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glam/frontend/public/schemas/20251121/linkml/modules/classes/BiologicalObject.yaml
kempersc 09674f7da2 Refactor schema slots and classes for improved consistency and clarity 
- Renamed `has_or_had_auxiliary_entities` to `is_or_was_associated_with` in DigitalPlatform.yaml to align with naming conventions.
- Updated examples in DigitalPlatform.yaml to reflect new slot names and types.
- Migrated `has_av_equipment` to `has_or_had_equipment` in EducationCenter.yaml, including detailed descriptions and examples.
- Consolidated archival references by migrating `archival_reference` to `has_or_had_identifier` in InformationCarrier.yaml.
- Removed deprecated slots: `has_authority_file_name`, `has_authority_file_url`, `has_auxiliary_place`, `has_auxiliary_place_type`, `has_auxiliary_platform`, `has_auxiliary_platform_type`, and `has_av_equipment`, archiving their definitions.
- Updated slot fixes to reflect the migration of various slots to more generic or appropriate counterparts, ensuring all changes are documented with processing notes.
2026-01-27 11:39:06 +01:00

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YAML
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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
# REMOVED 2026-01-15: ../slots/wikidata_id - inherits has_or_had_identifier from ExhibitedObject (Rule 53)
- ./WikiDataIdentifier
# associated_taxa REMOVED - migrated to is_or_was_associated_with (Rule 53)
- ../slots/is_or_was_associated_with
- ./Taxon
# has_associated_taxon REMOVED - migrated to has_or_had_hypernym + Taxon (Rule 53)
- ../slots/has_or_had_hypernym
# bold_id REMOVED - migrated to has_or_had_identifier with BOLDIdentifier class (Rule 53)
- ../slots/has_or_had_identifier
- ./BOLDIdentifier
# cites_appendix REMOVED - migrated to is_or_was_listed_in with CITESAppendix class (Rule 53, 2026-01-19)
- ../slots/is_or_was_listed_in
- ./CITESAppendix
# REMOVED 2026-01-19: collection_date - migrated to was_acquired_through + Acquisition (Rule 53)
- ../slots/was_acquired_through
- ./Acquisition
# REMOVED 2026-01-19: collection_locality_text - migrated to describes_or_described + Locality (Rule 53)
- ../slots/describes_or_described
- ./Locality
# REMOVED 2026-01-19: collection_location - migrated to has_or_had_place + CollectionEvent (Rule 53)
- ../slots/has_or_had_place
- ./CollectionEvent
# REMOVED 2026-01-22: ../slots/collector - migrated to is_or_was_acquired_by + Agent (Rule 53)
- ../slots/is_or_was_acquired_by
- ./Agent
# REMOVED 2026-01-22: ../slots/common_name - migrated to has_or_had_name + Name + has_or_had_type + NameType (Rule 53)
# REMOVED 2026-01-22: ../slots/common_name_language - migrated to Name.has_or_had_language (Rule 53)
- ../slots/has_or_had_name
- ./Name
- ./NameType
- ./NameTypes
- ../slots/has_or_had_custodian_type
- ./IdentificationEvent
- ../slots/is_or_was_identified_through # was: date_identified - migrated per Rule 53 (2026-01-23)
- ../slots/has_or_had_identifier # was: field_number - migrated per Rule 53 (2026-01-26)
- ./FieldNumber # for has_or_had_identifier range
- ../slots/gbif_id
- ../slots/genbank_accession
- ../slots/has_or_had_habitat # was: habitat - migrated per Rule 53 (2026-01-26)
- ./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/has_or_had_comment # was: taxon_remark - migrated per Rule 53
- ../slots/has_or_had_authority # was: taxonomic_authority - migrated per Rule 53/56 (2026-01-16)
- ./TaxonomicAuthority
- ../slots/has_or_had_rank # was: taxonomic_rank - migrated per Rule 53/56 (2026-01-17)
- ../slots/has_or_had_score # was: template_specificity - migrated per Rule 53 (2026-01-17)
# REMOVED 2026-01-14: ../slots/type_status - migrated to has_or_had_status with TypeStatus
- ../slots/has_or_had_status
- ./TypeStatus
- ./SpecificityAnnotation
- ./TemplateSpecificityScore # was: TemplateSpecificityScores - migrated per Rule 53 (2026-01-17)
- ./TemplateSpecificityType
- ./TemplateSpecificityTypes
# has_associated_taxon REMOVED - migrated to has_or_had_hypernym (Rule 53)
- ../slots/has_or_had_hypernym
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- `has_or_had_label` (TaxonName) → dwc:scientificName\n- `was_acquired_through` (Acquisition) → dwc:eventDate\
\n- `is_or_was_acquired_by` (Agent) → dwc:recordedBy\n- `preservation_method` → dwc:preparations\n- `gbif_id` → dwc:occurrenceID\
\ (GBIF)\n\n**Taxonomic Data Model**:\n\n```\nBiologicalObject\n │\n ├── has_or_had_label (TaxonName: \"Raphus\
\ cucullatus\")\n │ │\n │ ├── has_or_had_name (Name with type=CommonName: \"Dodo\")\n │ ├── has_or_had_rank (SPECIES)\n \
\ │ ├── has_or_had_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 REMOVED - migrated to is_or_was_listed_in with CITESAppendix (Rule 53, 2026-01-19)
- is_or_was_listed_in
# collection_date REMOVED - migrated to was_acquired_through + Acquisition (Rule 53, 2026-01-19)
- was_acquired_through
# collection_locality_text REMOVED - migrated to describes_or_described + Locality (Rule 53, 2026-01-19)
- describes_or_described
# collection_location REMOVED - migrated to has_or_had_place + CollectionEvent (Rule 53, 2026-01-19)
- has_or_had_place
# has_associated_taxon REMOVED - migrated to has_or_had_hypernym (Rule 53)
- has_or_had_hypernym
# REMOVED 2026-01-22: collector - migrated to is_or_was_acquired_by + Agent (Rule 53)
- is_or_was_acquired_by
# REMOVED 2026-01-22: common_name, common_name_language - migrated to has_or_had_name + Name (Rule 53)
- has_or_had_name
- has_or_had_custodian_type
- is_or_was_identified_through # was: date_identified - migrated per Rule 53 (2026-01-23)
- has_or_had_identifier # was: field_number - migrated per Rule 53 (2026-01-26)
- gbif_id
- genbank_accession
- has_or_had_habitat # was: 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
- has_or_had_comment # was: taxon_remark - migrated per Rule 53
- has_or_had_authority # was: taxonomic_authority - migrated per Rule 53/56 (2026-01-16)
- has_or_had_rank # was: taxonomic_rank - migrated per Rule 53/56 (2026-01-17)
- has_or_had_score # was: template_specificity - migrated per Rule 53 (2026-01-17)
# 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)
# MIGRATED 2026-01-22: common_name, common_name_language → has_or_had_name + Name (Rule 53)
has_or_had_name:
description: |
Common/vernacular names for this biological object.
MIGRATED from common_name and common_name_language per slot_fixes.yaml (Rule 53, 2026-01-22).
Uses Name class for structured representation including:
- Name value (has_or_had_label)
- Name type (has_or_had_type → NameType, e.g., CommonName)
- Language (has_or_had_language)
required: false
range: Name
multivalued: true
inlined: true
inlined_as_list: true
examples:
- value:
has_or_had_label: "Dodo"
has_or_had_type: CommonName
has_or_had_language: "en"
description: English common name
- value:
has_or_had_label: "Dronte"
has_or_had_type: CommonName
has_or_had_language: "nl"
description: Dutch common name
- value:
has_or_had_label: "Lion"
has_or_had_type: CommonName
has_or_had_language: "en"
- value:
has_or_had_label: "Coast Redwood"
has_or_had_type: CommonName
has_or_had_language: "en"
has_or_had_rank: # was: taxonomic_rank - migrated per Rule 53/56 (2026-01-17)
required: false
range: string
description: |
Taxonomic rank of the identification.
MIGRATED from taxonomic_rank per slot_fixes.yaml (Rule 53/56, 2026-01-17).
examples:
- value: SPECIES
- value: SUBSPECIES
- value: GENUS
description: When only identified to genus level
has_or_had_authority: # was: taxonomic_authority - migrated per Rule 53/56 (2026-01-16)
required: false
range: TaxonomicAuthority
inlined: true
description: |
Structured taxonomic authority information.
MIGRATED from taxonomic_authority per slot_fixes.yaml (Rule 53/56, 2026-01-16).
examples:
- value:
has_or_had_label: "Linnaeus, 1758"
has_or_had_author: ["Carl Linnaeus"]
has_or_had_date: 1758
is_or_was_recombined: false
nomenclatural_code: ICZN
description: Standard zoological authority
- value:
has_or_had_label: "(Gray, 1821)"
has_or_had_author: ["John Edward Gray"]
has_or_had_date: 1821
is_or_was_recombined: true
description: Parentheses indicate recombination from original genus
higher_classification:
required: false
range: string
examples:
- value: Animalia|Chordata|Aves|Columbiformes|Columbidae|Raphus
description: Dodo classification
has_or_had_comment: # was: taxon_remark - migrated per Rule 53
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
is_or_was_identified_through: # was: date_identified - migrated per Rule 53 (2026-01-23)
required: false
range: IdentificationEvent
inlined: true
description: |
Identification event for this specimen.
MIGRATED from date_identified per slot_fixes.yaml (Rule 53).
Uses IdentificationEvent class with temporal_extent for dates.
examples:
- value:
temporal_extent:
begin_of_the_begin: '2020-03-15'
identified_by:
- agent_name: "Dr. Jane Smith"
description: "Was date_identified: 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
# 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
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