773 lines
33 KiB
YAML
773 lines
33 KiB
YAML
id: https://nde.nl/ontology/hc/class/BiologicalObject
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name: BiologicalObject
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title: Biological Object Class
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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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crm: http://www.cidoc-crm.org/cidoc-crm/
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dcterms: http://purl.org/dc/terms/
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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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gbif: http://rs.gbif.org/terms/
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aat: http://vocab.getty.edu/aat/
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imports:
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- linkml:types
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- ../metadata
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- ./TimeSpan
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- ./CustodianPlace
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- ../enums/PreservationMethodEnum
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# REMOVED 2026-01-15: ../slots/wikidata_id - inherits has_or_had_identifier from ExhibitedObject (Rule 53)
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- ./WikiDataIdentifier
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# associated_taxa REMOVED - migrated to is_or_was_associated_with (Rule 53)
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- ../slots/is_or_was_associated_with
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- ./Taxon
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# has_associated_taxon REMOVED - migrated to has_or_had_hypernym + Taxon (Rule 53)
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- ../slots/has_or_had_hypernym
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# bold_id REMOVED - migrated to has_or_had_identifier with BOLDIdentifier class (Rule 53)
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- ../slots/has_or_had_identifier
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- ./BOLDIdentifier
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# cites_appendix REMOVED - migrated to is_or_was_listed_in with CITESAppendix class (Rule 53, 2026-01-19)
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- ../slots/is_or_was_listed_in
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- ./CITESAppendix
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# REMOVED 2026-01-19: collection_date - migrated to was_acquired_through + Acquisition (Rule 53)
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- ../slots/was_acquired_through
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- ./Acquisition
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# REMOVED 2026-01-19: collection_locality_text - migrated to describes_or_described + Locality (Rule 53)
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- ../slots/describes_or_described
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- ./Locality
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# REMOVED 2026-01-19: collection_location - migrated to has_or_had_place + CollectionEvent (Rule 53)
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- ../slots/has_or_had_place
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- ./CollectionEvent
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# REMOVED 2026-01-22: ../slots/collector - migrated to is_or_was_acquired_by + Agent (Rule 53)
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- ../slots/is_or_was_acquired_by
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- ./Agent
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# REMOVED 2026-01-22: ../slots/common_name - migrated to has_or_had_name + Name + has_or_had_type + NameType (Rule 53)
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# REMOVED 2026-01-22: ../slots/common_name_language - migrated to Name.has_or_had_language (Rule 53)
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- ../slots/has_or_had_name
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- ./Name
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- ./NameType
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- ./NameTypes
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- ../slots/has_or_had_custodian_type
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- ./IdentificationEvent
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- ../slots/is_or_was_identified_through # was: date_identified - migrated per Rule 53 (2026-01-23)
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- ../slots/has_or_had_identifier # was: field_number - migrated per Rule 53 (2026-01-26)
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- ./FieldNumber # for has_or_had_identifier range
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- ../slots/gbif_id
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- ../slots/genbank_accession
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- ../slots/has_or_had_habitat # was: habitat - migrated per Rule 53 (2026-01-26)
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- ./Habitat
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- ../slots/higher_classification
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- ../slots/identification_qualifier
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- ../slots/identified_by
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- ../slots/is_type_specimen
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- ../slots/iucn_status
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- ../slots/legal_provenance_note
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- ../slots/life_stage
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- ../slots/part_type
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- ../slots/preparation_date
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- ../slots/prepared_by
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- ../slots/preservation_method
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- ../slots/preservative_detail
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- ../slots/sex
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- ../slots/specificity_annotation
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- ../slots/specimen_count
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- ../slots/specimen_type
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# REMOVED 2026-01-14: ../slots/taxon_name - migrated to has_or_had_label with TaxonName (Rule 53)
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- ../slots/has_or_had_label
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- ./TaxonName
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- ../slots/has_or_had_comment # was: taxon_remark - migrated per Rule 53
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- ../slots/has_or_had_authority # was: taxonomic_authority - migrated per Rule 53/56 (2026-01-16)
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- ./TaxonomicAuthority
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- ../slots/has_or_had_rank # was: taxonomic_rank - migrated per Rule 53/56 (2026-01-17)
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- ../slots/has_or_had_score # was: template_specificity - migrated per Rule 53 (2026-01-17)
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# REMOVED 2026-01-14: ../slots/type_status - migrated to has_or_had_status with TypeStatus
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- ../slots/has_or_had_status
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- ./TypeStatus
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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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# has_associated_taxon REMOVED - migrated to has_or_had_hypernym (Rule 53)
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- ../slots/has_or_had_hypernym
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default_prefix: hc
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classes:
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BiologicalObject:
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class_uri: crm:E20_Biological_Object
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description: "A biological specimen or natural history object held in a heritage collection.\n\nModels organisms, parts\
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\ of organisms, or biological products preserved for\nscientific study, education, or display.\n\n**CIDOC-CRM Alignment**:\n\
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\nE20_Biological_Object - \"Physical objects that have been produced by \nbiological processes and include organisms,\
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\ parts of organisms, and \nbiological products.\"\n\n**Key Distinction from ExhibitedObject**:\n\n| Concept | Class\
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\ | Example |\n|---------|-------|---------|\n| General museum object | ExhibitedObject | \"Girl with a Pearl Earring\"\
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\ |\n| **Biological specimen** | **BiologicalObject** | **Dodo skeleton** |\n| Archaeological find | ExhibitedObject\
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\ | Roman pottery |\n\n**When to Use BiologicalObject**:\n\nUse for specimens that are primarily biological in nature:\n\
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- Taxidermy mounts (mammals, birds, fish)\n- Study skins and skeletal material\n- Herbarium specimens (pressed plants)\n\
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- Wet specimens (fluid-preserved animals)\n- Fossils of organisms\n- Entomological collections (pinned insects)\n- Paleontological\
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\ specimens\n- Living collection records (botanical gardens, zoos)\n\n**Darwin Core Integration**:\n\nBiologicalObject\
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\ aligns with Darwin Core (TDWG) occurrence/specimen standards:\n- `has_or_had_label` (TaxonName) → dwc:scientificName\n- `was_acquired_through` (Acquisition) → dwc:eventDate\
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\n- `is_or_was_acquired_by` (Agent) → dwc:recordedBy\n- `preservation_method` → dwc:preparations\n- `gbif_id` → dwc:occurrenceID\
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\ (GBIF)\n\n**Taxonomic Data Model**:\n\n```\nBiologicalObject\n │\n ├── has_or_had_label (TaxonName: \"Raphus\
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\ cucullatus\")\n │ │\n │ ├── has_or_had_name (Name with type=CommonName: \"Dodo\")\n │ ├── has_or_had_rank (SPECIES)\n \
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\ │ ├── has_or_had_authority (\"Linnaeus, 1758\")\n │ └── higher_classification (Aves → Columbiformes\
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\ → Columbidae)\n │\n ├── specimen_data\n │ │\n │ ├── specimen_type (HOLOTYPE, PARATYPE, etc.)\n\
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\ │ ├── is_type_specimen (boolean)\n │ ├── sex (MALE, FEMALE, UNKNOWN)\n │ ├── life_stage\
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\ (ADULT, JUVENILE, LARVA, etc.)\n │ └── part_type (SKELETON, SKIN, SHELL, etc.)\n │\n ├── preservation\n\
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\ │ │\n │ ├── preservation_method (PreservationMethodEnum)\n │ └── preservative_details (specific\
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\ chemicals, methods)\n │\n └── collection_event\n │\n ├── collection_date (when collected)\n\
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\ ├── collection_location (where collected)\n ├── collector (who collected)\n └── field_number\
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\ (collector's field ID)\n```\n\n**Conservation Status Integration**:\n\nFor specimens of conservation-sensitive species,\
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\ BiologicalObject supports:\n- IUCN Red List status tracking\n- CITES appendix listing\n- Provenance documentation\
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\ for legal compliance\n\n**Example**:\n\nOxford Dodo specimen at Oxford University Museum of Natural History:\n- taxon_name:\
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\ \"Raphus cucullatus\"\n- common_name: \"Dodo\"\n- specimen_type: Historical specimen\n- preservation_method: SKELETON\
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\ (partial)\n- significance: Last reliably dated dodo remains\n"
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exact_mappings:
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- crm:E20_Biological_Object
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close_mappings:
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- dwc:Occurrence
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- dwc:Organism
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- schema:Taxon
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related_mappings:
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- crm:E19_Physical_Object
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- crm:E22_Human-Made_Object
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- gbif:Specimen
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is_a: ExhibitedObject
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slots:
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# associated_taxa REMOVED - migrated to is_or_was_associated_with (Rule 53)
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- is_or_was_associated_with
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# bold_id REMOVED - migrated to has_or_had_identifier with BOLDIdentifier (Rule 53)
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- has_or_had_identifier
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# cites_appendix REMOVED - migrated to is_or_was_listed_in with CITESAppendix (Rule 53, 2026-01-19)
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- is_or_was_listed_in
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# collection_date REMOVED - migrated to was_acquired_through + Acquisition (Rule 53, 2026-01-19)
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- was_acquired_through
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# collection_locality_text REMOVED - migrated to describes_or_described + Locality (Rule 53, 2026-01-19)
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- describes_or_described
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# collection_location REMOVED - migrated to has_or_had_place + CollectionEvent (Rule 53, 2026-01-19)
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- has_or_had_place
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# has_associated_taxon REMOVED - migrated to has_or_had_hypernym (Rule 53)
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- has_or_had_hypernym
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# REMOVED 2026-01-22: collector - migrated to is_or_was_acquired_by + Agent (Rule 53)
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- is_or_was_acquired_by
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# REMOVED 2026-01-22: common_name, common_name_language - migrated to has_or_had_name + Name (Rule 53)
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- has_or_had_name
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- has_or_had_custodian_type
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- is_or_was_identified_through # was: date_identified - migrated per Rule 53 (2026-01-23)
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- has_or_had_identifier # was: field_number - migrated per Rule 53 (2026-01-26)
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- gbif_id
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- genbank_accession
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- has_or_had_habitat # was: habitat
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- higher_classification
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- identification_qualifier
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- identified_by
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- is_type_specimen
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- iucn_status
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- legal_provenance_note
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- life_stage
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- part_type
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- preparation_date
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- prepared_by
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- preservation_method
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- preservative_detail
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- sex
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- specificity_annotation
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- specimen_count
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- specimen_type
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# REMOVED 2026-01-14: taxon_name - migrated to has_or_had_label with TaxonName (Rule 53)
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- has_or_had_label # was: taxon_name - migrated per Rule 53
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- has_or_had_comment # was: taxon_remark - migrated per Rule 53
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- has_or_had_authority # was: taxonomic_authority - migrated per Rule 53/56 (2026-01-16)
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- has_or_had_rank # was: taxonomic_rank - migrated per Rule 53/56 (2026-01-17)
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- has_or_had_score # was: template_specificity - migrated per Rule 53 (2026-01-17)
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# REMOVED 2026-01-14: type_status - migrated to has_or_had_status with TypeStatus
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- has_or_had_status
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slot_usage:
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is_or_was_associated_with:
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description: >-
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MIGRATED from associated_taxa (Rule 53).
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Links biological object to associated taxa.
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Range narrowed to Taxon class.
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range: Taxon
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multivalued: true
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inlined_as_list: true
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examples:
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- value: https://nde.nl/ontology/hc/taxon/raphus-cucullatus
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description: Associated with Dodo taxon
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has_or_had_identifier:
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description: >-
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MIGRATED from bold_id (Rule 53).
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BOLD (Barcode of Life Data System) identifier for DNA barcode records.
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Range narrowed to BOLDIdentifier class.
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range: BOLDIdentifier
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multivalued: true
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inlined_as_list: true
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examples:
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- value:
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id: https://nde.nl/ontology/hc/bold-id/NLNAT001-21
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identifier_value: NLNAT001-21
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description: BOLD identifier for specimen
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# DEPRECATED: taxon_name - migrated to has_or_had_label (2026-01-14, Rule 53)
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# taxon_name:
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# required: true
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# range: string
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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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has_or_had_label: # was: taxon_name - migrated per Rule 53
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description: |
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Scientific taxonomic name for this biological object.
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MIGRATED from taxon_name per slot_fixes.yaml (Rule 53).
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Uses TaxonName class for structured representation.
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range: TaxonName
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inlined: true
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required: true
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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 with nomenclatural authority
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- value:
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scientific_name: "Panthera leo"
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taxonomic_rank: SPECIES
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description: Lion (authority omitted)
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# MIGRATED 2026-01-22: common_name, common_name_language → has_or_had_name + Name (Rule 53)
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has_or_had_name:
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description: |
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Common/vernacular names for this biological object.
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MIGRATED from common_name and common_name_language per slot_fixes.yaml (Rule 53, 2026-01-22).
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Uses Name class for structured representation including:
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- Name value (has_or_had_label)
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- Name type (has_or_had_type → NameType, e.g., CommonName)
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- Language (has_or_had_language)
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required: false
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range: Name
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multivalued: true
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inlined: true
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inlined_as_list: true
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examples:
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- value:
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has_or_had_label: "Dodo"
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has_or_had_type: CommonName
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has_or_had_language: "en"
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description: English common name
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- value:
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has_or_had_label: "Dronte"
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has_or_had_type: CommonName
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has_or_had_language: "nl"
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description: Dutch common name
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- value:
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has_or_had_label: "Lion"
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has_or_had_type: CommonName
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has_or_had_language: "en"
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- value:
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has_or_had_label: "Coast Redwood"
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has_or_had_type: CommonName
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has_or_had_language: "en"
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has_or_had_rank: # was: taxonomic_rank - migrated per Rule 53/56 (2026-01-17)
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required: false
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range: string
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description: |
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Taxonomic rank of the identification.
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MIGRATED from taxonomic_rank per slot_fixes.yaml (Rule 53/56, 2026-01-17).
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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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description: When only identified to genus level
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has_or_had_authority: # was: taxonomic_authority - migrated per Rule 53/56 (2026-01-16)
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required: false
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range: TaxonomicAuthority
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inlined: true
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description: |
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Structured taxonomic authority information.
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MIGRATED from taxonomic_authority per slot_fixes.yaml (Rule 53/56, 2026-01-16).
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examples:
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- value:
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has_or_had_label: "Linnaeus, 1758"
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has_or_had_author: ["Carl Linnaeus"]
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has_or_had_date: 1758
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is_or_was_recombined: false
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nomenclatural_code: ICZN
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description: Standard zoological authority
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- value:
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has_or_had_label: "(Gray, 1821)"
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has_or_had_author: ["John Edward Gray"]
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has_or_had_date: 1821
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is_or_was_recombined: true
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description: Parentheses indicate recombination from original genus
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higher_classification:
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required: false
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range: string
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examples:
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- value: Animalia|Chordata|Aves|Columbiformes|Columbidae|Raphus
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description: Dodo classification
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has_or_had_comment: # was: taxon_remark - migrated per Rule 53
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required: false
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range: string
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examples:
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- value: Previously classified as Didus ineptus
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identification_qualifier:
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required: false
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range: string
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examples:
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- value: cf.
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description: Uncertain, compare with named taxon
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- value: aff.
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description: Related to but distinct from named taxon
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identified_by:
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required: false
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range: string
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multivalued: true
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examples:
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- value: Dr. Jane Smith
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is_or_was_identified_through: # was: date_identified - migrated per Rule 53 (2026-01-23)
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required: false
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range: IdentificationEvent
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inlined: true
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description: |
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Identification event for this specimen.
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MIGRATED from date_identified per slot_fixes.yaml (Rule 53).
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Uses IdentificationEvent class with temporal_extent for dates.
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examples:
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- value:
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temporal_extent:
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begin_of_the_begin: '2020-03-15'
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identified_by:
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- agent_name: "Dr. Jane Smith"
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description: "Was date_identified: 2020-03-15"
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specimen_type:
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required: false
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range: string
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examples:
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- value: HOLOTYPE
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- value: PARATYPE
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is_type_specimen:
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required: false
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range: boolean
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examples:
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- value: true
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description: Type specimen
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# REMOVED 2026-01-14: type_status - migrated to has_or_had_status with TypeStatus
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# type_status:
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# required: false
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# range: string
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# examples:
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# - value: Holotype of Raphus cucullatus Linnaeus, 1758
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has_or_had_status:
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range: TypeStatus
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inlined: true
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description: |
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Type status designation for this specimen.
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MIGRATED 2026-01-14: Replaces type_status slot.
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required: false
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examples:
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- value: |
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TypeStatus:
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status_value: "Holotype of Raphus cucullatus Linnaeus, 1758"
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status_type: "nomenclatural"
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description: Holotype status
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sex:
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required: false
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range: string
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examples:
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- value: MALE
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- value: FEMALE
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- value: UNKNOWN
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life_stage:
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required: false
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range: string
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examples:
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- value: ADULT
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- value: LARVA
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- value: FLOWERING
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part_type:
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required: false
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range: string
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multivalued: true
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examples:
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- value: SKELETON
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- value: SKULL
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- value: SKIN
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specimen_count:
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required: false
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range: integer
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examples:
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- value: 1
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- value: 50
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description: Lot of 50 insects on one pin/slide
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preservation_method:
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required: false
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range: PreservationMethodEnum
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examples:
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- value: TAXIDERMY_MOUNT
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- value: FLUID_ETHANOL
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- value: DRIED_PRESSED
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- value: FROZEN_TISSUE
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preservative_detail:
|
|
required: false
|
|
range: string
|
|
examples:
|
|
- value: 70% ethanol
|
|
- value: Formalin-fixed, ethanol-transferred
|
|
- value: Silica gel dried, stored at -20°C
|
|
preparation_date:
|
|
required: false
|
|
range: date
|
|
examples:
|
|
- value: '2020-06-15'
|
|
prepared_by:
|
|
required: false
|
|
range: string
|
|
examples:
|
|
- value: Natural History Museum Preparation Lab
|
|
- value: J. van der Berg
|
|
# MIGRATED 2026-01-19: collection_date → was_acquired_through + Acquisition (Rule 53)
|
|
was_acquired_through:
|
|
required: false
|
|
range: Acquisition
|
|
inlined: true
|
|
inlined_as_list: true
|
|
description: >-
|
|
Acquisition event capturing when and how specimen was collected.
|
|
Replaces simple collection_date with structured acquisition data.
|
|
examples:
|
|
- value: |
|
|
acquisition_method: FIELD_COLLECTION
|
|
temporal_extent:
|
|
begin_of_the_begin: "2020-06-15"
|
|
end_of_the_end: "2020-06-15"
|
|
acquisition_date_text: "2020-06-15"
|
|
- value: |
|
|
acquisition_method: FIELD_COLLECTION
|
|
temporal_extent:
|
|
begin_of_the_begin: "2020-06-01"
|
|
end_of_the_end: "2020-07-31"
|
|
acquisition_date_text: "2020-06/2020-07"
|
|
acquisition_notes: "Collected sometime in June-July 2020"
|
|
- value: |
|
|
acquisition_method: FIELD_COLLECTION
|
|
temporal_extent:
|
|
begin_of_the_begin: "1870-01-01"
|
|
end_of_the_end: "1879-12-31"
|
|
acquisition_date_text: "1870s"
|
|
acquisition_notes: "Historical specimen with approximate date"
|
|
# MIGRATED 2026-01-19: collection_location → has_or_had_place + CollectionEvent (Rule 53)
|
|
has_or_had_place:
|
|
required: false
|
|
range: CustodianPlace
|
|
inlined: true
|
|
description: >-
|
|
Structured location where specimen was collected.
|
|
MIGRATED from collection_location per slot_fixes.yaml (Rule 53, 2026-01-19).
|
|
|
|
Uses CustodianPlace for detailed location including coordinates.
|
|
examples:
|
|
- value:
|
|
place_name: Mauritius
|
|
country: MU
|
|
latitude: -20.2
|
|
longitude: 57.5
|
|
# MIGRATED 2026-01-19: collection_locality_text → describes_or_described + Locality (Rule 53)
|
|
describes_or_described:
|
|
required: false
|
|
range: Locality
|
|
inlined: true
|
|
inlined_as_list: true
|
|
description: >-
|
|
Verbatim locality description as recorded on specimen label.
|
|
MIGRATED from collection_locality_text per slot_fixes.yaml (Rule 53, 2026-01-19).
|
|
|
|
Uses Locality class for structured representation including
|
|
original text, language, and provenance.
|
|
examples:
|
|
- value:
|
|
verbatim_text: "Mauritius, near Port Louis, in forest"
|
|
original_language: "en"
|
|
description: Locality for Dodo specimen
|
|
- value:
|
|
verbatim_text: "Indonesia: Java: Mt. Gede, 1500m"
|
|
original_language: "en"
|
|
interpretation_notes: "Mt. Gede is Gunung Gede volcano"
|
|
description: Indonesian specimen with elevation
|
|
# MIGRATED 2026-01-22: collector → is_or_was_acquired_by + Agent (Rule 53)
|
|
is_or_was_acquired_by:
|
|
description: |
|
|
The person(s) or organization(s) who collected this specimen.
|
|
Migrated from collector per slot_fixes.yaml revision.
|
|
required: false
|
|
range: Agent
|
|
multivalued: true
|
|
inlined: true
|
|
inlined_as_list: true
|
|
examples:
|
|
- value:
|
|
agent_name: "Alfred Russel Wallace"
|
|
agent_type: person
|
|
agent_role: collector
|
|
description: Victorian naturalist collector
|
|
- value:
|
|
agent_name: "Charles Darwin"
|
|
agent_type: person
|
|
agent_role: collector
|
|
description: HMS Beagle expedition collector
|
|
# field_number - MIGRATED to has_or_had_identifier with FieldNumber (Rule 53, 2026-01-26)
|
|
has_or_had_identifier:
|
|
description: |
|
|
Identifiers for this biological object, including field numbers.
|
|
MIGRATED from field_number (2026-01-26).
|
|
|
|
Use has_or_had_type to distinguish identifier types:
|
|
- FieldNumber (dwc:fieldNumber)
|
|
- BOLDIdentifier (BOLD ID)
|
|
- WikiDataIdentifier (Wikidata Q-number)
|
|
range: Identifier
|
|
multivalued: true
|
|
inlined: true
|
|
inlined_as_list: true
|
|
required: false
|
|
any_of:
|
|
- range: FieldNumber
|
|
- range: BOLDIdentifier
|
|
- range: WikiDataIdentifier
|
|
- range: uriorcurie
|
|
examples:
|
|
- value:
|
|
identifier_value: "ARW-1234"
|
|
has_or_had_type: FieldNumber
|
|
description: Field number (was field_number)
|
|
- value:
|
|
id: https://nde.nl/ontology/hc/bold-id/NLNAT001-21
|
|
identifier_value: NLNAT001-21
|
|
has_or_had_type: BOLDIdentifier
|
|
description: BOLD identifier (was bold_id)
|
|
- value:
|
|
qid: "Q193493"
|
|
label: "Oxford Dodo"
|
|
has_or_had_type: WikiDataIdentifier
|
|
description: Wikidata identifier (from ExhibitedObject)
|
|
has_or_had_habitat:
|
|
required: false
|
|
range: Habitat
|
|
inlined: true
|
|
examples:
|
|
- value:
|
|
has_or_had_label: Tropical rainforest
|
|
has_or_had_description: Understory
|
|
- value:
|
|
has_or_had_label: Coral reef
|
|
has_or_had_description: Depth 15m
|
|
has_or_had_hypernym: # was: has_associated_taxon - migrated per Rule 53
|
|
description: |
|
|
Associated taxon (e.g. host, parasite) relationship.
|
|
MIGRATED from has_associated_taxon per slot_fixes.yaml (Rule 53).
|
|
Uses Taxon class.
|
|
required: false
|
|
range: Taxon
|
|
multivalued: true
|
|
inlined: true
|
|
inlined_as_list: true
|
|
examples:
|
|
- value:
|
|
has_or_had_label: "Quercus robur"
|
|
description: "host:Quercus robur"
|
|
description: Insect collected from oak tree
|
|
- value:
|
|
has_or_had_label: "Cervus elaphus"
|
|
description: "parasite of:Cervus elaphus"
|
|
iucn_status:
|
|
required: false
|
|
range: string
|
|
examples:
|
|
- value: EX
|
|
description: Extinct (e.g., Dodo)
|
|
- value: CR
|
|
description: Critically Endangered
|
|
# cites_appendix REMOVED - migrated to is_or_was_listed_in with CITESAppendix (Rule 53, 2026-01-19)
|
|
is_or_was_listed_in:
|
|
description: >-
|
|
CITES (Convention on International Trade in Endangered Species) listing.
|
|
MIGRATED from cites_appendix per slot_fixes.yaml (Rule 53, 2026-01-19).
|
|
|
|
Uses CITESAppendix class for structured representation including
|
|
appendix level, listing date, and exemption notes.
|
|
|
|
Important for legal compliance in specimen transfers between institutions.
|
|
range: CITESAppendix
|
|
inlined: true
|
|
required: false
|
|
examples:
|
|
- value:
|
|
has_or_had_type: APPENDIX_I
|
|
has_or_had_label: "CITES Appendix I - Most Endangered"
|
|
listing_effective_date: "1975-07-01"
|
|
species_covered: "Loxodonta africana"
|
|
description: African elephant - highest CITES protection
|
|
- value:
|
|
has_or_had_type: NOT_LISTED
|
|
has_or_had_label: "Not regulated under CITES"
|
|
species_covered: "Raphus cucullatus"
|
|
exemption_note: "Extinct species - historical specimens pre-date CITES"
|
|
description: Dodo - extinct, not subject to CITES restrictions
|
|
legal_provenance_note:
|
|
required: false
|
|
range: string
|
|
examples:
|
|
- value: 'Collected pre-CITES (1975). Import permit #12345.'
|
|
gbif_id:
|
|
required: false
|
|
range: string
|
|
examples:
|
|
- value: https://www.gbif.org/occurrence/1234567890
|
|
bold_id:
|
|
required: false
|
|
range: string
|
|
examples:
|
|
- value: BOLD:AAA0001
|
|
genbank_accession:
|
|
required: false
|
|
range: string
|
|
multivalued: true
|
|
examples:
|
|
- value: MW123456
|
|
- value: MN987654
|
|
has_or_had_custodian_type:
|
|
equals_expression: '["hc:BioCustodianType", "hc:MuseumType", "hc:ResearchOrganizationType"]'
|
|
comments:
|
|
- BiologicalObject extends ExhibitedObject with biological specimen-specific fields
|
|
- Aligned with Darwin Core (TDWG) vocabulary for biodiversity data
|
|
- Supports natural history museum, botanical garden, and zoo collections
|
|
- Includes taxonomic, preservation, collection event, and conservation data
|
|
- Links to GBIF, BOLD, and GenBank for molecular data integration
|
|
see_also:
|
|
- https://cidoc-crm.org/html/cidoc_crm_v7.1.3.html#E20
|
|
- https://dwc.tdwg.org/terms/
|
|
- https://www.gbif.org/
|
|
- https://www.iucnredlist.org/
|
|
examples:
|
|
- value:
|
|
object_id: https://nde.nl/ontology/hc/object/oum-dodo-head
|
|
object_name: Oxford Dodo
|
|
object_description: "The only surviving dodo soft tissue - a head with preserved skin and \\nfeathers, plus associated\\\n \\ foot. The most complete dodo specimen known.\\nDonated by Elias Ashmole in 1683.\\n"
|
|
# taxon_name: Raphus cucullatus (Linnaeus, 1758) - MIGRATED to has_or_had_label (2026-01-14)
|
|
has_or_had_label:
|
|
scientific_name: "Raphus cucullatus (Linnaeus, 1758)"
|
|
authorship: "Linnaeus, 1758"
|
|
taxonomic_rank: SPECIES
|
|
# MIGRATED 2026-01-22: common_name → has_or_had_name + Name (Rule 53)
|
|
has_or_had_name:
|
|
- has_or_had_label: "Dodo"
|
|
has_or_had_type: CommonName
|
|
has_or_had_language: "en"
|
|
- has_or_had_label: "Dronte"
|
|
has_or_had_type: CommonName
|
|
has_or_had_language: "nl"
|
|
has_or_had_rank: SPECIES # was: taxonomic_rank - migrated per Rule 53/56 (2026-01-17)
|
|
higher_classification: Animalia|Chordata|Aves|Columbiformes|Columbidae|Raphus
|
|
part_type:
|
|
- HEAD
|
|
- FOOT
|
|
preservation_method: DRIED_WHOLE
|
|
# MIGRATED 2026-01-19: collection_date → was_acquired_through (Rule 53)
|
|
was_acquired_through:
|
|
- acquisition_method: FIELD_COLLECTION
|
|
acquisition_date_text: "pre-1662"
|
|
temporal_extent:
|
|
begin_of_the_begin: "1600-01-01"
|
|
end_of_the_end: "1662-12-31"
|
|
notes: "Pre-1662 (before Great Fire of London destroyed records)"
|
|
# MIGRATED 2026-01-19: collection_location → has_or_had_place (Rule 53)
|
|
has_or_had_place:
|
|
place_name: Mauritius
|
|
country: MU
|
|
iucn_status: EX
|
|
current_keeper: https://nde.nl/ontology/hc/custodian/uk/oxford-museum-natural-history
|
|
accession_number: OUM 11605
|
|
# MIGRATED 2026-01-15: wikidata_id → has_or_had_identifier (Rule 53)
|
|
has_or_had_identifier:
|
|
- qid: "Q193493"
|
|
label: "Oxford Dodo"
|
|
description: Oxford Dodo - most complete dodo specimen, Oxford University Museum
|
|
- value:
|
|
object_id: https://nde.nl/ontology/hc/object/naturalis-megatherium
|
|
object_name: Megatherium skeleton
|
|
object_description: 'Nearly complete skeleton of giant ground sloth from Pleistocene Argentina.
|
|
|
|
One of the finest examples of this extinct megafauna.
|
|
|
|
'
|
|
# taxon_name: Megatherium americanum Cuvier, 1796 - MIGRATED to has_or_had_label (2026-01-14)
|
|
has_or_had_label:
|
|
scientific_name: "Megatherium americanum Cuvier, 1796"
|
|
authorship: "Cuvier, 1796"
|
|
taxonomic_rank: SPECIES
|
|
# MIGRATED 2026-01-22: common_name → has_or_had_name + Name (Rule 53)
|
|
has_or_had_name:
|
|
- has_or_had_label: "Giant Ground Sloth"
|
|
has_or_had_type: CommonName
|
|
has_or_had_language: "en"
|
|
has_or_had_rank: SPECIES # was: taxonomic_rank - migrated per Rule 53/56 (2026-01-17)
|
|
part_type:
|
|
- SKELETON
|
|
preservation_method: FOSSIL_PREPARED
|
|
# MIGRATED 2026-01-19: collection_locality_text → describes_or_described (Rule 53)
|
|
describes_or_described:
|
|
- verbatim_text: "Argentina, Buenos Aires Province"
|
|
original_language: "en"
|
|
iucn_status: EX
|
|
current_keeper: https://nde.nl/ontology/hc/custodian/nl/naturalis
|
|
description: Megatherium skeleton at Naturalis Biodiversity Center
|
|
- value:
|
|
object_id: https://nde.nl/ontology/hc/object/kew-type-specimen
|
|
object_name: Quercus robur type specimen
|
|
object_description: 'Herbarium type specimen of English Oak collected by Linnaeus.
|
|
|
|
'
|
|
# taxon_name: Quercus robur L. - MIGRATED to has_or_had_label (2026-01-14)
|
|
has_or_had_label:
|
|
scientific_name: "Quercus robur L."
|
|
authorship: "L."
|
|
taxonomic_rank: SPECIES
|
|
# MIGRATED 2026-01-22: common_name → has_or_had_name + Name (Rule 53)
|
|
has_or_had_name:
|
|
- has_or_had_label: "English Oak"
|
|
has_or_had_type: CommonName
|
|
has_or_had_language: "en"
|
|
- has_or_had_label: "Pedunculate Oak"
|
|
has_or_had_type: CommonName
|
|
has_or_had_language: "en"
|
|
has_or_had_rank: SPECIES # was: taxonomic_rank - migrated per Rule 53/56 (2026-01-17)
|
|
has_or_had_authority: # was: taxonomic_authority - migrated per Rule 53/56 (2026-01-16)
|
|
has_or_had_label: "Linnaeus, 1753"
|
|
has_or_had_author: ["Carl Linnaeus"]
|
|
has_or_had_date: 1753
|
|
nomenclatural_code: ICN
|
|
specimen_type: LECTOTYPE
|
|
is_type_specimen: true
|
|
has_or_had_status: # was: type_status
|
|
status_value: Lectotype of Quercus robur L., designated by Schwarz (1936)
|
|
status_type: nomenclatural
|
|
part_type:
|
|
- LEAF
|
|
- FLOWER
|
|
preservation_method: DRIED_PRESSED
|
|
# MIGRATED 2026-01-19: collection_date → was_acquired_through (Rule 53)
|
|
was_acquired_through:
|
|
- acquisition_method: FIELD_COLLECTION
|
|
acquisition_date_text: "1750s"
|
|
temporal_extent:
|
|
begin_of_the_begin: "1750-01-01"
|
|
end_of_the_end: "1759-12-31"
|
|
notes: "Collected by Linnaeus in the 1750s"
|
|
# MIGRATED 2026-01-22: collector → is_or_was_acquired_by + Agent (Rule 53)
|
|
is_or_was_acquired_by:
|
|
- agent_name: "Carl Linnaeus"
|
|
agent_type: person
|
|
agent_role: collector
|
|
current_keeper: https://nde.nl/ontology/hc/custodian/uk/royal-botanic-gardens-kew
|
|
description: Oak type specimen at Royal Botanic Gardens, Kew
|