110 lines
3.5 KiB
YAML
110 lines
3.5 KiB
YAML
id: https://nde.nl/ontology/hc/class/Taxon
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name: taxon_class
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title: Taxon Class
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description: >-
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Biological taxon (species, genus, family, etc.) associated with heritage objects.
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Follows Schema.org Taxon pattern for biological classification.
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Used primarily for natural history collections.
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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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schema: http://schema.org/
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dwc: http://rs.tdwg.org/dwc/terms/
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skos: http://www.w3.org/2004/02/skos/core#
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default_prefix: hc
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imports:
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- linkml:types
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- ../slots/id
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- ../slots/has_or_had_label
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- ../slots/description
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- ../slots/specificity_annotation
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- ../slots/has_or_had_score # was: template_specificity - migrated per Rule 53 (2026-01-17)
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- ./SpecificityAnnotation
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- ./TemplateSpecificityScore # was: TemplateSpecificityScores - migrated per Rule 53 (2026-01-17)
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- ./TemplateSpecificityType
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- ./TemplateSpecificityTypes
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classes:
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Taxon:
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class_uri: schema:Taxon
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description: >-
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A biological taxon (species, genus, family, order, etc.) that can be
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associated with heritage objects in natural history collections.
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**USE CASES**:
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1. **Specimen Classification**: Link BiologicalObject to its taxonomic identification
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2. **Collection Scope**: Define taxa covered by a natural history collection
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3. **Research Context**: Document species studied in research archives
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**DARWIN CORE ALIGNMENT**:
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Uses Darwin Core terms for taxonomic data:
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- dwc:scientificName - Full scientific name
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- dwc:taxonRank - Level in hierarchy (species, genus, etc.)
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- dwc:kingdom, dwc:phylum, dwc:class, dwc:order, dwc:family, dwc:genus
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**EXTERNAL IDENTIFIERS**:
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Link to authoritative taxonomic databases:
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- GBIF (Global Biodiversity Information Facility)
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- NCBI Taxonomy
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- Wikidata (Q-numbers for taxa)
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- BOLD (Barcode of Life)
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exact_mappings:
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- schema:Taxon
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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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- id
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- has_or_had_label
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- description
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- specificity_annotation
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- has_or_had_score # was: template_specificity - migrated per Rule 53 (2026-01-17)
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slot_usage:
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id:
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identifier: true
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required: true
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range: uriorcurie
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pattern: ^https://nde\.nl/ontology/hc/taxon/[a-z0-9-]+$
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examples:
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- value: https://nde.nl/ontology/hc/taxon/raphus-cucullatus
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description: Dodo (extinct species)
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has_or_had_label:
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description: Scientific name of the taxon.
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range: string
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required: true
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examples:
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- value: Raphus cucullatus
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description: Dodo scientific name
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- value: Homo sapiens
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description: Human scientific name
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description:
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range: string
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examples:
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- value: Extinct flightless bird endemic to Mauritius
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comments:
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- Used for taxonomic associations in natural history collections
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- Link to GBIF, NCBI, or Wikidata for authoritative identifiers
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- Range should be narrowed via slot_usage when used
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examples:
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- value:
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id: https://nde.nl/ontology/hc/taxon/raphus-cucullatus
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has_or_had_label: Raphus cucullatus
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description: >-
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Dodo - an extinct flightless bird that was endemic to the island
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of Mauritius. Last confirmed sighting in 1662.
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description: Dodo taxon for natural history specimen
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