id: https://nde.nl/ontology/hc/class/BiologicalObject
name: BiologicalObject
title: Biological Object Class
prefixes:
  linkml: https://w3id.org/linkml/
  hc: https://nde.nl/ontology/hc/
  schema: http://schema.org/
  crm: http://www.cidoc-crm.org/cidoc-crm/
  dcterms: http://purl.org/dc/terms/
  skos: http://www.w3.org/2004/02/skos/core#
  dwc: http://rs.tdwg.org/dwc/terms/
  gbif: http://rs.gbif.org/terms/
  aat: http://vocab.getty.edu/aat/
imports:
- linkml:types
- ../metadata
- ./TimeSpan
- ./CustodianPlace
- ../enums/PreservationMethodEnum
- ../slots/wikidata_id
# associated_taxa REMOVED - migrated to is_or_was_associated_with (Rule 53)
- ../slots/is_or_was_associated_with
- ./Taxon
# bold_id REMOVED - migrated to has_or_had_identifier with BOLDIdentifier class (Rule 53)
- ../slots/has_or_had_identifier
- ./BOLDIdentifier
- ../slots/cites_appendix
- ../slots/collection_date
- ../slots/collection_locality_text
- ../slots/collection_location
- ../slots/collector
- ../slots/common_name
- ../slots/common_name_language
- ../slots/has_or_had_custodian_type
- ../slots/date_identified
- ../slots/field_number
- ../slots/gbif_id
- ../slots/genbank_accession
- ../slots/habitat
- ../slots/higher_classification
- ../slots/identification_qualifier
- ../slots/identified_by
- ../slots/is_type_specimen
- ../slots/iucn_status
- ../slots/legal_provenance_note
- ../slots/life_stage
- ../slots/part_type
- ../slots/preparation_date
- ../slots/prepared_by
- ../slots/preservation_method
- ../slots/preservative_detail
- ../slots/sex
- ../slots/specificity_annotation
- ../slots/specimen_count
- ../slots/specimen_type
# REMOVED 2026-01-14: ../slots/taxon_name - migrated to has_or_had_label with TaxonName (Rule 53)
- ../slots/has_or_had_label
- ./TaxonName
- ../slots/taxon_remark
- ../slots/taxonomic_authority
- ../slots/taxonomic_rank
- ../slots/template_specificity
# REMOVED 2026-01-14: ../slots/type_status - migrated to has_or_had_status with TypeStatus
- ../slots/has_or_had_status
- ./TypeStatus
- ./SpecificityAnnotation
- ./TemplateSpecificityScores
- ../slots/has_associated_taxon
default_prefix: hc
classes:
  BiologicalObject:
    class_uri: crm:E20_Biological_Object
    description: "A biological specimen or natural history object held in a heritage collection.\n\nModels organisms, parts\
      \ of organisms, or biological products preserved for\nscientific study, education, or display.\n\n**CIDOC-CRM Alignment**:\n\
      \nE20_Biological_Object - \"Physical objects that have been produced by \nbiological processes and include organisms,\
      \ parts of organisms, and \nbiological products.\"\n\n**Key Distinction from ExhibitedObject**:\n\n| Concept | Class\
      \ | Example |\n|---------|-------|---------|\n| General museum object | ExhibitedObject | \"Girl with a Pearl Earring\"\
      \ |\n| **Biological specimen** | **BiologicalObject** | **Dodo skeleton** |\n| Archaeological find | ExhibitedObject\
      \ | Roman pottery |\n\n**When to Use BiologicalObject**:\n\nUse for specimens that are primarily biological in nature:\n\
      - Taxidermy mounts (mammals, birds, fish)\n- Study skins and skeletal material\n- Herbarium specimens (pressed plants)\n\
      - Wet specimens (fluid-preserved animals)\n- Fossils of organisms\n- Entomological collections (pinned insects)\n- Paleontological\
      \ specimens\n- Living collection records (botanical gardens, zoos)\n\n**Darwin Core Integration**:\n\nBiologicalObject\
      \ aligns with Darwin Core (TDWG) occurrence/specimen standards:\n- `taxon_name` → dwc:scientificName\n- `collection_date`\
      \ → dwc:eventDate\n- `collector` → dwc:recordedBy\n- `preservation_method` → dwc:preparations\n- `gbif_id` → dwc:occurrenceID\
      \ (GBIF)\n\n**Taxonomic Data Model**:\n\n```\nBiologicalObject\n    │\n    ├── taxon_name (scientific name: \"Raphus\
      \ cucullatus\")\n    │       │\n    │       ├── common_name (\"Dodo\")\n    │       ├── taxonomic_rank (SPECIES)\n \
      \   │       ├── taxonomic_authority (\"Linnaeus, 1758\")\n    │       └── higher_classification (Aves → Columbiformes\
      \ → Columbidae)\n    │\n    ├── specimen_data\n    │       │\n    │       ├── specimen_type (HOLOTYPE, PARATYPE, etc.)\n\
      \    │       ├── is_type_specimen (boolean)\n    │       ├── sex (MALE, FEMALE, UNKNOWN)\n    │       ├── life_stage\
      \ (ADULT, JUVENILE, LARVA, etc.)\n    │       └── part_type (SKELETON, SKIN, SHELL, etc.)\n    │\n    ├── preservation\n\
      \    │       │\n    │       ├── preservation_method (PreservationMethodEnum)\n    │       └── preservative_details (specific\
      \ chemicals, methods)\n    │\n    └── collection_event\n            │\n            ├── collection_date (when collected)\n\
      \            ├── collection_location (where collected)\n            ├── collector (who collected)\n            └── field_number\
      \ (collector's field ID)\n```\n\n**Conservation Status Integration**:\n\nFor specimens of conservation-sensitive species,\
      \ BiologicalObject supports:\n- IUCN Red List status tracking\n- CITES appendix listing\n- Provenance documentation\
      \ for legal compliance\n\n**Example**:\n\nOxford Dodo specimen at Oxford University Museum of Natural History:\n- taxon_name:\
      \ \"Raphus cucullatus\"\n- common_name: \"Dodo\"\n- specimen_type: Historical specimen\n- preservation_method: SKELETON\
      \ (partial)\n- significance: Last reliably dated dodo remains\n"
    exact_mappings:
    - crm:E20_Biological_Object
    close_mappings:
    - dwc:Occurrence
    - dwc:Organism
    - schema:Taxon
    related_mappings:
    - crm:E19_Physical_Object
    - crm:E22_Human-Made_Object
    - gbif:Specimen
    is_a: ExhibitedObject
    slots:
    # associated_taxa REMOVED - migrated to is_or_was_associated_with (Rule 53)
    - is_or_was_associated_with
    # bold_id REMOVED - migrated to has_or_had_identifier with BOLDIdentifier (Rule 53)
    - has_or_had_identifier
    - cites_appendix
    - collection_date
    - collection_locality_text
    - collection_location
    - collector
    - common_name
    - common_name_language
    - has_or_had_custodian_type
    - date_identified
    - field_number
    - gbif_id
    - genbank_accession
    - habitat
    - higher_classification
    - identification_qualifier
    - identified_by
    - is_type_specimen
    - iucn_status
    - legal_provenance_note
    - life_stage
    - part_type
    - preparation_date
    - prepared_by
    - preservation_method
    - preservative_detail
    - sex
    - specificity_annotation
    - specimen_count
    - specimen_type
    # REMOVED 2026-01-14: taxon_name - migrated to has_or_had_label with TaxonName (Rule 53)
    - has_or_had_label  # was: taxon_name - migrated per Rule 53
    - taxon_remark
    - taxonomic_authority
    - taxonomic_rank
    - template_specificity
    # REMOVED 2026-01-14: type_status - migrated to has_or_had_status with TypeStatus
    - has_or_had_status
    slot_usage:
      is_or_was_associated_with:
        description: >-
          MIGRATED from associated_taxa (Rule 53).
          Links biological object to associated taxa.
          Range narrowed to Taxon class.
        range: Taxon
        multivalued: true
        inlined_as_list: true
        examples:
          - value: https://nde.nl/ontology/hc/taxon/raphus-cucullatus
            description: Associated with Dodo taxon
      has_or_had_identifier:
        description: >-
          MIGRATED from bold_id (Rule 53).
          BOLD (Barcode of Life Data System) identifier for DNA barcode records.
          Range narrowed to BOLDIdentifier class.
        range: BOLDIdentifier
        multivalued: true
        inlined_as_list: true
        examples:
          - value:
              id: https://nde.nl/ontology/hc/bold-id/NLNAT001-21
              identifier_value: NLNAT001-21
            description: BOLD identifier for specimen
      # DEPRECATED: taxon_name - migrated to has_or_had_label (2026-01-14, Rule 53)
      # taxon_name:
      #   required: true
      #   range: string
      #   examples:
      #   - value: Raphus cucullatus (Linnaeus, 1758)
      #     description: Dodo with nomenclatural authority
      #   - value: Panthera leo
      #     description: Lion (authority omitted)
      has_or_had_label:  # was: taxon_name - migrated per Rule 53
        description: |
          Scientific taxonomic name for this biological object.
          MIGRATED from taxon_name per slot_fixes.yaml (Rule 53).
          
          Uses TaxonName class for structured representation.
        range: TaxonName
        inlined: true
        required: true
        examples:
        - value:
            scientific_name: "Raphus cucullatus (Linnaeus, 1758)"
            authorship: "Linnaeus, 1758"
            taxonomic_rank: SPECIES
          description: Dodo with nomenclatural authority
        - value:
            scientific_name: "Panthera leo"
            taxonomic_rank: SPECIES
          description: Lion (authority omitted)
      common_name:
        required: false
        range: string
        multivalued: true
        examples:
        - value: Dodo
        - value: Lion
        - value: Coast Redwood
      common_name_language:
        required: false
        range: string
        multivalued: true
        examples:
        - value: en
        - value: nl
      taxonomic_rank:
        required: false
        range: string
        examples:
        - value: SPECIES
        - value: SUBSPECIES
        - value: GENUS
          description: When only identified to genus level
      taxonomic_authority:
        required: false
        range: string
        examples:
        - value: Linnaeus, 1758
        - value: (Gray, 1821)
          description: Parentheses indicate original genus differs
      higher_classification:
        required: false
        range: string
        examples:
        - value: Animalia|Chordata|Aves|Columbiformes|Columbidae|Raphus
          description: Dodo classification
      taxon_remark:
        required: false
        range: string
        examples:
        - value: Previously classified as Didus ineptus
      identification_qualifier:
        required: false
        range: string
        examples:
        - value: cf.
          description: Uncertain, compare with named taxon
        - value: aff.
          description: Related to but distinct from named taxon
      identified_by:
        required: false
        range: string
        multivalued: true
        examples:
        - value: Dr. Jane Smith
      date_identified:
        required: false
        range: date
        examples:
        - value: '2020-03-15'
      specimen_type:
        required: false
        range: string
        examples:
        - value: HOLOTYPE
        - value: PARATYPE
      is_type_specimen:
        required: false
        range: boolean
        examples:
        - value: true
          description: Type specimen
      # REMOVED 2026-01-14: type_status - migrated to has_or_had_status with TypeStatus
      # type_status:
      #   required: false
      #   range: string
      #   examples:
      #   - value: Holotype of Raphus cucullatus Linnaeus, 1758
      has_or_had_status:
        range: TypeStatus
        inlined: true
        description: |
          Type status designation for this specimen.
          MIGRATED 2026-01-14: Replaces type_status slot.
        required: false
        examples:
        - value: |
            TypeStatus:
              status_value: "Holotype of Raphus cucullatus Linnaeus, 1758"
              status_type: "nomenclatural"
          description: Holotype status
      sex:
        required: false
        range: string
        examples:
        - value: MALE
        - value: FEMALE
        - value: UNKNOWN
      life_stage:
        required: false
        range: string
        examples:
        - value: ADULT
        - value: LARVA
        - value: FLOWERING
      part_type:
        required: false
        range: string
        multivalued: true
        examples:
        - value: SKELETON
        - value: SKULL
        - value: SKIN
      specimen_count:
        required: false
        range: integer
        examples:
        - value: 1
        - value: 50
          description: Lot of 50 insects on one pin/slide
      preservation_method:
        required: false
        range: PreservationMethodEnum
        examples:
        - value: TAXIDERMY_MOUNT
        - value: FLUID_ETHANOL
        - value: DRIED_PRESSED
        - value: FROZEN_TISSUE
      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
      collection_date:
        required: false
        range: string
        examples:
        - value: '2020-06-15'
        - value: 2020-06/2020-07
          description: Collected sometime in June-July 2020
        - value: 1870s
          description: Historical specimen with approximate date
      collection_location:
        required: false
        range: CustodianPlace
        inlined: true
        examples:
        - value:
            place_name: Mauritius
            country: MU
            latitude: -20.2
            longitude: 57.5
      collection_locality_text:
        required: false
        range: string
        examples:
        - value: Mauritius, near Port Louis, in forest
        - value: 'Indonesia: Java: Mt. Gede, 1500m'
      collector:
        required: false
        range: string
        multivalued: true
        examples:
        - value: Alfred Russel Wallace
        - value: Charles Darwin
      field_number:
        required: false
        range: string
        examples:
        - value: ARW-1234
        - value: CD-HMS Beagle-567
      habitat:
        required: false
        range: string
        examples:
        - value: Tropical rainforest, understory
        - value: Coral reef, depth 15m
      has_associated_taxon:
        required: false
        range: string
        multivalued: true
        examples:
        - value: host:Quercus robur
          description: Insect collected from oak tree
        - value: 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:
        required: false
        range: string
        examples:
        - value: APPENDIX_I
          description: Most endangered, trade prohibited
      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
        common_name:
        - Dodo
        - Dronte
        taxonomic_rank: SPECIES
        higher_classification: Animalia|Chordata|Aves|Columbiformes|Columbidae|Raphus
        part_type:
        - HEAD
        - FOOT
        preservation_method: DRIED_WHOLE
        collection_date: pre-1662
        collection_location:
          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
        wikidata_id: Q193493
      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
        common_name:
        - Giant Ground Sloth
        taxonomic_rank: SPECIES
        part_type:
        - SKELETON
        preservation_method: FOSSIL_PREPARED
        collection_locality_text: Argentina, Buenos Aires Province
        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
        common_name:
        - English Oak
        - Pedunculate Oak
        taxonomic_rank: SPECIES
        taxonomic_authority: Linnaeus, 1753
        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
        collection_date: 1750s
        collector:
        - Carl Linnaeus
        current_keeper: https://nde.nl/ontology/hc/custodian/uk/royal-botanic-gardens-kew
      description: Oak type specimen at Royal Botanic Gardens, Kew