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