source-qualified meaning must be recorded for type and nomenclatural act reference?", "kind": "evidence", "answer_data": [ "Type and nomenclatural act reference", "Authoritative identifier or controlled value", "Source classification and version", "Explicit unknown or not-applicable reason" ] }, { "id": "type-and-nomenclatural-act-reference-q02", "text": "Which authority, source, method and evidence establish type and nomenclatural act reference, with what confidence, effective time and limitations?", "kind": "evidence", "answer_data": [ "Authority or steward reference", "Source and method reference", "Evidence and confidence", "Effective and recorded timestamps" ] }, { "id": "type-and-nomenclatural-act-reference-q03", "text": "How must type and nomenclatural act reference be related, validated and preserved when classifications disagree or change?", "kind": "validation", "answer_data": [ "Typed related concept or external reference", "Validation and conflict result", "Predecessor or successor link", "Provenance and retention decision" ] } ], "data_elements": [ { "id": "type-and-nomenclatural-act-reference-record", "name": "Type and nomenclatural act reference record", "description": "Structured source-qualified values for type and nomenclatural act reference, including authority, version, provenance, uncertainty and applicable time.", "value_kind": "collection", "cardinality": "0..n", "required": false, "source_refs": [ "SRC-001", "SRC-002", "SRC-004", "SRC-005" ] } ], "artifacts": [ { "id": "type-and-nomenclatural-act-reference-artifact", "name": "Typification and act evidence", "description": "Versioned evidence or exchange artifact supporting type and nomenclatural act reference without replacing the authoritative master record.", "media_or_form": [ "JSON", "YAML", "RDF or CSV when mapped", "Human-readable record" ], "serial": true, "identity_strategy": "Use the authoritative taxon-concept ID plus immutable assertion or event ID; never use a scientific name, date, filename or hash alone as semantic identity.", "source_refs": [ "SRC-001", "SRC-002", "SRC-004", "SRC-005" ] } ], "inline_only_rationale": null } ] }, { "id": "vernacular-usage", "name": "Vernacular usage", "description": "Human-language names with geographic and community context.", "source_refs": [ "SRC-001", "SRC-002", "SRC-003" ], "findings": [ { "id": "vernacular-name-language-and-script", "name": "Vernacular name, language and script", "description": "Records a vernacular label, normalized and verbatim forms, language, script, grammatical notes and source citation.", "source_refs": [ "SRC-001", "SRC-002", "SRC-003" ], "questions": [ { "id": "vernacular-name-language-and-script-q01", "text": "What exact values and source-qualified meaning must be recorded for vernacular name, language and script?", "kind": "definition", "answer_data": [ "Vernacular name, language and script", "Authoritative identifier or controlled value", "Source classification and version", "Explicit unknown or not-applicable reason" ] }, { "id": "vernacular-name-language-and-script-q02", "text": "Which authority, source, method and evidence establish vernacular name, language and script, with what confidence, effective time and limitations?", "kind": "evidence", "answer_data": [ "Authority or steward reference", "Source and method reference", "Evidence and confidence", "Effective and recorded timestamps" ] }, { "id": "vernacular-name-language-and-script-q03", "text": "How must vernacular name, language and script be related, validated and preserved when classifications disagree or change?", "kind": "validation", "answer_data": [ "Typed related concept or external reference", "Validation and conflict result", "Predecessor or successor link", "Provenance and retention decision" ] } ], "data_elements": [ { "id": "vernacular-name-language-and-script-record", "name": "Vernacular name, language and script record", "description": "Structured source-qualified values for vernacular name, language and script, including authority, version, provenance, uncertainty and applicable time.", "value_kind": "collection", "cardinality": "0..n", "required": false, "source_refs": [ "SRC-001", "SRC-002", "SRC-003" ] } ], "artifacts": [ { "id": "vernacular-name-language-and-script-artifact", "name": "Vernacular name record", "description": "Versioned evidence or exchange artifact supporting vernacular name, language and script without replacing the authoritative master record.", "media_or_form": [ "JSON", "YAML", "RDF or CSV when mapped", "Human-readable record" ], "serial": true, "identity_strategy": "Use the authoritative taxon-concept ID plus immutable assertion or event ID; never use a scientific name, date, filename or hash alone as semantic identity.", "source_refs": [ "SRC-001", "SRC-002", "SRC-003" ] } ], "inline_only_rationale": null }, { "id": "regional-preference-community-and-source", "name": "Regional preference, community and source", "description": "Qualifies geographic scope, community, preferred or deprecated use, season or context, evidence and responsible steward.", "source_refs": [ "SRC-001", "SRC-002", "SRC-003" ], "questions": [ { "id": "regional-preference-community-and-source-q01", "text": "What exact values and source-qualified meaning must be recorded for regional preference, community and source?", "kind": "spatial", "answer_data": [ "Regional preference, community and source", "Authoritative identifier or controlled value", "Source classification and version", "Explicit unknown or not-applicable reason" ] }, { "id": "regional-preference-community-and-source-q02", "text": "Which authority, source, method and evidence establish regional preference, community and source, with what confidence, effective time and limitations?", "kind": "evidence", "answer_data": [ "Authority or steward reference", "Source and method reference", "Evidence and confidence", "Effective and recorded timestamps" ] }, { "id": "regional-preference-community-and-source-q03", "text": "How must regional preference, community and source be related, validated and preserved when classifications disagree or change?", "kind": "validation", "answer_data": [ "Typed related concept or external reference", "Validation and conflict result", "Predecessor or successor link", "Provenance and retention decision" ] } ], "data_elements": [ { "id": "regional-preference-community-and-source-record", "name": "Regional preference, community and source record", "description": "Structured source-qualified values for regional preference, community and source, including authority, version, provenance, uncertainty and applicable time.", "value_kind": "collection", "cardinality": "0..n", "required": false, "source_refs": [ "SRC-001", "SRC-002", "SRC-003" ] } ], "artifacts": [ { "id": "regional-preference-community-and-source-artifact", "name": "Vernacular usage assertion", "description": "Versioned evidence or exchange artifact supporting regional preference, community and source without replacing the authoritative master record.", "media_or_form": [ "JSON", "YAML", "RDF or CSV when mapped", "Human-readable record" ], "serial": true, "identity_strategy": "Use the authoritative taxon-concept ID plus immutable assertion or event ID; never use a scientific name, date, filename or hash alone as semantic identity.", "source_refs": [ "SRC-001", "SRC-002", "SRC-003" ] } ], "inline_only_rationale": null } ] } ] }, { "id": "classification-placement-and-membership", "name": "Classification placement and membership", "description": "Represents rank or rankless placement, parentage, paths and direct members inside a named classification version.", "rationale": "Placement is an assertion owned by a classification, not an intrinsic universal property of a taxon concept.", "source_refs": [ "SRC-001", "SRC-002", "SRC-003", "SRC-006", "SRC-007", "SRC-008" ], "layers": [ { "id": "rank-parentage-and-root", "name": "Rank, parentage and root", "description": "Immediate governed placement within one classification.", "source_refs": [ "SRC-001", "SRC-002", "SRC-003" ], "findings": [ { "id": "rank-or-rankless-placement", "name": "Rank or rankless placement", "description": "Records the exact rank term, vocabulary and source, or an explicit rankless treatment without forcing a Linnaean rank.", "source_refs": [ "SRC-001", "SRC-003", "SRC-006", "SRC-008" ], "questions": [ { "id": "rank-or-rankless-placement-q01", "text": "What exact values and source-qualified meaning must be recorded for rank or rankless placement?", "kind": "classification", "answer_data": [ "Rank or rankless placement", "Authoritative identifier or controlled value", "Source classification and version", "Explicit unknown or not-applicable reason" ] }, { "id": "rank-or-rankless-placement-q02", "text": "Which authority, source, method and evidence establish rank or rankless placement, with what confidence, effective time and limitations?", "kind": "evidence", "answer_data": [ "Authority or steward reference", "Source and method reference", "Evidence and confidence", "Effective and recorded timestamps" ] }, { "id": "rank-or-rankless-placement-q03", "text": "How must rank or rankless placement be related, validated and preserved when classifications disagree or change?", "kind": "validation", "answer_data": [ "Typed related concept or external reference", "Validation and conflict result", "Predecessor or successor link", "Provenance and retention decision" ] } ], "data_elements": [ { "id": "rank-or-rankless-placement-record", "name": "Rank or rankless placement record", "description": "Structured source-qualified values for rank or rankless placement, including authority, version, provenance, uncertainty and applicable time.", "value_kind": "object", "cardinality": "0..n", "required": false, "source_refs": [ "SRC-001", "SRC-003", "SRC-006", "SRC-008" ] } ], "artifacts": [ { "id": "rank-or-rankless-placement-artifact", "name": "Rank placement assertion", "description": "Versioned evidence or exchange artifact supporting rank or rankless placement without replacing the authoritative master record.", "media_or_form": [ "JSON", "YAML", "RDF or CSV when mapped", "Human-readable record" ], "serial": true, "identity_strategy": "Use the authoritative taxon-concept ID plus immutable assertion or event ID; never use a scientific name, date, filename or hash alone as semantic identity.", "source_refs": [ "SRC-001", "SRC-003", "SRC-006", "SRC-008" ] } ], "inline_only_rationale": null }, { "id": "parent-concept-and-classification-root", "name": "Parent concept and classification root", "description": "Links the immediate parent and root in the same classification release, with placement authority and effective interval.", "source_refs": [ "SRC-001", "SRC-002", "SRC-003", "SRC-006" ], "questions": [ { "id": "parent-concept-and-classification-root-q01", "text": "What exact values and source-qualified meaning must be recorded for parent concept and classification root?", "kind": "relationship", "answer_data": [ "Parent concept and classification root", "Authoritative identifier or controlled value", "Source classification and version", "Explicit unknown or not-applicable reason" ] }, { "id": "parent-concept-and-classification-root-q02", "text": "Which authority, source, method and evidence establish parent concept and classification root, with what confidence, effective time and limitations?", "kind": "evidence", "answer_data": [ "Authority or steward reference", "Source and method reference", "Evidence and confidence", "Effective and recorded timestamps" ] }, { "id": "parent-concept-and-classification-root-q03", "text": "How must parent concept and classification root be related, validated and preserved when classifications disagree or change?", "kind": "validation", "answer_data": [ "Typed related concept or external reference", "Validation and conflict result", "Predecessor or successor link", "Provenance and retention decision" ] } ], "data_elements": [ { "id": "parent-concept-and-classification-root-record", "name": "Parent concept and classification root record", "description": "Structured source-qualified values for parent concept and classification root, including authority, version, provenance, uncertainty and applicable time.", "value_kind": "collection", "cardinality": "1", "required": true, "source_refs": [ "SRC-001", "SRC-002", "SRC-003", "SRC-006" ] } ], "artifacts": [ { "id": "parent-concept-and-classification-root-artifact", "name": "Parentage assertion", "description": "Versioned evidence or exchange artifact supporting parent concept and classification root without replacing the authoritative master record.", "media_or_form": [ "JSON", "YAML", "RDF or CSV when mapped", "Human-readable record" ], "serial": true, "identity_strategy": "Use the authoritative taxon-concept ID plus immutable assertion or event ID; never use a scientific name, date, filename or hash alone as semantic identity.", "source_refs": [ "SRC-001", "SRC-002", "SRC-003", "SRC-006" ] } ], "inline_only_rationale": null } ] }, { "id": "path-membership-and-uncertain-placement", "name": "Path, membership and uncertain placement", "description": "Ancestor path, direct children and unresolved position.", "source_refs": [ "SRC-001", "SRC-002", "SRC-003", "SRC-006", "SRC-007" ], "findings": [ { "id": "classification-path-and-child-membership", "name": "Classification path and child membership", "description": "Records ordered ancestor references, directly included child concepts, membership role, source release and consistency evidence.", "source_refs": [ "SRC-001", "SRC-002", "SRC-006", "SRC-007" ], "questions": [ { "id": "classification-path-and-child-membership-q01", "text": "What exact values and source-qualified meaning must be recorded for classification path and child membership?", "kind": "composition", "answer_data": [ "Classification path and child membership", "Authoritative identifier or controlled value", "Source classification and version", "Explicit unknown or not-applicable reason" ] }, { "id": "classification-path-and-child-membership-q02", "text": "Which authority, source, method and evidence establish classification path and child membership, with what confidence, effective time and limitations?", "kind": "evidence", "answer_data": [ "Authority or steward reference", "Source and method reference", "Evidence and confidence", "Effective and recorded timestamps" ] }, { "id": "classification-path-and-child-membership-q03", "text": "How must classification path and child membership be related, validated and preserved when classifications disagree or change?", "kind": "validation", "answer_data": [ "Typed related concept or external reference", "Validation and conflict result", "Predecessor or successor link", "Provenance and retention decision" ] } ], "data_elements": [ { "id": "classification-path-and-child-membership-record", "name": "Classification path and child membership record", "description": "Structured source-qualified values for classification path and child membership, including authority, version, provenance, uncertainty and applicable time.", "value_kind": "collection", "cardinality": "1", "required": true, "source_refs": [ "SRC-001", "SRC-002", "SRC-006", "SRC-007" ] } ], "artifacts": [ { "id": "classification-path-and-child-membership-artifact", "name": "Classification path projection", "description": "Versioned evidence or exchange artifact supporting classification path and child membership without replacing the authoritative master record.", "media_or_form": [ "JSON", "YAML", "RDF or CSV when mapped", "Human-readable record" ], "serial": true, "identity_strategy": "Use the authoritative taxon-concept ID plus immutable assertion or event ID; never use a scientific name, date, filename or hash alone as semantic identity.", "source_refs": [ "SRC-001", "SRC-002", "SRC-006", "SRC-007" ] } ], "inline_only_rationale": null }, { "id": "uncertain-placement-and-incertae-sedis", "name": "Uncertain placement and incertae sedis", "description": "Records unresolved, provisional or competing placements, candidate parents, reason, method, evidence, confidence and review status.", "source_refs": [ "SRC-001", "SRC-003", "SRC-006" ], "questions": [ { "id": "uncertain-placement-and-incertae-sedis-q01", "text": "What exact values and source-qualified meaning must be recorded for uncertain placement and incertae sedis?", "kind": "quality", "answer_data": [ "Uncertain placement and incertae sedis", "Authoritative identifier or controlled value", "Source classification and version", "Explicit unknown or not-applicable reason" ] }, { "id": "uncertain-placement-and-incertae-sedis-q02", "text": "Which authority, source, method and evidence establish uncertain placement and incertae sedis, with what confidence, effective time and limitations?", "kind": "evidence", "answer_data": [ "Authority or steward reference", "Source and method reference", "Evidence and confidence", "Effective and recorded timestamps" ] }, { "id": "uncertain-placement-and-incertae-sedis-q03", "text": "How must uncertain placement and incertae sedis be related, validated and preserved when classifications disagree or change?", "kind": "validation", "answer_data": [ "Typed related concept or external reference", "Validation and conflict result", "Predecessor or successor link", "Provenance and retention decision" ] } ], "data_elements": [ { "id": "uncertain-placement-and-incertae-sedis-record", "name": "Uncertain placement and incertae sedis record", "description": "Structured source-qualified values for uncertain placement and incertae sedis, including authority, version, provenance, uncertainty and applicable time.", "value_kind": "collection", "cardinality": "0..n", "required": false, "source_refs": [ "SRC-001", "SRC-003", "SRC-006" ] } ], "artifacts": [ { "id": "uncertain-placement-and-incertae-sedis-artifact", "name": "Uncertain placement assessment", "description": "Versioned evidence or exchange artifact supporting uncertain placement and incertae sedis without replacing the authoritative master record.", "media_or_form": [ "JSON", "YAML", "RDF or CSV when mapped", "Human-readable record" ], "serial": true, "identity_strategy": "Use the authoritative taxon-concept ID plus immutable assertion or event ID; never use a scientific name, date, filename or hash alone as semantic identity.", "source_refs": [ "SRC-001", "SRC-003", "SRC-006" ] } ], "inline_only_rationale": null } ] } ] }, { "id": "concept-relations-and-reconciliation", "name": "Concept relations and reconciliation", "description": "Preserves taxonomic change and maps concepts across classifications using explicit evidence-bearing semantics.", "rationale": "Similarity of names or identifiers is insufficient for concept equivalence; mappings need direction, scope, provenance and uncertainty.", "source_refs": [ "SRC-001", "SRC-002", "SRC-003", "SRC-006", "SRC-009" ], "layers": [ { "id": "within-classification-relations", "name": "Within-classification relations", "description": "Name relationships and concept succession inside an authority context.", "source_refs": [ "SRC-001", "SRC-002", "SRC-003", "SRC-004", "SRC-005" ], "findings": [ { "id": "synonymy-basionym-and-combination", "name": "Synonymy, basionym and combination", "description": "Records typed name and usage relationships, direction, applicable code, source assertion and exceptions without treating every synonym as concept identity.", "source_refs": [ "SRC-001", "SRC-002", "SRC-003", "SRC-004", "SRC-005" ], "questions": [ { "id": "synonymy-basionym-and-combination-q01", "text": "What exact values and source-qualified meaning must be recorded for synonymy, basionym and combination?", "kind": "relationship", "answer_data": [ "Synonymy, basionym and combination", "Authoritative identifier or controlled value", "Source classification and version", "Explicit unknown or not-applicable reason" ] }, { "id": "synonymy-basionym-and-combination-q02", "text": "Which authority, source, method and evidence establish synonymy, basionym and combination, with what confidence, effective time and limitations?", "kind": "evidence", "answer_data": [ "Authority or steward reference", "Source and method reference", "Evidence and confidence", "Effective and recorded timestamps" ] }, { "id": "synonymy-basionym-and-combination-q03", "text": "How must synonymy, basionym and combination be related, validated and preserved when classifications disagree or change?", "kind": "validation", "answer_data": [ "Typed related concept or external reference", "Validation and conflict result", "Predecessor or successor link", "Provenance and retention decision" ] } ], "data_elements": [ { "id": "synonymy-basionym-and-combination-record", "name": "Synonymy, basionym and combination record", "description": "Structured source-qualified values for synonymy, basionym and combination, including authority, version, provenance, uncertainty and applicable time.", "value_kind": "collection", "cardinality": "1", "required": true, "source_refs": [ "SRC-001", "SRC-002", "SRC-003", "SRC-004", "SRC-005" ] } ], "artifacts": [ { "id": "synonymy-basionym-and-combination-artifact", "name": "Nomenclatural relationship assertion", "description": "Versioned evidence or exchange artifact supporting synonymy, basionym and combination without replacing the authoritative master record.", "media_or_form": [ "JSON", "YAML", "RDF or CSV when mapped", "Human-readable record" ], "serial": true, "identity_strategy": "Use the authoritative taxon-concept ID plus immutable assertion or event ID; never use a scientific name, date, filename or hash alone as semantic identity.", "source_refs": [ "SRC-001", "SRC-002", "SRC-003", "SRC-004", "SRC-005" ] } ], "inline_only_rationale": null }, { "id": "split-lump-replacement-and-successor", "name": "Split, lump, replacement and successor", "description": "Records taxonomic revision events that create successor concepts, retained portions, split or merged scopes and change rationale.", "source_refs": [ "SRC-001", "SRC-002", "SRC-006", "SRC-009" ], "questions": [ { "id": "split-lump-replacement-and-successor-q01", "text": "What exact values and source-qualified meaning must be recorded for split, lump, replacement and successor?", "kind": "lifecycle", "answer_data": [ "Split, lump, replacement and successor", "Authoritative identifier or controlled value", "Source classification and version", "Explicit unknown or not-applicable reason" ] }, { "id": "split-lump-replacement-and-successor-q02", "text": "Which authority, source, method and evidence establish split, lump, replacement and successor, with what confidence, effective time and limitations?", "kind": "evidence", "answer_data": [ "Authority or steward reference", "Source and method reference", "Evidence and confidence", "Effective and recorded timestamps" ] }, { "id": "split-lump-replacement-and-successor-q03", "text": "How must split, lump, replacement and successor be related, validated and preserved when classifications disagree or change?", "kind": "validation", "answer_data": [ "Typed related concept or external reference", "Validation and conflict result", "Predecessor or successor link", "Provenance and retention decision" ] } ], "data_elements": [ { "id": "split-lump-replacement-and-successor-record", "name": "Split, lump, replacement and successor record", "description": "Structured source-qualified values for split, lump, replacement and successor, including authority, version, provenance, uncertainty and applicable time.", "value_kind": "collection", "cardinality": "1", "required": true, "source_refs": [ "SRC-001", "SRC-002", "SRC-006", "SRC-009" ] } ], "artifacts": [ { "id": "split-lump-replacement-and-successor-artifact", "name": "Concept succession map", "description": "Versioned evidence or exchange artifact supporting split, lump, replacement and successor without replacing the authoritative master record.", "media_or_form": [ "JSON", "YAML", "RDF or CSV when mapped", "Human-readable record" ], "serial": true, "identity_strategy": "Use the authoritative taxon-concept ID plus immutable assertion or event ID; never use a scientific name, date, filename or hash alone as semantic identity.", "source_refs": [ "SRC-001", "SRC-002", "SRC-006", "SRC-009" ] } ], "inline_only_rationale": null } ] }, { "id": "cross-classification-mapping", "name": "Cross-classification mapping", "description": "Set-theoretic concept relationships across authorities and releases.", "source_refs": [ "SRC-001", "SRC-002", "SRC-006", "SRC-009" ], "findings": [ { "id": "congruence-inclusion-and-direction", "name": "Congruence, inclusion and direction", "description": "Records congruent, includes or is-included-in relationships between source-qualified concepts, including direction and compared circumscriptions.", "source_refs": [ "SRC-001", "SRC-002", "SRC-009" ], "questions": [ { "id": "congruence-inclusion-and-direction-q01", "text": "What exact values and source-qualified meaning must be recorded for congruence, inclusion and direction?", "kind": "relationship", "answer_data": [ "Congruence, inclusion and direction", "Authoritative identifier or controlled value", "Source classification and version", "Explicit unknown or not-applicable reason" ] }, { "id": "congruence-inclusion-and-direction-q02", "text": "Which authority, source, method and evidence establish congruence, inclusion and direction, with what confidence, effective time and limitations?", "kind": "evidence", "answer_data": [ "Authority or steward reference", "Source and method reference", "Evidence and confidence", "Effective and recorded timestamps" ] }, { "id": "congruence-inclusion-and-direction-q03", "text": "How must congruence, inclusion and direction be related, validated and preserved when classifications disagree or change?", "kind": "validation", "answer_data": [ "Typed related concept or external reference", "Validation and conflict result", "Predecessor or successor link", "Provenance and retention decision" ] } ], "data_elements": [ { "id": "congruence-inclusion-and-direction-record", "name": "Congruence, inclusion and direction record", "description": "Structured source-qualified values for congruence, inclusion and direction, including authority, version, provenance, uncertainty and applicable time.", "value_kind": "collection", "cardinality": "1", "required": true, "source_refs": [ "SRC-001", "SRC-002", "SRC-009" ] } ], "artifacts": [ { "id": "congruence-inclusion-and-direction-artifact", "name": "Concept inclusion mapping", "description": "Versioned evidence or exchange artifact supporting congruence, inclusion and direction without replacing the authoritative master record.", "media_or_form": [ "JSON", "YAML", "RDF or CSV when mapped", "Human-readable record" ], "serial": true, "identity_strategy": "Use the authoritative taxon-concept ID plus immutable assertion or event ID; never use a scientific name, date, filename or hash alone as semantic identity.", "source_refs": [ "SRC-001", "SRC-002", "SRC-009" ] } ], "inline_only_rationale": null }, { "id": "overlap-disjointness-and-mapping-provenance", "name": "Overlap, disjointness and mapping provenance", "description": "Records partial overlap, disjointness or unresolved relation with mapper, method, evidence, confidence, date and supersession.", "source_refs": [ "SRC-001", "SRC-002", "SRC-006", "SRC-009" ], "questions": [ { "id": "overlap-disjointness-and-mapping-provenance-q01", "text": "What exact values and source-qualified meaning must be recorded for overlap, disjointness and mapping provenance?", "kind": "evidence", "answer_data": [ "Overlap, disjointness and mapping provenance", "Authoritative identifier or controlled value", "Source classification and version", "Explicit unknown or not-applicable reason" ] }, { "id": "overlap-disjointness-and-mapping-provenance-q02", "text": "Which authority, source, method and evidence establish overlap, disjointness and mapping provenance, with what confidence, effective time and limitations?", "kind": "evidence", "answer_data": [ "Authority or steward reference", "Source and method reference", "Evidence and confidence", "Effective and recorded timestamps" ] }, { "id": "overlap-disjointness-and-mapping-provenance-q03", "text": "How must overlap, disjointness and mapping provenance be related, validated and preserved when classifications disagree or change?", "kind": "validation", "answer_data": [ "Typed related concept or external reference", "Validation and conflict result", "Predecessor or successor link", "Provenance and retention decision" ] } ], "data_elements": [ { "id": "overlap-disjointness-and-mapping-provenance-record", "name": "Overlap, disjointness and mapping provenance record", "description": "Structured source-qualified values for overlap, disjointness and mapping provenance, including authority, version, provenance, uncertainty and applicable time.", "value_kind": "collection", "cardinality": "1", "required": true, "source_refs": [ "SRC-001", "SRC-002", "SRC-006", "SRC-009" ] } ], "artifacts": [ { "id": "overlap-disjointness-and-mapping-provenance-artifact", "name": "Concept reconciliation record", "description": "Versioned evidence or exchange artifact supporting overlap, disjointness and mapping provenance without replacing the authoritative master record.", "media_or_form": [ "JSON", "YAML", "RDF or CSV when mapped", "Human-readable record" ], "serial": true, "identity_strategy": "Use the authoritative taxon-concept ID plus immutable assertion or event ID; never use a scientific name, date, filename or hash alone as semantic identity.", "source_refs": [ "SRC-001", "SRC-002", "SRC-006", "SRC-009" ] } ], "inline_only_rationale": null } ] } ] }, { "id": "diagnosis-evidence-and-uncertainty", "name": "Diagnosis, evidence and uncertainty", "description": "Captures how the concept is recognized and what supports or disputes its circumscription without absorbing evidence-object masters.", "rationale": "Agents need diagnostic and confidence context to distinguish a taxon concept from neighboring concepts and to avoid presenting unresolved judgment as fact.", "source_refs": [ "SRC-001", "SRC-003", "SRC-004", "SRC-005", "SRC-008", "SRC-009" ], "layers": [ { "id": "diagnosis-and-recognition", "name": "Diagnosis and recognition", "description": "Defining description and differential characters.", "source_refs": [ "SRC-001", "SRC-003", "SRC-004", "SRC-005" ], "findings": [ { "id": "diagnostic-description-and-source", "name": "Diagnostic description and source", "description": "Records the concept diagnosis, character statement, covered life stage or sex, method, source, language and applicability limits.", "source_refs": [ "SRC-001", "SRC-003", "SRC-004", "SRC-005" ], "questions": [ { "id": "diagnostic-description-and-source-q01", "text": "What exact values and source-qualified meaning must be recorded for diagnostic description and source?", "kind": "definition", "answer_data": [ "Diagnostic description and source", "Authoritative identifier or controlled value", "Source classification and version", "Explicit unknown or not-applicable reason" ] }, { "id": "diagnostic-description-and-source-q02", "text": "Which authority, source, method and evidence establish diagnostic description and source, with what confidence, effective time and limitations?", "kind": "evidence", "answer_data": [ "Authority or steward reference", "Source and method reference", "Evidence and confidence", "Effective and recorded timestamps" ] }, { "id": "diagnostic-description-and-source-q03", "text": "How must diagnostic description and source be related, validated and preserved when classifications disagree or change?", "kind": "validation", "answer_data": [ "Typed related concept or external reference", "Validation and conflict result", "Predecessor or successor link", "Provenance and retention decision" ] } ], "data_elements": [ { "id": "diagnostic-description-and-source-record", "name": "Diagnostic description and source record", "description": "Structured source-qualified values for diagnostic description and source, including authority, version, provenance, uncertainty and applicable time.", "value_kind": "collection", "cardinality": "1", "required": true, "source_refs": [ "SRC-001", "SRC-003", "SRC-004", "SRC-005" ] } ], "artifacts": [ { "id": "diagnostic-description-and-source-artifact", "name": "Diagnostic description", "description": "Versioned evidence or exchange artifact supporting diagnostic description and source without replacing the authoritative master record.", "media_or_form": [ "JSON", "YAML", "RDF or CSV when mapped", "Human-readable record" ], "serial": true, "identity_strategy": "Use the authoritative taxon-concept ID plus immutable assertion or event ID; never use a scientific name, date, filename or hash alone as semantic identity.", "source_refs": [ "SRC-001", "SRC-003", "SRC-004", "SRC-005" ] } ], "inline_only_rationale": null }, { "id": "differential-characters-and-confusing-concepts", "name": "Differential characters and confusing concepts", "description": "Records features that distinguish the concept from named alternatives, observation method, conditions, thresholds, uncertainty and failure modes.", "source_refs": [ "SRC-001", "SRC-003" ], "questions": [ { "id": "differential-characters-and-confusing-concepts-q01", "text": "What exact values and source-qualified meaning must be recorded for differential characters and confusing concepts?", "kind": "validation", "answer_data": [ "Differential characters and confusing concepts", "Authoritative identifier or controlled value", "Source classification and version", "Explicit unknown or not-applicable reason" ] }, { "id": "differential-characters-and-confusing-concepts-q02", "text": "Which authority, source, method and evidence establish differential characters and confusing concepts, with what confidence, effective time and limitations?", "kind": "evidence", "answer_data": [ "Authority or steward reference", "Source and method reference", "Evidence and confidence", "Effective and recorded timestamps" ] }, { "id": "differential-characters-and-confusing-concepts-q03", "text": "How must differential characters and confusing concepts be related, validated and preserved when classifications disagree or change?", "kind": "validation", "answer_data": [ "Typed related concept or external reference", "Validation and conflict result", "Predecessor or successor link", "Provenance and retention decision" ] } ], "data_elements": [ { "id": "differential-characters-and-confusing-concepts-record", "name": "Differential characters and confusing concepts record", "description": "Structured source-qualified values for differential characters and confusing concepts, including authority, version, provenance, uncertainty and applicable time.", "value_kind": "collection", "cardinality": "0..n", "required": false, "source_refs": [ "SRC-001", "SRC-003" ] } ], "artifacts": [ { "id": "differential-characters-and-confusing-concepts-artifact", "name": "Differential diagnosis matrix", "description": "Versioned evidence or exchange artifact supporting differential characters and confusing concepts without replacing the authoritative master record.", "media_or_form": [ "JSON", "YAML", "RDF or CSV when mapped", "Human-readable record" ], "serial": true, "identity_strategy": "Use the authoritative taxon-concept ID plus immutable assertion or event ID; never use a scientific name, date, filename or hash alone as semantic identity.", "source_refs": [ "SRC-001", "SRC-003" ] } ], "inline_only_rationale": null } ] }, { "id": "specimen-sequence-literature-and-expert-evidence", "name": "Specimen, sequence, literature and expert evidence", "description": "External evidence references and their role in concept support.", "source_refs": [ "SRC-001", "SRC-003", "SRC-004", "SRC-005", "SRC-008", "SRC-009" ], "findings": [ { "id": "specimen-and-sequence-evidence-reference", "name": "Specimen and sequence evidence reference", "description": "Links type, voucher, collection, material sample or sequence identifiers with evidence role, custody source, quality and access marking.", "source_refs": [ "SRC-001", "SRC-003", "SRC-004", "SRC-005", "SRC-008" ], "questions": [ { "id": "specimen-and-sequence-evidence-reference-q01", "text": "What exact values and source-qualified meaning must be recorded for specimen and sequence evidence reference?", "kind": "evidence", "answer_data": [ "Specimen and sequence evidence reference", "Authoritative identifier or controlled value", "Source classification and version", "Explicit unknown or not-applicable reason" ] }, { "id": "specimen-and-sequence-evidence-reference-q02", "text": "Which authority, source, method and evidence establish specimen and sequence evidence reference, with what confidence, effective time and limitations?", "kind": "evidence", "answer_data": [ "Authority or steward reference", "Source and method reference", "Evidence and confidence", "Effective and recorded timestamps" ] }, { "id": "specimen-and-sequence-evidence-reference-q03", "text": "How must specimen and sequence evidence reference be related, validated and preserved when classifications disagree or change?", "kind": "validation", "answer_data": [ "Typed related concept or external reference", "Validation and conflict result", "Predecessor or successor link", "Provenance and retention decision" ] } ], "data_elements": [ { "id": "specimen-and-sequence-evidence-reference-record", "name": "Specimen and sequence evidence reference record", "description": "Structured source-qualified values for specimen and sequence evidence reference, including authority, version, provenance, uncertainty and applicable time.", "value_kind": "collection", "cardinality": "0..n", "required": false, "source_refs": [ "SRC-001", "SRC-003", "SRC-004", "SRC-005", "SRC-008" ] } ], "artifacts": [ { "id": "specimen-and-sequence-evidence-reference-artifact", "name": "Material and sequence evidence index", "description": "Versioned evidence or exchange artifact supporting specimen and sequence evidence reference without replacing the authoritative master record.", "media_or_form": [ "JSON", "YAML", "RDF or CSV when mapped", "Human-readable record" ], "serial": true, "identity_strategy": "Use the authoritative taxon-concept ID plus immutable assertion or event ID; never use a scientific name, date, filename or hash alone as semantic identity.", "source_refs": [ "SRC-001", "SRC-003", "SRC-004", "SRC-005", "SRC-008" ] } ], "inline_only_rationale": null }, { "id": "literature-and-expert-assertion", "name": "Literature and expert assertion", "description": "Links supporting or rejecting publications, datasets and expert judgments with claim, author, method, review status and provenance.", "source_refs": [ "SRC-001", "SRC-003", "SRC-009" ], "questions": [ { "id": "literature-and-expert-assertion-q01", "text": "What exact values and source-qualified meaning must be recorded for literature and expert assertion?", "kind": "provenance", "answer_data": [ "Literature and expert assertion", "Authoritative identifier or controlled value", "Source classification and version", "Explicit unknown or not-applicable reason" ] }, { "id": "literature-and-expert-assertion-q02", "text": "Which authority, source, method and evidence establish literature and expert assertion, with what confidence, effective time and limitations?", "kind": "evidence", "answer_data": [ "Authority or steward reference", "Source and method reference", "Evidence and confidence", "Effective and recorded timestamps" ] }, { "id": "literature-and-expert-assertion-q03", "text": "How must literature and expert assertion be related, validated and preserved when classifications disagree or change?", "kind": "validation", "answer_data": [ "Typed related concept or external reference", "Validation and conflict result", "Predecessor or successor link", "Provenance and retention decision" ] } ], "data_elements": [ { "id": "literature-and-expert-assertion-record", "name": "Literature and expert assertion record", "description": "Structured source-qualified values for literature and expert assertion, including authority, version, provenance, uncertainty and applicable time.", "value_kind": "collection", "cardinality": "1", "required": true, "source_refs": [ "SRC-001", "SRC-003", "SRC-009" ] } ], "artifacts": [ { "id": "literature-and-expert-assertion-artifact", "name": "Evidence and assertion bundle", "description": "Versioned evidence or exchange artifact supporting literature and expert assertion without replacing the authoritative master record.", "media_or_form": [ "JSON", "YAML", "RDF or CSV when mapped", "Human-readable record" ], "serial": true, "identity_strategy": "Use the authoritative taxon-concept ID plus immutable assertion or event ID; never use a scientific name, date, filename or hash alone as semantic identity.", "source_refs": [ "SRC-001", "SRC-003", "SRC-009" ] } ], "inline_only_rationale": null } ] }, { "id": "confidence-dispute-and-revision-need", "name": "Confidence, dispute and revision need", "description": "Assessment quality and visible unresolved taxonomic judgment.", "source_refs": [ "SRC-001", "SRC-003", "SRC-006", "SRC-009" ], "findings": [ { "id": "confidence-method-and-review-status", "name": "Confidence, method and review status", "description": "Records confidence scale, assessment method, reviewer, evidence cut-off, result, limitations and next review trigger.", "source_refs": [ "SRC-001", "SRC-006", "SRC-009" ], "questions": [ { "id": "confidence-method-and-review-status-q01", "text": "What exact values and source-qualified meaning must be recorded for confidence, method and review status?", "kind": "measurement", "answer_data": [ "Confidence, method and review status", "Authoritative identifier or controlled value", "Source classification and version", "Explicit unknown or not-applicable reason" ] }, { "id": "confidence-method-and-review-status-q02", "text": "Which authority, source, method and evidence establish confidence, method and review status, with what confidence, effective time and limitations?", "kind": "evidence", "answer_data": [ "Authority or steward reference", "Source and method reference", "Evidence and confidence", "Effective and recorded timestamps" ] }, { "id": "confidence-method-and-review-status-q03", "text": "How must confidence, method and review status be related, validated and preserved when classifications disagree or change?", "kind": "validation", "answer_data": [ "Typed related concept or external reference", "Validation and conflict result", "Predecessor or successor link", "Provenance and retention decision" ] } ], "data_elements": [ { "id": "confidence-method-and-review-status-record", "name": "Confidence, method and review status record", "description": "Structured source-qualified values for confidence, method and review status, including authority, version, provenance, uncertainty and applicable time.", "value_kind": "object", "cardinality": "1", "required": true, "source_refs": [ "SRC-001", "SRC-006", "SRC-009" ] } ], "artifacts": [ { "id": "confidence-method-and-review-status-artifact", "name": "Concept confidence assessment", "description": "Versioned evidence or exchange artifact supporting confidence, method and review status without replacing the authoritative master record.", "media_or_form": [ "JSON", "YAML", "RDF or CSV when mapped", "Human-readable record" ], "serial": true, "identity_strategy": "Use the authoritative taxon-concept ID plus immutable assertion or event ID; never use a scientific name, date, filename or hash alone as semantic identity.", "source_refs": [ "SRC-001", "SRC-006", "SRC-009" ] } ], "inline_only_rationale": null }, { "id": "dispute-species-complex-and-pending-revision", "name": "Dispute, species complex and pending revision", "description": "Preserves competing circumscriptions, unresolved identification, cryptic complex, disputed placement and planned revision without forcing consensus.", "source_refs": [ "SRC-001", "SRC-003", "SRC-006", "SRC-009" ], "questions": [ { "id": "dispute-species-complex-and-pending-revision-q01", "text": "What exact values and source-qualified meaning must be recorded for dispute, species complex and pending revision?", "kind": "exception", "answer_data": [ "Dispute, species complex and pending revision", "Authoritative identifier or controlled value", "Source classification and version", "Explicit unknown or not-applicable reason" ] }, { "id": "dispute-species-complex-and-pending-revision-q02", "text": "Which authority, source, method and evidence establish dispute, species complex and pending revision, with what confidence, effective time and limitations?", "kind": "evidence", "answer_data": [ "Authority or steward reference", "Source and method reference", "Evidence and confidence", "Effective and recorded timestamps" ] }, { "id": "dispute-species-complex-and-pending-revision-q03", "text": "How must dispute, species complex and pending revision be related, validated and preserved when classifications disagree or change?", "kind": "validation", "answer_data": [ "Typed related concept or external reference", "Validation and conflict result", "Predecessor or successor link", "Provenance and retention decision" ] } ], "data_elements": [ { "id": "dispute-species-complex-and-pending-revision-record", "name": "Dispute, species complex and pending revision record", "description": "Structured source-qualified values for dispute, species complex and pending revision, including authority, version, provenance, uncertainty and applicable time.", "value_kind": "collection", "cardinality": "0..n", "required": false, "source_refs": [ "SRC-001", "SRC-003", "SRC-006", "SRC-009" ] } ], "artifacts": [ { "id": "dispute-species-complex-and-pending-revision-artifact", "name": "Taxonomic dispute record", "description": "Versioned evidence or exchange artifact supporting dispute, species complex and pending revision without replacing the authoritative master record.", "media_or_form": [ "JSON", "YAML", "RDF or CSV when mapped", "Human-readable record" ], "serial": true, "identity_strategy": "Use the authoritative taxon-concept ID plus immutable assertion or event ID; never use a scientific name, date, filename or hash alone as semantic identity.", "source_refs": [ "SRC-001", "SRC-003", "SRC-006", "SRC-009" ] } ], "inline_only_rationale": null } ] } ] }, { "id": "lifecycle-stewardship-and-governance", "name": "Lifecycle, stewardship and governance", "description": "Controls immutable versions, review authority, access, licence, retention and non-destructive retirement.", "rationale": "Taxonomic concepts are cited and reused over long periods, so revision must preserve resolvability, provenance and historical meaning.", "source_refs": [ "SRC-001", "SRC-003", "SRC-006", "SRC-009", "SRC-010" ], "layers": [ { "id": "version-lifecycle-and-change", "name": "Version lifecycle and change", "description": "Release identity, effective time and succession.", "source_refs": [ "SRC-001", "SRC-006", "SRC-009", "SRC-010" ], "findings": [ { "id": "concept-version-effective-and-record-time", "name": "Concept version, effective and record time", "description": "Records immutable concept version, release, effective interval, publication date, review time, ingestion time and assertion status as distinct values.", "source_refs": [ "SRC-001", "SRC-006", "SRC-009", "SRC-010" ], "questions": [ { "id": "concept-version-effective-and-record-time-q01", "text": "What exact values and source-qualified meaning must be recorded for concept version, effective and record time?", "kind": "temporal", "answer_data": [ "Concept version, effective and record time", "Authoritative identifier or controlled value", "Source classification and version", "Explicit unknown or not-applicable reason" ] }, { "id": "concept-version-effective-and-record-time-q02", "text": "Which authority, source, method and evidence establish concept version, effective and record time, with what confidence, effective time and limitations?", "kind": "evidence", "answer_data": [ "Authority or steward reference", "Source and method reference", "Evidence and confidence", "Effective and recorded timestamps" ] }, { "id": "concept-version-effective-and-record-time-q03", "text": "How must concept version, effective and record time be related, validated and preserved when classifications disagree or change?", "kind": "validation", "answer_data": [ "Typed related concept or external reference", "Validation and conflict result", "Predecessor or successor link", "Provenance and retention decision" ] } ], "data_elements": [ { "id": "concept-version-effective-and-record-time-record", "name": "Concept version, effective and record time record", "description": "Structured source-qualified values for concept version, effective and record time, including authority, version, provenance, uncertainty and applicable time.", "value_kind": "collection", "cardinality": "1", "required": true, "source_refs": [ "SRC-001", "SRC-006", "SRC-009", "SRC-010" ] } ], "artifacts": [ { "id": "concept-version-effective-and-record-time-artifact", "name": "Version and time record", "description": "Versioned evidence or exchange artifact supporting concept version, effective and record time without replacing the authoritative master record.", "media_or_form": [ "JSON", "YAML", "RDF or CSV when mapped", "Human-readable record" ], "serial": true, "identity_strategy": "Use the authoritative taxon-concept ID plus immutable assertion or event ID; never use a scientific name, date, filename or hash alone as semantic identity.", "source_refs": [ "SRC-001", "SRC-006", "SRC-009", "SRC-010" ] } ], "inline_only_rationale": null }, { "id": "supersession-deprecation-and-change-rationale", "name": "Supersession, deprecation and change rationale", "description": "Links predecessor and successor concepts, changed boundary, name or placement, reason, authority, migration impact and continued resolution policy.", "source_refs": [ "SRC-001", "SRC-002", "SRC-006", "SRC-009" ], "questions": [ { "id": "supersession-deprecation-and-change-rationale-q01", "text": "What exact values and source-qualified meaning must be recorded for supersession, deprecation and change rationale?", "kind": "lifecycle", "answer_data": [ "Supersession, deprecation and change rationale", "Authoritative identifier or controlled value", "Source classification and version", "Explicit unknown or not-applicable reason" ] }, { "id": "supersession-deprecation-and-change-rationale-q02", "text": "Which authority, source, method and evidence establish supersession, deprecation and change rationale, with what confidence, effective time and limitations?", "kind": "evidence", "answer_data": [ "Authority or steward reference", "Source and method reference", "Evidence and confidence", "Effective and recorded timestamps" ] }, { "id": "supersession-deprecation-and-change-rationale-q03", "text": "How must supersession, deprecation and change rationale be related, validated and preserved when classifications disagree or change?", "kind": "validation", "answer_data": [ "Typed related concept or external reference", "Validation and conflict result", "Predecessor or successor link", "Provenance and retention decision" ] } ], "data_elements": [ { "id": "supersession-deprecation-and-change-rationale-record", "name": "Supersession, deprecation and change rationale record", "description": "Structured source-qualified values for supersession, deprecation and change rationale, including authority, version, provenance, uncertainty and applicable time.", "value_kind": "collection", "cardinality": "1", "required": true, "source_refs": [ "SRC-001", "SRC-002", "SRC-006", "SRC-009" ] } ], "artifacts": [ { "id": "supersession-deprecation-and-change-rationale-artifact", "name": "Concept change set", "description": "Versioned evidence or exchange artifact supporting supersession, deprecation and change rationale without replacing the authoritative master record.", "media_or_form": [ "JSON", "YAML", "RDF or CSV when mapped", "Human-readable record" ], "serial": true, "identity_strategy": "Use the authoritative taxon-concept ID plus immutable assertion or event ID; never use a scientific name, date, filename or hash alone as semantic identity.", "source_refs": [ "SRC-001", "SRC-002", "SRC-006", "SRC-009" ] } ], "inline_only_rationale": null } ] }, { "id": "stewardship-access-and-retention", "name": "Stewardship, access and retention", "description": "Responsibility, review, rights and preservation.", "source_refs": [ "SRC-003", "SRC-006", "SRC-009" ], "findings": [ { "id": "taxonomic-authority-review-and-provenance", "name": "Taxonomic authority, review and provenance", "description": "Records asserting authority, steward, editor, reviewer, delegated role, method, source chain, decision and accountable timestamps.", "source_refs": [ "SRC-001", "SRC-006", "SRC-009", "SRC-010" ], "questions": [ { "id": "taxonomic-authority-review-and-provenance-q01", "text": "What exact values and source-qualified meaning must be recorded for taxonomic authority, review and provenance?", "kind": "ownership", "answer_data": [ "Taxonomic authority, review and provenance", "Authoritative identifier or controlled value", "Source classification and version", "Explicit unknown or not-applicable reason" ] }, { "id": "taxonomic-authority-review-and-provenance-q02", "text": "Which authority, source, method and evidence establish taxonomic authority, review and provenance, with what confidence, effective time and limitations?", "kind": "evidence", "answer_data": [ "Authority or steward reference", "Source and method reference", "Evidence and confidence", "Effective and recorded timestamps" ] }, { "id": "taxonomic-authority-review-and-provenance-q03", "text": "How must taxonomic authority, review and provenance be related, validated and preserved when classifications disagree or change?", "kind": "validation", "answer_data": [ "Typed related concept or external reference", "Validation and conflict result", "Predecessor or successor link", "Provenance and retention decision" ] } ], "data_elements": [ { "id": "taxonomic-authority-review-and-provenance-record", "name": "Taxonomic authority, review and provenance record", "description": "Structured source-qualified values for taxonomic authority, review and provenance, including authority, version, provenance, uncertainty and applicable time.", "value_kind": "collection", "cardinality": "1", "required": true, "source_refs": [ "SRC-001", "SRC-006", "SRC-009", "SRC-010" ] } ], "artifacts": [ { "id": "taxonomic-authority-review-and-provenance-artifact", "name": "Review and provenance record", "description": "Versioned evidence or exchange artifact supporting taxonomic authority, review and provenance without replacing the authoritative master record.", "media_or_form": [ "JSON", "YAML", "RDF or CSV when mapped", "Human-readable record" ], "serial": true, "identity_strategy": "Use the authoritative taxon-concept ID plus immutable assertion or event ID; never use a scientific name, date, filename or hash alone as semantic identity.", "source_refs": [ "SRC-001", "SRC-006", "SRC-009", "SRC-010" ] } ], "inline_only_rationale": null }, { "id": "licence-access-retention-and-tombstone", "name": "Licence, access, retention and tombstone", "description": "Records license, attribution, sensitive evidence, withholding or generalization, retention, legal hold, deletion authority and tombstone behavior.", "source_refs": [ "SRC-003", "SRC-006", "SRC-009" ], "questions": [ { "id": "licence-access-retention-and-tombstone-q01", "text": "What exact values and source-qualified meaning must be recorded for licence, access, retention and tombstone?", "kind": "retention", "answer_data": [ "Licence, access, retention and tombstone", "Authoritative identifier or controlled value", "Source classification and version", "Explicit unknown or not-applicable reason" ] }, { "id": "licence-access-retention-and-tombstone-q02", "text": "Which authority, source, method and evidence establish licence, access, retention and tombstone, with what confidence, effective time and limitations?", "kind": "evidence", "answer_data": [ "Authority or steward reference", "Source and method reference", "Evidence and confidence", "Effective and recorded timestamps" ] }, { "id": "licence-access-retention-and-tombstone-q03", "text": "How must licence, access, retention and tombstone be related, validated and preserved when classifications disagree or change?", "kind": "validation", "answer_data": [ "Typed related concept or external reference", "Validation and conflict result", "Predecessor or successor link", "Provenance and retention decision" ] } ], "data_elements": [ { "id": "licence-access-retention-and-tombstone-record", "name": "Licence, access, retention and tombstone record", "description": "Structured source-qualified values for licence, access, retention and tombstone, including authority, version, provenance, uncertainty and applicable time.", "value_kind": "collection", "cardinality": "1", "required": true, "source_refs": [ "SRC-003", "SRC-006", "SRC-009" ] } ], "artifacts": [ { "id": "licence-access-retention-and-tombstone-artifact", "name": "Access and retention policy record", "description": "Versioned evidence or exchange artifact supporting licence, access, retention and tombstone without replacing the authoritative master record.", "media_or_form": [ "JSON", "YAML", "RDF or CSV when mapped", "Human-readable record" ], "serial": true, "identity_strategy": "Use the authoritative taxon-concept ID plus immutable assertion or event ID; never use a scientific name, date, filename or hash alone as semantic identity.", "source_refs": [ "SRC-003", "SRC-006", "SRC-009" ] } ], "inline_only_rationale": null } ] } ] }, { "id": "interoperability-and-projections", "name": "Interoperability and projections", "description": "Maps the semantic model to biodiversity standards, registries, APIs and serializations without coupling identity to a format.", "rationale": "Each external system has a source-relative classification and may lose semantics, so projections require pinned versions, mappings and round-trip limits.", "source_refs": [ "SRC-001", "SRC-002", "SRC-003", "SRC-006", "SRC-007", "SRC-008" ], "layers": [ { "id": "standard-and-registry-bindings", "name": "Standard and registry bindings", "description": "Pinned mappings to principal taxonomic exchange systems.", "source_refs": [ "SRC-001", "SRC-003", "SRC-006", "SRC-007", "SRC-008" ], "findings": [ { "id": "tcs-and-darwin-core-binding", "name": "TCS and Darwin Core binding", "description": "Maps concept, name, according-to, parent, child, accepted usage, synonym and mapping fields to pinned TCS and Darwin Core terms with loss disclosure.", "source_refs": [ "SRC-001", "SRC-002", "SRC-003" ], "questions": [ { "id": "tcs-and-darwin-core-binding-q01", "text": "What exact values and source-qualified meaning must be recorded for tcs and darwin core binding?", "kind": "interoperability", "answer_data": [ "TCS and Darwin Core binding", "Authoritative identifier or controlled value", "Source classification and version", "Explicit unknown or not-applicable reason" ] }, { "id": "tcs-and-darwin-core-binding-q02", "text": "Which authority, source, method and evidence establish tcs and darwin core binding, with what confidence, effective time and limitations?", "kind": "evidence", "answer_data": [ "Authority or steward reference", "Source and method reference", "Evidence and confidence", "Effective and recorded timestamps" ] }, { "id": "tcs-and-darwin-core-binding-q03", "text": "How must tcs and darwin core binding be related, validated and preserved when classifications disagree or change?", "kind": "validation", "answer_data": [ "Typed related concept or external reference", "Validation and conflict result", "Predecessor or successor link", "Provenance and retention decision" ] } ], "data_elements": [ { "id": "tcs-and-darwin-core-binding-record", "name": "TCS and Darwin Core binding record", "description": "Structured source-qualified values for tcs and darwin core binding, including authority, version, provenance, uncertainty and applicable time.", "value_kind": "collection", "cardinality": "1", "required": true, "source_refs": [ "SRC-001", "SRC-002", "SRC-003" ] } ], "artifacts": [ { "id": "tcs-and-darwin-core-binding-artifact", "name": "TCS and Darwin Core crosswalk", "description": "Versioned evidence or exchange artifact supporting tcs and darwin core binding without replacing the authoritative master record.", "media_or_form": [ "JSON", "YAML", "RDF or CSV when mapped", "Human-readable record" ], "serial": true, "identity_strategy": "Use the authoritative taxon-concept ID plus immutable assertion or event ID; never use a scientific name, date, filename or hash alone as semantic identity.", "source_refs": [ "SRC-001", "SRC-002", "SRC-003" ] } ], "inline_only_rationale": null }, { "id": "catalogue-of-life-gbif-and-ncbi-binding", "name": "Catalogue of Life, GBIF and NCBI binding", "description": "Maps source dataset, release, taxon identifiers, name usage, hierarchy and reconciliation status to each registry without claiming universal equivalence.", "source_refs": [ "SRC-006", "SRC-007", "SRC-008" ], "questions": [ { "id": "catalogue-of-life-gbif-and-ncbi-binding-q01", "text": "What exact values and source-qualified meaning must be recorded for catalogue of life, gbif and ncbi binding?", "kind": "interoperability", "answer_data": [ "Catalogue of Life, GBIF and NCBI binding", "Authoritative identifier or controlled value", "Source classification and version", "Explicit unknown or not-applicable reason" ] }, { "id": "catalogue-of-life-gbif-and-ncbi-binding-q02", "text": "Which authority, source, method and evidence establish catalogue of life, gbif and ncbi binding, with what confidence, effective time and limitations?", "kind": "evidence", "answer_data": [ "Authority or steward reference", "Source and method reference", "Evidence and confidence", "Effective and recorded timestamps" ] }, { "id": "catalogue-of-life-gbif-and-ncbi-binding-q03", "text": "How must catalogue of life, gbif and ncbi binding be related, validated and preserved when classifications disagree or change?", "kind": "validation", "answer_data": [ "Typed related concept or external reference", "Validation and conflict result", "Predecessor or successor link", "Provenance and retention decision" ] } ], "data_elements": [ { "id": "catalogue-of-life-gbif-and-ncbi-binding-record", "name": "Catalogue of Life, GBIF and NCBI binding record", "description": "Structured source-qualified values for catalogue of life, gbif and ncbi binding, including authority, version, provenance, uncertainty and applicable time.", "value_kind": "collection", "cardinality": "0..n", "required": false, "source_refs": [ "SRC-006", "SRC-007", "SRC-008" ] } ], "artifacts": [ { "id": "catalogue-of-life-gbif-and-ncbi-binding-artifact", "name": "Registry identifier crosswalk", "description": "Versioned evidence or exchange artifact supporting catalogue of life, gbif and ncbi binding without replacing the authoritative master record.", "media_or_form": [ "JSON", "YAML", "RDF or CSV when mapped", "Human-readable record" ], "serial": true, "identity_strategy": "Use the authoritative taxon-concept ID plus immutable assertion or event ID; never use a scientific name, date, filename or hash alone as semantic identity.", "source_refs": [ "SRC-006", "SRC-007", "SRC-008" ] } ], "inline_only_rationale": null } ] }, { "id": "canonical-and-serialized-projections", "name": "Canonical and serialized projections", "description": "Resolvable citation, integrity and representation variants.", "source_refs": [ "SRC-001", "SRC-003", "SRC-006", "SRC-009" ], "findings": [ { "id": "canonical-uri-citation-and-digest", "name": "Canonical URI, citation and digest", "description": "Records stable resolution URI, human citation, source snapshot, media type, byte length and digest for a concept version and mapping set.", "source_refs": [ "SRC-001", "SRC-003", "SRC-006", "SRC-009" ], "questions": [ { "id": "canonical-uri-citation-and-digest-q01", "text": "What exact values and source-qualified meaning must be recorded for canonical uri, citation and digest?", "kind": "provenance", "answer_data": [ "Canonical URI, citation and digest", "Authoritative identifier or controlled value", "Source classification and version", "Explicit unknown or not-applicable reason" ] }, { "id": "canonical-uri-citation-and-digest-q02", "text": "Which authority, source, method and evidence establish canonical uri, citation and digest, with what confidence, effective time and limitations?", "kind": "evidence", "answer_data": [ "Authority or steward reference", "Source and method reference", "Evidence and confidence", "Effective and recorded timestamps" ] }, { "id": "canonical-uri-citation-and-digest-q03", "text": "How must canonical uri, citation and digest be related, validated and preserved when classifications disagree or change?", "kind": "validation", "answer_data": [ "Typed related concept or external reference", "Validation and conflict result", "Predecessor or successor link", "Provenance and retention decision" ] } ], "data_elements": [ { "id": "canonical-uri-citation-and-digest-record", "name": "Canonical URI, citation and digest record", "description": "Structured source-qualified values for canonical uri, citation and digest, including authority, version, provenance, uncertainty and applicable time.", "value_kind": "collection", "cardinality": "1", "required": true, "source_refs": [ "SRC-001", "SRC-003", "SRC-006", "SRC-009" ] } ], "artifacts": [ { "id": "canonical-uri-citation-and-digest-artifact", "name": "Canonical concept citation", "description": "Versioned evidence or exchange artifact supporting canonical uri, citation and digest without replacing the authoritative master record.", "media_or_form": [ "JSON", "YAML", "RDF or CSV when mapped", "Human-readable record" ], "serial": true, "identity_strategy": "Use the authoritative taxon-concept ID plus immutable assertion or event ID; never use a scientific name, date, filename or hash alone as semantic identity.", "source_refs": [ "SRC-001", "SRC-003", "SRC-006", "SRC-009" ] } ], "inline_only_rationale": null }, { "id": "machine-human-and-round-trip-projections", "name": "Machine, human and round-trip projections", "description": "Defines JSON, RDF, CSV, Darwin Core Archive, API and human-card projections with schema, ordering, omitted values and round-trip tests.", "source_refs": [ "SRC-001", "SRC-002", "SRC-003", "SRC-006", "SRC-007" ], "questions": [ { "id": "machine-human-and-round-trip-projections-q01", "text": "What exact values and source-qualified meaning must be recorded for machine, human and round-trip projections?", "kind": "interoperability", "answer_data": [ "Machine, human and round-trip projections", "Authoritative identifier or controlled value", "Source classification and version", "Explicit unknown or not-applicable reason" ] }, { "id": "machine-human-and-round-trip-projections-q02", "text": "Which authority, source, method and evidence establish machine, human and round-trip projections, with what confidence, effective time and limitations?", "kind": "evidence", "answer_data": [ "Authority or steward reference", "Source and method reference", "Evidence and confidence", "Effective and recorded timestamps" ] }, { "id": "machine-human-and-round-trip-projections-q03", "text": "How must machine, human and round-trip projections be related, validated and preserved when classifications disagree or change?", "kind": "validation", "answer_data": [ "Typed related concept or external reference", "Validation and conflict result", "Predecessor or successor link", "Provenance and retention decision" ] } ], "data_elements": [ { "id": "machine-human-and-round-trip-projections-record", "name": "Machine, human and round-trip projections record", "description": "Structured source-qualified values for machine, human and round-trip projections, including authority, version, provenance, uncertainty and applicable time.", "value_kind": "collection", "cardinality": "0..n", "required": false, "source_refs": [ "SRC-001", "SRC-002", "SRC-003", "SRC-006", "SRC-007" ] } ], "artifacts": [ { "id": "machine-human-and-round-trip-projections-artifact", "name": "Projection conformance pack", "description": "Versioned evidence or exchange artifact supporting machine, human and round-trip projections without replacing the authoritative master record.", "media_or_form": [ "JSON", "YAML", "RDF or CSV when mapped", "Human-readable record" ], "serial": true, "identity_strategy": "Use the authoritative taxon-concept ID plus immutable assertion or event ID; never use a scientific name, date, filename or hash alone as semantic identity.", "source_refs": [ "SRC-001", "SRC-002", "SRC-003", "SRC-006", "SRC-007" ] } ], "inline_only_rationale": null } ] } ] } ] }, "functions": [ { "id": "register-taxon-concept", "name": "Register taxon concept", "description": "Create a stable source-qualified concept identity and initial circumscription.", "inputs": [ "According-to source", "Concept identifier", "Circumscription", "Authority" ], "outputs": [ "Immutable concept version", "Validation result" ], "preconditions": [ "Source and identity authority are resolved" ], "effects": [ "Registers concept without treating a name as its identity" ], "source_refs": [ "SRC-001", "SRC-003", "SRC-006" ] }, { "id": "bind-name-usage", "name": "Bind name usage", "description": "Attach a scientific or vernacular name usage with source-relative status.", "inputs": [ "Concept version", "Name reference", "Usage status", "Code profile" ], "outputs": [ "Name usage assertion" ], "preconditions": [ "Concept and name identities are resolved" ], "effects": [ "Adds typed usage without merging concept and name lifecycles" ], "source_refs": [ "SRC-001", "SRC-002", "SRC-003", "SRC-004", "SRC-005" ] }, { "id": "place-in-classification", "name": "Place in classification", "description": "Assert rank or rankless parentage in one classification release.", "inputs": [ "Concept version", "Classification release", "Parent", "Rank or rankless marker" ], "outputs": [ "Placement assertion", "Cycle check" ], "preconditions": [ "Parent and release are resolved" ], "effects": [ "Creates source-specific placement and path evidence" ], "source_refs": [ "SRC-001", "SRC-003", "SRC-006" ] }, { "id": "revise-circumscription", "name": "Revise circumscription", "description": "Create a successor concept for a boundary, split, lump or placement change.", "inputs": [ "Predecessor", "New circumscription", "Change reason", "Authority" ], "outputs": [ "Successor version", "Change set" ], "preconditions": [ "Published predecessor is immutable" ], "effects": [ "Preserves lineage and leaves predecessor resolvable" ], "source_refs": [ "SRC-001", "SRC-002", "SRC-006", "SRC-009" ] }, { "id": "map-taxon-concepts", "name": "Map taxon concepts", "description": "Record congruence, inclusion, overlap, disjointness or unresolved relation across classifications.", "inputs": [ "Source concept", "Target concept", "Mapping relation", "Evidence" ], "outputs": [ "Qualified mapping assertion" ], "preconditions": [ "Both concepts and classification versions are resolved" ], "effects": [ "Adds directional evidence-bearing reconciliation without rewriting either source" ], "source_refs": [ "SRC-001", "SRC-002", "SRC-009" ] }, { "id": "attach-diagnostic-evidence", "name": "Attach diagnostic evidence", "description": "Reference diagnosis, distinguishing characters, specimens, sequences, literature or expert assertions.", "inputs": [ "Concept version", "Evidence reference", "Evidence role", "Access marking" ], "outputs": [ "Evidence binding" ], "preconditions": [ "External evidence identity and provenance are available" ], "effects": [ "Supports or challenges the concept without importing evidence lifecycle" ], "source_refs": [ "SRC-001", "SRC-003", "SRC-004", "SRC-005", "SRC-008", "SRC-009" ] }, { "id": "review-taxonomic-assertion", "name": "Review taxonomic assertion", "description": "Record an accountable assessment of identity, placement, mapping or evidence.", "inputs": [ "Assertion", "Reviewer", "Method", "Evidence cut-off" ], "outputs": [ "Review decision", "Confidence assessment" ], "preconditions": [ "Reviewer authority and conflicts are declared" ], "effects": [ "Adds review provenance and next-review trigger" ], "source_refs": [ "SRC-006", "SRC-009", "SRC-010" ] }, { "id": "validate-classification", "name": "Validate classification", "description": "Check identifiers, parentage, source bindings, code applicability, mappings and version lineage.", "inputs": [ "Classification release", "Validation profile" ], "outputs": [ "Validation report" ], "preconditions": [ "Pinned rules and references are available" ], "effects": [ "Reports cycles, broken links, ambiguity and semantic conflicts without silent repair" ], "source_refs": [ "SRC-001", "SRC-003", "SRC-006" ] }, { "id": "deprecate-taxon-concept", "name": "Deprecate taxon concept", "description": "Retire a concept version while preserving citation and successor navigation.", "inputs": [ "Concept version", "Authority", "Reason", "Successor references" ], "outputs": [ "Deprecation event", "Tombstone projection" ], "preconditions": [ "Retention and dependent citations are checked" ], "effects": [ "Stops new use while preserving historical identity and provenance" ], "source_refs": [ "SRC-006", "SRC-009", "SRC-010" ] }, { "id": "publish-checklist-projection", "name": "Publish checklist projection", "description": "Render a governed classification or checklist without changing source concepts.", "inputs": [ "Concept versions", "Projection profile", "Release metadata" ], "outputs": [ "Checklist artifact", "Digest", "Conformance report" ], "preconditions": [ "All required concepts and mappings validate" ], "effects": [ "Creates immutable machine and human projections" ], "source_refs": [ "SRC-001", "SRC-003", "SRC-006", "SRC-007" ] }, { "id": "reconcile-registry-identifiers", "name": "Reconcile registry identifiers", "description": "Link Catalogue of Life, GBIF, NCBI and other source identifiers with explicit match semantics.", "inputs": [ "Concept version", "Registry records", "Matching method" ], "outputs": [ "Identifier crosswalk", "Unresolved candidates" ], "preconditions": [ "Registry versions and evidence are pinned" ], "effects": [ "Adds mappings without claiming name equality as concept equivalence" ], "source_refs": [ "SRC-006", "SRC-007", "SRC-008" ] }, { "id": "export-taxon-concept", "name": "Export taxon concept", "description": "Produce a selected format or API representation with declared omissions and round-trip limits.", "inputs": [ "Concept version", "Target profile", "Access scope" ], "outputs": [ "Serialized projection", "Loss report" ], "preconditions": [ "Access policy and profile version permit export" ], "effects": [ "Provides portable output while semantic identity remains format-independent" ], "source_refs": [ "SRC-001", "SRC-003", "SRC-006", "SRC-007" ] } ], "composition": [ { "target": "Scientific Name, Nomenclatural Act, Publication and Type Specimen models", "relation": "REFERENCE", "purpose": "Bind code-governed name and evidence identities without importing their lifecycle.", "required": true, "source_refs": [ "SRC-001", "SRC-002", "SRC-004", "SRC-005" ] }, { "target": "Organism, Population, Specimen, Occurrence, Sequence, Trait, Distribution, Habitat and Conservation models", "relation": "REFERENCE", "purpose": "Connect observations and domain evidence while retaining their direct properties and mastership externally.", "required": false, "source_refs": [ "SRC-003", "SRC-006", "SRC-008" ] }, { "target": "Classification, Evidence, Provenance, Person, Organization, Language and Geography models", "relation": "REFERENCE", "purpose": "Resolve source authority, mappings, review, vernacular context and provenance by typed identities.", "required": false, "source_refs": [ "SRC-001", "SRC-003", "SRC-009" ] }, { "target": "Taxon Concept Standard", "relation": "ALIGN", "purpose": "Supports format-independent Taxon Concept, Taxon Name, Mapping and Nomenclatural Type semantics.", "required": false, "source_refs": [ "SRC-001", "SRC-002" ] }, { "target": "Darwin Core", "relation": "ALIGN", "purpose": "Supports broad biodiversity exchange while requiring explicit concept-versus-name-usage interpretation.", "required": false, "source_refs": [ "SRC-003" ] }, { "target": "Catalogue of Life, GBIF and NCBI taxonomy services", "relation": "ALIGN", "purpose": "Supports operational identifier, checklist, hierarchy and reconciliation projections with source-relative scope.", "required": false, "source_refs": [ "SRC-006", "SRC-007", "SRC-008" ] } ], "serviceLayers": { "dimension": { "owner_package_requirements": [ "Dimension identity, owner, accountable taxonomic steward and namespace", "Taxon, name, classification, evidence, publication, organization, person, access and provenance registries", "Master-system and federation mappings for external taxonomy services", "Authority, review, access, retention, licensing and publication policies" ], "namespace_guidance": "Mint taxon concept, concept version, placement, mapping, review and local assertion identifiers in the adopting Dimension namespace only when no authoritative source identifier exists; keep names, organisms, specimens, occurrences, sequences, publications and external registry identities as typed references.", "registry_links": [ "https://ver.cy/models/", "https://ver.cy/model-agent-protocol.md", "Dimension-local taxon concept, classification, mapping, evidence and provenance registries" ] }, "canon_and_patch": { "canonicalization_rules": [ "Canonicalize by authoritative source, source release and taxon-concept identifier, never by scientific name text alone.", "Keep concept, name usage, placement assertion, mapping, evidence object and conservation assessment distinct; preserve competing classifications and source-relative accepted status." ], "patch_rules": [ "Additive extensions declare target bundle, layer or finding, namespace, source, authority, code profile, compatibility and interoperability effect.", "A circumscription, identity or relation-semantics change creates a successor version with migration and rollback mappings rather than mutating a cited release." ], "compatibility_rules": [ "Consumers may ignore unknown additive fields only when concept identity, according-to source, circumscription, classification placement, name-usage status, provenance and lifecycle meaning remain intact.", "TCS, Darwin Core, Catalogue of Life, GBIF, NCBI and code projections pin source and target versions and disclose transformed, omitted or non-round-trippable semantics." ] }, "artifact_rules": { "identity_priority": [ "Authoritative checklist, taxonomic publication or taxonomy master-system concept identifier plus source release.", "Governed globally resolvable taxon-concept IRI qualified by according-to authority.", "Adopting-Dimension UUID or ULID when no authoritative external concept identifier exists." ], "timestamp_rule": "Record event timestamps in RFC 3339 with seconds and an explicit UTC offset or Z; keep nomenclatural publication date, concept effective time, review time, ingestion time, mapping time and retirement time distinct.", "serial_naming_rule": "Name serial artifacts as {taxon-concept-id}--{artifact-kind}--{assertion-or-event-id}; never use a scientific name, date, filename or hash alone as taxon concept identity.", "integrity_rule": "Store digest, media type, byte length, source release, creator, licence, access marking, effective time, provenance and assurance for every retained serial artifact and projection." }, "policies": [ "The adopting Dimension declares who may register, revise, map, review, publish, deprecate, disclose and remove taxon concept records.", "Accepted, synonym and placement status are always qualified by classification, source release and effective time; disagreement remains visible.", "Agents never infer concept equivalence from matching names, ranks or registry labels alone and never fabricate physical properties for a taxon concept.", "Nomenclatural codes, publications, names, specimens, organisms, occurrences, sequences, distributions, habitats and conservation assessments remain in their owning systems and are referenced.", "Automated agents may resolve, validate and project published low-risk concept data within policy, while new circumscription, destructive consolidation, restricted-evidence disclosure and irreversible retirement require accountable authority." ], "crud": { "read": [ "Resolve active Dimension, authoritative concept ID, source classification and release, applicable code, version, access scope and requested projection; return the minimum permitted evidence-bearing view." ], "create": [ "Create stable source-qualified concept identity, circumscription, authority, placement, name usage, provenance and explicit unknowns before publication." ], "update": [ "Create an immutable successor with actor, authority, reason, semantic change class, RFC 3339 effective time, predecessor links and before-and-after validation; never overwrite a cited concept version." ], "delete": [ "Apply citation, dependency, retention, licence and legal-hold policy; prefer deprecation and tombstone, preserve identity and lineage, and never cascade into referenced names, specimens, organisms, occurrences, sequences or evidence." ] }, "roles": [ { "name": "Dimension owner", "responsibilities": [ "Own namespace, mastership, autonomy, access, retention and federation rules." ] }, { "name": "Taxonomic authority or concept author", "responsibilities": [ "Own circumscription, placement, revision rationale and scientific judgment." ] }, { "name": "Nomenclatural steward", "responsibilities": [ "Interpret applicable code, name usage, authorship, typification and acts." ] }, { "name": "Checklist or registry publisher", "responsibilities": [ "Own releases, identifiers, resolution, availability, licence and distribution metadata." ] }, { "name": "Data curator", "responsibilities": [ "Maintain mappings, references, quality flags, provenance and issue queues." ] }, { "name": "Reviewer or mapping expert", "responsibilities": [ "Assess evidence, competing concepts, mappings, confidence and conformance." ] }, { "name": "Evidence custodian", "responsibilities": [ "Own specimen, sequence, publication or dataset records and their access controls." ] }, { "name": "Access and compliance authority", "responsibilities": [ "Govern restricted evidence, licensing, disclosure, retention and audit." ] } ], "access": { "default_rule": "Deny mutation and restricted-evidence disclosure unless the active Dimension, role, purpose, source licence and field policy grant the action; preserve public concept identifiers and citations when policy permits.", "scopes": [ "bundle", "layer", "finding", "artifact" ], "exceptions": [ "Emergency correction of harmful misidentification must be time-limited, attributable and independently reviewed, and must not erase the prior cited concept, evidence or audit trail." ], "audit_requirements": [ "Log actor, agent, role, purpose, concept and version, source release, action, policy and code profile, RFC 3339 timestamp with offset, affected scope, evidence, validation result and successor or rollback reference." ] }, "agents_bootstrap": { "filename": "AGENTS.md", "required_fields": [ "Name", "Type", "Specification URL", "Storage type URL", "Interface URL", "Processes URL" ], "read_order": [ "Read the nearest Dimension-owner AGENTS.md, taxonomy-source, authority, access, licensing, retention and federation policies.", "Read this model AGENTS.md, pinned spec.yaml and required name, organism, specimen, occurrence, sequence, publication, classification, evidence and provenance model instructions before mutation." ] } }, "coverage": { "claim": "A source-grounded reviewable draft of Taxon across the current TDWG Taxon Concept Standard, Darwin Core, ICZN and ICN nomenclature, Catalogue of Life, GBIF, NCBI Taxonomy, W3C provenance and RFC 3339, without a claim of universal classification, code-profile, registry-crosswalk or taxonomic completeness.", "confidence": "medium", "checklist": [ { "dimension": "identity", "status": "covered", "notes": "Authoritative source, release and concept identifier are distinct from name strings and local aliases." }, { "dimension": "classification and definition", "status": "covered", "notes": "Circumscription, according-to authority, taxonomic domain, code applicability, rank or rankless status and placement are explicit." }, { "dimension": "direct properties", "status": "covered", "notes": "Native informational properties include identity, source, circumscription, placement, status and diagnosis; physical geometry, mass and material do not apply to a concept." }, { "dimension": "recognition and observation", "status": "covered", "notes": "Diagnosis, differential characters, confusing concepts, method, conditions, evidence, confidence and failure modes support recognition." }, { "dimension": "capabilities and possible actions", "status": "covered", "notes": "Registration, name binding, placement, revision, mapping, evidence attachment, review, validation, retirement, projection, reconciliation and export are controlled functions." }, { "dimension": "lifecycle", "status": "covered", "notes": "Immutable versions, effective times, split, lump, succession, deprecation and tombstones preserve cited history." }, { "dimension": "relationships", "status": "covered", "notes": "Names, parents, children, concepts, classifications, evidence, authorities, mappings and successors use typed source-qualified relations." }, { "dimension": "temporal", "status": "covered", "notes": "Publication, effective, review, ingestion, mapping and retirement times remain distinct." }, { "dimension": "spatial", "status": "covered", "notes": "Geography qualifies vernacular usage and source scope; organism distribution remains external." }, { "dimension": "provenance", "status": "covered", "notes": "Sources, authors, stewards, reviews, evidence, mappings, revisions and projections retain attribution and derivation." }, { "dimension": "ownership", "status": "covered", "notes": "Dimension owner, taxonomic authority, nomenclatural steward, publisher, curator, reviewer, evidence custodian and access authority are separated." }, { "dimension": "validation and quality", "status": "covered", "notes": "Uniqueness, source resolution, code applicability, parent cycles, lineage, mapping semantics, confidence and round trips are checked." }, { "dimension": "access", "status": "covered", "notes": "Licensing, restricted evidence, withholding, generalization, role and purpose govern projections." }, { "dimension": "retention and deletion", "status": "covered", "notes": "Cited versions are retained or tombstoned and deletion never cascades into external biological or evidence masters." }, { "dimension": "interoperability", "status": "covered", "notes": "TCS, Darwin Core, Catalogue of Life, GBIF and NCBI mappings pin versions and disclose loss." } ], "known_omissions": [ "Code-specific botanical, zoological, prokaryotic and viral nomenclature require separate expert profiles.", "Organism, population, specimen, occurrence, sequence, trait, distribution, habitat and conservation-assessment lifecycles remain in neighboring models.", "Certified registry crosswalks, full TCS conformance fixtures, phylogenetic rankless profiles and mapping benchmarks remain future work." ], "conflicts": [ "TCS now distinguishes Taxon Concept and Taxon Name explicitly, while many Darwin Core and registry records use a broader Taxon or name-usage record; projections must disclose the chosen interpretation.", "Accepted status and parentage vary by source and release, so no single classification is treated as universal truth.", "Nomenclatural codes govern names and types but do not determine taxonomic circumscription or scientific acceptance." ], "regional_assumptions": [ "Applicable nomenclatural code depends on organismal domain and edition, not geography alone.", "Catalogue of Life, GBIF and NCBI are authoritative for their own releases and scopes, not universal arbiters of all taxonomy.", "Vernacular names and preferences are language, community and region specific." ], "adversarial_checks": [ "Reject identity based only on scientific-name text, rank or a local display label.", "Reject a parent, accepted name or synonym assertion that lacks a source classification and release.", "Reject inferred congruence from matching names when circumscriptions or evidence have not been compared.", "Reject mutation of a cited concept version or deletion that breaks historical references.", "Reject physical organism, specimen, occurrence, distribution or conservation facts copied into the taxon concept as intrinsic properties." ] }, "researchAdjudication": { "providerMode": "single-provider-waiver", "activeProviders": [ "codex" ], "waivedProviders": [ "claude", "grok" ], "providerPolicy": { "contract_version": "1.0.0", "mode": "single-provider-waiver", "effective_at": "2026-09-06T00:00:00Z", "scope": "Canonical single-stream subject-model research after the six-workstream consolidation", "active_providers": [ "codex" ], "waived_providers": [ { "provider": "claude", "authorized_by": "repository owner", "authorized_at": "2026-09-06T00:00:00Z", "reason": "Claude produced no result on prior 1800-second and 900-second attempts and again timed out on bounded 600-second Sonnet and 300-second Haiku passes. The owner prioritized completion over provider availability." }, { "provider": "grok", "authorized_by": "repository owner", "authorized_at": "2026-09-06T00:00:00Z", "reason": "The repository owner authorized completion without Grok when Grok is unavailable, slow or schema-invalid. Grok may still be attempted as a bounded supplemental reviewer, but its failure never blocks a valid Claude plus no-tools result." } ], "review_rule": "Codex may complete source-grounded fallback research after bounded Claude and Grok attempts fail. It requires a separate no-tools adversarial audit and remains reviewable-draft with a visible absence-of-external-review hold.", "supplemental_provider_attempts": [ { "provider": "claude", "required": false, "maximum_attempts": 1, "failure_policy": "record-and-continue", "admission_rule": "Use only a locally schema-valid result whose sources and boundaries survive adjudication." }, { "provider": "grok", "required": false, "maximum_attempts": 1, "failure_policy": "record-and-continue", "admission_rule": "Use only a locally schema-valid result whose sources and boundaries survive adjudication." } ] }, "boundaryDecision": { "entry_kind": "entity", "status": "accepted as a source-qualified taxon concept", "rationale": "The model represents a stable conceptual biological grouping according to a named classification and release. Names, organisms, populations, specimens, occurrences, sequences, publications, nomenclatural acts, habitats, distributions and conservation assessments remain distinct linked objects." }, "decisions": [ { "concept": "Taxon concept and scientific name", "disposition": "accepted as distinct linked identities", "rationale": "The same name may denote different circumscriptions and a concept may carry several name usages, so name text is never sufficient concept identity." }, { "concept": "According-to authority", "disposition": "accepted as mandatory qualification", "rationale": "Circumscription, placement, acceptance and synonymy are assertions made by a named classification, checklist, revision or database release." }, { "concept": "Competing classifications", "disposition": "accepted as parallel truths with mappings", "rationale": "Source classifications remain intact and cross-source reconciliation records congruence, inclusion, overlap, disjointness or uncertainty without last-write-wins collapse." }, { "concept": "Rankless and phylogenetic concepts", "disposition": "accepted without forced Linnaean rank", "rationale": "Rank is source-qualified and may be absent where the source classification deliberately uses rankless placement." }, { "concept": "Nomenclatural codes", "disposition": "accepted as external versioned governance", "rationale": "Codes govern names, typification and acts for different organismal domains but do not determine taxonomic circumscription or scientific acceptance." }, { "concept": "Organism and evidence-object properties", "disposition": "accepted as external references", "rationale": "Physical, spatial, custody and observation properties belong to organisms, specimens, occurrences, sequences and evidence records, not to the abstract taxon concept." }, { "concept": "Diagnosis and recognition", "disposition": "accepted with method and uncertainty", "rationale": "Diagnostic descriptions and differential characters need applicability, observation conditions, evidence, confidence and confusing alternatives rather than unqualified prose." }, { "concept": "Concept revision", "disposition": "accepted as immutable successor lineage", "rationale": "Split, lump, boundary and placement changes create successor versions and explicit change sets while cited predecessors remain resolvable." }, { "concept": "TCS and Darwin Core", "disposition": "accepted as related but non-identical projections", "rationale": "TCS explicitly separates concepts, names, mappings and types, while broad Darwin Core Taxon records require a declared concept-versus-name-usage interpretation." }, { "concept": "Catalogue of Life, GBIF and NCBI", "disposition": "accepted as source-relative registry bindings", "rationale": "Each service owns its identifiers, releases and coverage and cannot be treated as a universal arbiter of all taxonomy." }, { "concept": "Approved registry composition", "disposition": "held pending relation governance", "rationale": "The approved relation ledger contains no outgoing WM-LIV-001 rows, so proposed sibling composition remains draft." }, { "concept": "Question and function coverage", "disposition": "accepted as reviewable draft", "rationale": "The structure covers identity, scope, names, nomenclature, placement, reconciliation, diagnosis, evidence, uncertainty, governance, lifecycle and interoperability, while specialist code profiles remain deferred." } ], "publicationHolds": [ "Claude and Grok timed out during their bounded attempts, so independent external review is absent and explicitly waived for this published reviewable draft.", "The approved relationship ledger contains no outgoing relation rows for WM-LIV-001, so proposed links to name, organism, specimen, occurrence, sequence, classification, habitat, distribution and conservation models remain draft.", "Botanical, zoological, prokaryotic and viral nomenclature, rankless phylogenetic treatment and jurisdiction-specific sensitive-species access require expert profiles.", "Certified TCS, Darwin Core, Catalogue of Life, GBIF and NCBI crosswalks, conformance fixtures, identifier mappings and round-trip suites remain unverified.", "Independent external review was explicitly waived by the repository owner; this codex-only result remains a reviewable draft." ], "deferredResearch": [ "Validate separate ICN, ICZN, ICNP and ICTV nomenclatural profiles and their name, type, authorship and act mappings.", "Create rankless, hybrid, fossil, microbial, viral and species-complex recipes with explicit applicability and evidence rules.", "Develop deterministic fixtures for parent cycles, split and lump lineage, RCC-5 mappings, source disagreement, tombstones and loss-aware projections.", "Approve sibling model identifiers and relation cardinalities for names, organisms, populations, specimens, occurrences, sequences, classifications, evidence, traits, distributions, habitats and conservation assessments." ] }, "statistics": { "sources": 10, "bundles": 7, "layers": 16, "findings": 32, "questions": 96, "artifacts": 32, "functions": 12 } }