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glam/schemas/20251121/linkml/modules/classes/BiologicalObject.yaml
kempersc fc405445c6 Refactor and update schema definitions 
- Removed obsolete slots: `has_or_had_custodian_observation`, `provider`, and `specificity_annotation`.
- Updated `has_or_had_score` slot to use `SpecificityScore` class and modified its description and examples.
- Added new slots: `end_seconds`, `end_time`, `has_archive_path`, `has_or_had_custodian_name`, `protocol_name`, and `protocol_version`.
- Introduced a script `check_annotation_types.py` to validate the presence and structure of `custodian_types` in YAML files.
- Added a script `update_specificity.py` to automate updates related to `SpecificityAnnotation` to `SpecificityScore`.
2026-02-01 19:55:38 +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
- ../enums/PreservationMethodEnum
- ../metadata
- ../slots/describes_or_described
- ../slots/has_or_had_authority
- ../slots/has_or_had_comment
- ../slots/has_or_had_habitat
- ../slots/has_or_had_hypernym
- ../slots/has_or_had_identifier
- ../slots/has_or_had_label
- ../slots/has_or_had_name
- ../slots/has_or_had_place
- ../slots/has_or_had_rank
- ../slots/has_or_had_score
- ../slots/has_or_had_status
- ../slots/has_or_had_type
- ../slots/is_or_was_acquired_by
- ../slots/is_or_was_associated_with
- ../slots/is_or_was_identified_through
- ../slots/is_or_was_listed_in
- ../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/specimen_count
- ../slots/specimen_type
- ../slots/was_acquired_through
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) \u2192 dwc:scientificName\n- `was_acquired_through` (Acquisition) \u2192 dwc:eventDate\n- `is_or_was_acquired_by` (Agent) \u2192 dwc:recordedBy\n- `preservation_method` \u2192 dwc:preparations\n- `gbif_id` \u2192 dwc:occurrenceID (GBIF)\n\n**Taxonomic Data Model**:\n\n```\nBiologicalObject\n \u2502\n \u251C\u2500\u2500 has_or_had_label (TaxonName: \"Raphus cucullatus\")\n \u2502 \u2502\n \u2502 \u251C\u2500\u2500 has_or_had_name (Name with type=CommonName: \"Dodo\")\n \u2502 \u251C\u2500\u2500 has_or_had_rank (SPECIES)\n \u2502 \u251C\u2500\u2500 has_or_had_authority (\"Linnaeus, 1758\")\n \u2502 \u2514\u2500\u2500 higher_classification (Aves \u2192\
\ Columbiformes \u2192 Columbidae)\n \u2502\n \u251C\u2500\u2500 specimen_data\n \u2502 \u2502\n \u2502 \u251C\u2500\u2500 specimen_type (HOLOTYPE, PARATYPE, etc.)\n \u2502 \u251C\u2500\u2500 is_type_specimen (boolean)\n \u2502 \u251C\u2500\u2500 sex (MALE, FEMALE, UNKNOWN)\n \u2502 \u251C\u2500\u2500 life_stage (ADULT, JUVENILE, LARVA, etc.)\n \u2502 \u2514\u2500\u2500 part_type (SKELETON, SKIN, SHELL, etc.)\n \u2502\n \u251C\u2500\u2500 preservation\n \u2502 \u2502\n \u2502 \u251C\u2500\u2500 preservation_method (PreservationMethodEnum)\n \u2502 \u2514\u2500\u2500 preservative_details (specific chemicals, methods)\n \u2502\n \u2514\u2500\u2500 collection_event\n \u2502\n \u251C\u2500\u2500 collection_date (when collected)\n \u251C\u2500\u2500 collection_location (where collected)\n \u251C\u2500\u2500 collector (who collected)\n \
\ \u2514\u2500\u2500 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:
- is_or_was_associated_with
- has_or_had_identifier
- is_or_was_listed_in
- was_acquired_through
- describes_or_described
- has_or_had_place
- has_or_had_hypernym
- is_or_was_acquired_by
- has_or_had_name
- has_or_had_type
- is_or_was_identified_through
- has_or_had_habitat
- is_type_specimen
- iucn_status
- legal_provenance_note
- life_stage
- part_type
- preparation_date
- prepared_by
- preservation_method
- preservative_detail
- sex
- specimen_count
- specimen_type
- has_or_had_label
- has_or_had_comment
- has_or_had_authority
- has_or_had_rank
- has_or_had_score
- has_or_had_status
slot_usage:
is_or_was_associated_with:
range: Taxon
multivalued: true
inlined_as_list: true
examples:
- value: https://nde.nl/ontology/hc/taxon/raphus-cucullatus
has_or_had_identifier:
range: uriorcurie
multivalued: true
inlined: true
inlined_as_list: true
required: false
any_of:
- range: FieldNumber
- range: BOLDIdentifier
- range: WikiDataIdentifier
- range: uriorcurie
examples:
- value:
has_or_had_type: FieldNumber
- value:
id: https://nde.nl/ontology/hc/bold-id/NLNAT001-21
has_or_had_type: BOLDIdentifier
- value:
has_or_had_type: WikiDataIdentifier
has_or_had_label:
range: TaxonName
inlined: true
required: true
examples:
- value:
- value:
has_or_had_name:
description: "Common/vernacular names for this biological object.\nMIGRATED from common_name and common_name_language per slot_fixes.yaml (Rule 53, 2026-01-22).\n\nUses Name class for structured representation including:\n- Name value (has_or_had_label)\n- Name type (has_or_had_type \u2192 NameType, e.g., CommonName)\n- Language (has_or_had_language)\n"
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
- value:
has_or_had_label: Dronte
has_or_had_type: CommonName
has_or_had_language: nl
- 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:
required: false
range: string
examples:
- value: SPECIES
- value: SUBSPECIES
- value: GENUS
has_or_had_authority:
required: false
range: TaxonomicAuthority
inlined: true
examples:
- value:
has_or_had_label: Linnaeus, 1758
has_or_had_author:
- Carl Linnaeus
- value:
has_or_had_label: (Gray, 1821)
has_or_had_author:
- John Edward Gray
has_or_had_comment:
required: false
range: string
examples:
- value: Previously classified as Didus ineptus
- value: aff.
is_or_was_identified_through:
required: false
range: IdentificationEvent
inlined: true
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
has_or_had_status:
range: TypeStatus
inlined: true
required: false
examples:
- value: "TypeStatus:\n status_value: \"Holotype of Raphus cucullatus Linnaeus, 1758\"\n status_type: \"nomenclatural\"\n"
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
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\xB0C"
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
was_acquired_through:
required: false
range: Acquisition
inlined: true
inlined_as_list: true
examples:
- value: "acquisition_method: FIELD_COLLECTION\ntemporal_extent:\n begin_of_the_begin: \"2020-06-15\"\n end_of_the_end: \"2020-06-15\"\nacquisition_date_text: \"2020-06-15\"\n"
- value: "acquisition_method: FIELD_COLLECTION\ntemporal_extent:\n begin_of_the_begin: \"2020-06-01\"\n end_of_the_end: \"2020-07-31\"\nacquisition_date_text: \"2020-06/2020-07\"\nacquisition_notes: \"Collected sometime in June-July 2020\"\n"
- value: "acquisition_method: FIELD_COLLECTION\ntemporal_extent:\n begin_of_the_begin: \"1870-01-01\"\n end_of_the_end: \"1879-12-31\"\nacquisition_date_text: \"1870s\"\nacquisition_notes: \"Historical specimen with approximate date\"\n"
has_or_had_place:
required: false
range: CustodianPlace
inlined: true
examples:
- value:
place_name: Mauritius
country: MU
latitude: -20.2
longitude: 57.5
describes_or_described:
required: false
range: Locality
inlined: true
inlined_as_list: true
examples:
- value:
- value:
verbatim_text: 'Indonesia: Java: Mt. Gede, 1500m'
is_or_was_acquired_by:
required: false
range: Agent
multivalued: true
inlined: true
inlined_as_list: true
examples:
- value:
- value:
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:
required: false
range: Taxon
multivalued: true
inlined: true
inlined_as_list: true
examples:
- value:
has_or_had_label: Quercus robur
description: host:Quercus robur
- value:
has_or_had_label: Cervus elaphus
description: parasite of:Cervus elaphus
iucn_status:
required: false
range: string
examples:
- value: EX
- value: CR
is_or_was_listed_in:
range: CITESAppendix
inlined: true
required: false
examples:
- value:
has_or_had_type: APPENDIX_I
has_or_had_label: CITES Appendix I - Most Endangered
- value:
has_or_had_type: NOT_LISTED
has_or_had_label: Not regulated under CITES
legal_provenance_note:
required: false
range: string
examples:
- value: 'Collected pre-CITES (1975). Import permit #12345.'
has_or_had_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"
has_or_had_label:
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
part_type:
- HEAD
- FOOT
preservation_method: DRIED_WHOLE
was_acquired_through:
- acquisition_method: FIELD_COLLECTION
temporal_extent:
begin_of_the_begin: '1600-01-01'
end_of_the_end: '1662-12-31'
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
has_or_had_identifier:
- qid: Q193493
- 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.
'
has_or_had_label:
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
part_type:
- SKELETON
preservation_method: FOSSIL_PREPARED
describes_or_described:
- verbatim_text: Argentina, Buenos Aires Province
iucn_status: EX
current_keeper: https://nde.nl/ontology/hc/custodian/nl/naturalis
- 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.
'
has_or_had_label:
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
has_or_had_authority:
has_or_had_label: Linnaeus, 1753
has_or_had_author:
- Carl Linnaeus
specimen_type: LECTOTYPE
is_type_specimen: true
has_or_had_status:
status_value: Lectotype of Quercus robur L., designated by Schwarz (1936)
part_type:
- LEAF
- FLOWER
preservation_method: DRIED_PRESSED
was_acquired_through:
- acquisition_method: FIELD_COLLECTION
temporal_extent:
begin_of_the_begin: '1750-01-01'
end_of_the_end: '1759-12-31'
is_or_was_acquired_by:
- agent_name: Carl Linnaeus
current_keeper: https://nde.nl/ontology/hc/custodian/uk/royal-botanic-gardens-kew
annotations:
specificity_score: 0.1
specificity_rationale: Generic utility class/slot created during migration
custodian_types: "['*']"
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