37d923cae1
- Migrated `was_generated_by` to `is_or_was_generated_by` and `was_derived_from` to `is_or_was_derived_from` across multiple YAML schema files as per Rule 53. - Updated relevant imports, slot lists, and slot usage keys to reflect the new naming conventions. - Added migration comments for clarity and tracking. - Introduced a migration script to automate the changes across all affected files.
110 lines
3.3 KiB
YAML
110 lines
3.3 KiB
YAML
# TaxonName - Scientific taxonomic name class
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#
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# Created per slot_fixes.yaml migration for: taxon_name
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# Creation date: 2026-01-14
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# Rule compliance: 0b (Type/Types pattern), 38 (slot centralization), 53 (full migration)
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id: https://nde.nl/ontology/hc/class/TaxonName
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name: TaxonName
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title: Taxon Name
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prefixes:
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linkml: https://w3id.org/linkml/
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hc: https://nde.nl/ontology/hc/
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skos: http://www.w3.org/2004/02/skos/core#
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dwc: http://rs.tdwg.org/dwc/terms/
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default_prefix: hc
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imports:
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- linkml:types
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- ../slots/has_or_had_label
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- ../slots/has_or_had_code
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classes:
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TaxonName:
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class_uri: dwc:Taxon
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description: |
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A scientific taxonomic name (Linnaean binomial or trinomial).
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**PURPOSE**:
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Structured representation of scientific names following taxonomic nomenclature
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standards (ICZN for animals, ICN for plants/fungi/algae).
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**FORMAT**:
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- Binomial: "Genus species (Author, Year)"
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- Trinomial: "Genus species subspecies Author, Year"
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- With authority: "Raphus cucullatus (Linnaeus, 1758)"
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- Without authority: "Panthera leo"
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**DARWIN CORE ALIGNMENT**:
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- Aligns with dwc:scientificName
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- Supports dwc:scientificNameAuthorship
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**MIGRATION NOTE**:
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Created to replace string-based taxon_name slot per slot_fixes.yaml (Rule 53).
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exact_mappings:
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- dwc:Taxon
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close_mappings:
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- skos:Concept
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slots:
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- has_or_had_label
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- has_or_had_code
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attributes:
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scientific_name:
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description: |
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Full scientific name including author citation.
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Format: "Genus species (Author, Year)"
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range: string
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required: true
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slot_uri: dwc:scientificName
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examples:
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- value: "Raphus cucullatus (Linnaeus, 1758)"
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description: Dodo with nomenclatural authority
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- value: "Panthera leo"
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description: Lion (authority omitted)
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authorship:
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description: |
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The authorship information for this scientific name.
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Parentheses indicate original genus differs from current placement.
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range: string
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required: false
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slot_uri: dwc:scientificNameAuthorship
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examples:
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- value: "Linnaeus, 1758"
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- value: "(Gray, 1821)"
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description: Parentheses indicate genus changed
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taxonomic_rank:
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description: |
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Taxonomic rank of this name (SPECIES, GENUS, FAMILY, etc.).
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range: string
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required: false
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slot_uri: dwc:taxonRank
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examples:
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- value: SPECIES
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- value: SUBSPECIES
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- value: GENUS
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annotations:
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specificity_score: "0.70"
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specificity_rationale: "Specific to natural history collections - taxonomic nomenclature."
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custodian_types: '["B", "M", "R"]'
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custodian_types_rationale: "Botanical gardens, Museums (natural history), Research centers"
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examples:
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- value:
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scientific_name: "Raphus cucullatus (Linnaeus, 1758)"
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authorship: "Linnaeus, 1758"
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taxonomic_rank: "SPECIES"
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description: Dodo scientific name with full authority
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- value:
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scientific_name: "Quercus robur L."
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authorship: "L."
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taxonomic_rank: "SPECIES"
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description: English Oak with abbreviated author
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