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/20260202_matang/describe - ../slots/20260202_matang/has_authority - ../slots/20260202_matang/commented_on - ../slots/20260202_matang/has_habitat - ../slots/20260202_matang/has_hypernym - ../slots/20260202_matang/identified_by - ../slots/20260202_matang/has_label - ../slots/20260202_matang/has_name - ../slots/20260202_matang/in_place - ../slots/20260202_matang/has_rank - ../slots/20260202_matang/has_score - ../slots/20260202_matang/has_status - ../slots/20260202_matang/has_type - ../slots/20260202_matang/acquired_by - ../slots/20260202_matang/associated_with - ../slots/20260202_matang/identified_through - ../slots/20260202_matang/listed_in - ../slots/20260202_matang/new/is_type_specimen - ../slots/20260202_matang/new/iucn_status - ../slots/20260202_matang/new/legal_provenance_note - ../slots/20260202_matang/new/life_stage - ../slots/20260202_matang/new/part_type - ../slots/20260202_matang/new/preparation_date - ../slots/20260202_matang/new/prepared_by - ../slots/20260202_matang/new/preservation_method - ../slots/20260202_matang/new/preservative_detail - ../slots/20260202_matang/new/sex - ../slots/20260202_matang/new/specimen_count - ../slots/20260202_matang/new/specimen_type - ../slots/20260202_matang/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_label` (TaxonName) \u2192 dwc:scientificName\n- `was_acquired_through` (Acquisition) \u2192 dwc:eventDate\n- `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_label (TaxonName: \"Raphus cucullatus\")\n \u2502 \u2502\n \u2502 \u251C\u2500\u2500 has_name (Name with type=CommonName: \"Dodo\")\n \u2502 \u251C\u2500\u2500 has_rank (SPECIES)\n \u2502 \u251C\u2500\u2500 has_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: - associated_with - identified_by - listed_in - was_acquired_through - describe - has_place - has_hypernym - acquired_by - has_name - has_type - identified_through - has_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_label - commented_on - has_authority - has_rank - has_score - has_status slot_usage: associated_with: range: Taxon multivalued: true inlined_as_list: true examples: - value: https://nde.nl/ontology/hc/taxon/raphus-cucullatus identified_by: # range: string # uriorcurie multivalued: true inlined: false # Fixed invalid inline for primitive type inlined_as_list: false # Fixed invalid inline for primitive type required: false any_of: - range: FieldNumber - range: BOLDIdentifier - range: WikiDataIdentifier - range: string # uriorcurie examples: - value: has_type: FieldNumber - value: id: https://nde.nl/ontology/hc/bold-id/NLNAT001-21 has_type: BOLDIdentifier - value: has_type: WikiDataIdentifier has_label: range: TaxonName inlined: true required: true examples: - value: - value: has_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_label)\n- Name type (has_type \u2192 NameType, e.g., CommonName)\n- Language (has_language)\n" required: false range: Name multivalued: true inlined: true inlined_as_list: true examples: - value: has_label: Dodo has_type: CommonName has_language: en - value: has_label: Dronte has_type: CommonName has_language: nl - value: has_label: Lion has_type: CommonName has_language: en - value: has_label: Coast Redwood has_type: CommonName has_language: en has_rank: required: false # range: string examples: - value: SPECIES - value: SUBSPECIES - value: GENUS has_authority: required: false range: TaxonomicAuthority inlined: true examples: - value: has_label: Linnaeus, 1758 has_author: - Carl Linnaeus - value: has_label: (Gray, 1821) has_author: - John Edward Gray commented_on: required: false # range: string examples: - value: Previously classified as Didus ineptus - value: aff. 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_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_place: required: false range: CustodianPlace inlined: true examples: - value: place_name: Mauritius country: MU latitude: -20.2 longitude: 57.5 describe: required: false range: Locality inlined: true inlined_as_list: true examples: - value: - value: verbatim_text: 'Indonesia: Java: Mt. Gede, 1500m' acquired_by: required: false range: Agent multivalued: true inlined: true inlined_as_list: true examples: - value: - value: has_habitat: required: false range: Habitat inlined: true examples: - value: has_label: Tropical rainforest has_description: Understory - value: has_label: Coral reef has_description: Depth 15m has_hypernym: required: false range: Taxon multivalued: true inlined: true inlined_as_list: true examples: - value: has_label: Quercus robur description: host:Quercus robur - value: has_label: Cervus elaphus description: parasite of:Cervus elaphus iucn_status: required: false # range: string examples: - value: EX - value: CR listed_in: range: CITESAppendix inlined: true required: false examples: - value: has_type: APPENDIX_I has_label: CITES Appendix I - Most Endangered - value: has_type: NOT_LISTED has_label: Not regulated under CITES legal_provenance_note: required: false # range: string examples: - value: 'Collected pre-CITES (1975). Import permit #12345.' has_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_label: has_name: - has_label: Dodo has_type: CommonName has_language: en - has_label: Dronte has_type: CommonName has_language: nl has_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_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 identified_by: - 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_label: has_name: - has_label: Giant Ground Sloth has_type: CommonName has_language: en has_rank: SPECIES part_type: - SKELETON preservation_method: FOSSIL_PREPARED describe: - 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_label: has_name: - has_label: English Oak has_type: CommonName has_language: en - has_label: Pedunculate Oak has_type: CommonName has_language: en has_rank: SPECIES has_authority: has_label: Linnaeus, 1753 has_author: - Carl Linnaeus specimen_type: LECTOTYPE is_type_specimen: true has_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' 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: "['*']"