glam/schemas/20251121/linkml/modules/classes/BiologicalObject.yaml
kempersc c1946e93f9 Refactor VideoPost and WebObservation schemas; remove deprecated slots and migrate to new structures
- Updated VideoPost.yaml to include new slots and remove deprecated ones, enhancing video-specific properties.
- Removed extraction_confidence from WebObservation.yaml, streamlining the schema.
- Deleted obsolete slot files: characteristics.yaml, class_definition.yaml, confidence.yaml, confidence_method.yaml, confidence_score.yaml, confidence_value.yaml, count.yaml, and hosts_branch.yaml.
- Introduced ghost_slots.txt to track unused slots.
- Archived previous versions of characteristics, class_definition, confidence, confidence_method, confidence_score, confidence_value, count, and hosts_branch slots for historical reference.
- Added new slots: has_or_had_citation, has_or_had_city_code, and is_or_was_location_of with appropriate descriptions and mappings.
2026-01-28 15:04:11 +01:00

664 lines
26 KiB
YAML

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
- ./WikiDataIdentifier
- ../slots/is_or_was_associated_with
- ./Taxon
- ../slots/has_or_had_hypernym
- ../slots/has_or_had_identifier
- ./BOLDIdentifier
- ../slots/is_or_was_listed_in
- ./CITESAppendix
- ../slots/was_acquired_through
- ./Acquisition
- ../slots/describes_or_described
- ./Locality
- ../slots/has_or_had_place
- ./CollectionEvent
- ../slots/is_or_was_acquired_by
- ./Agent
- ../slots/has_or_had_name
- ./Name
- ./NameType
- ./NameTypes
- ../slots/has_or_had_type
- ./IdentificationEvent
- ../slots/is_or_was_identified_through
- ../slots/has_or_had_identifier
- ./FieldNumber
- ../slots/gbif_id
- ../slots/genbank_accession
- ../slots/has_or_had_habitat
- ./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
- ../slots/has_or_had_label
- ./TaxonName
- ../slots/has_or_had_comment
- ../slots/has_or_had_authority
- ./TaxonomicAuthority
- ../slots/has_or_had_rank
- ../slots/has_or_had_score
- ../slots/has_or_had_status
- ./TypeStatus
- ./SpecificityAnnotation
- ./TemplateSpecificityScore
- ./TemplateSpecificityType
- ./TemplateSpecificityTypes
- ../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) \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_identifier
- gbif_id
- genbank_accession
- has_or_had_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
- 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:
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: '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_label:
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)
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
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:
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:
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:
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:
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
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:\n status_value: \"Holotype of Raphus cucullatus Linnaeus, 1758\"\n status_type: \"nomenclatural\"\n"
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\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
description: Acquisition event capturing when and how specimen was collected. Replaces simple collection_date with structured acquisition data.
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
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
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
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
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:
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
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
genbank_accession:
required: false
range: string
multivalued: true
examples:
- value: MW123456
- value: MN987654
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:
scientific_name: Raphus cucullatus (Linnaeus, 1758)
authorship: Linnaeus, 1758
taxonomic_rank: SPECIES
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
higher_classification: Animalia|Chordata|Aves|Columbiformes|Columbidae|Raphus
part_type:
- HEAD
- FOOT
preservation_method: DRIED_WHOLE
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)
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
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.
'
has_or_had_label:
scientific_name: Megatherium americanum Cuvier, 1796
authorship: Cuvier, 1796
taxonomic_rank: SPECIES
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
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.
'
has_or_had_label:
scientific_name: Quercus robur L.
authorship: L.
taxonomic_rank: SPECIES
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
has_or_had_date: 1753
nomenclatural_code: ICN
specimen_type: LECTOTYPE
is_type_specimen: true
has_or_had_status:
status_value: Lectotype of Quercus robur L., designated by Schwarz (1936)
status_type: nomenclatural
part_type:
- LEAF
- FLOWER
preservation_method: DRIED_PRESSED
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
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
annotations:
specificity_score: 0.1
specificity_rationale: Generic utility class/slot created during migration
custodian_types:
- '*'
custodian_types_rationale: Universal utility concept