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: - ./ExhibitedObject - linkml:types - ../enums/PreservationMethodEnum - ../metadata - ../slots/describe - ../slots/has_authority - ../slots/commented_on - ../slots/has_habitat - ../slots/has_hypernym - ../slots/identified_by - ../slots/has_label - ../slots/has_name - ../slots/in_place - ../slots/has_rank - ../slots/has_score - ../slots/has_status - ../slots/has_type - ../slots/acquired_by - ../slots/associated_with - ../slots/identified_through - ../slots/listed_in - ../slots/symbolize - ../slots/has_provenance - ../slots/has_stage - ../slots/contain - ../slots/prepared_on - ../slots/prepared_by - ../slots/has_method - ../slots/has_detail - ../slots/has_gender - ../slots/has_quantity - ../slots/has_specimen - ../slots/acquired_through default_prefix: hc classes: BiologicalObject: is_a: ExhibitedObject class_uri: crm:E20_Biological_Object description: >- Natural specimen or organism-derived item held in a heritage collection, with associated taxonomic identification and preservation metadata. alt_descriptions: nl: >- Natuurlijk specimen of organisme-afgeleid item in een erfgoedcollectie, met bijbehorende taxonomische identificatie en conserveringsmetadata. de: >- Natürliches Exemplar oder organismusabgeleitetes Objekt in einer Kulturgutsammlung mit zugehöriger taxonomischer Identifikation und Konservierungsmetadaten. fr: >- Spécimen naturel ou objet dérivé d'organisme dans une collection patrimoniale, avec identification taxonomique et métadonnées de préservation associées. es: >- Espécimen natural u objeto derivado de organismo en una colección patrimonial, con identificación taxonómica y metadatos de preservación asociados. ar: >- عينة طبيعية أو عنصر مشتق من كائن حي في مجموعة تراثية، مع تحديد تصنيفي وبيانات الحفظ المرتبطة. id: >- Spesimen alami atau benda turunan organisme dalam koleksi warisan, dengan identifikasi taksonomi dan metadata pengawetan terkait. zh: >- 遗产收藏中的自然标本或生物衍生物品，带有相关分类学鉴定和保存元数据。 structured_aliases: - literal_form: biologisch object predicate: EXACT_SYNONYM in_language: nl - literal_form: natuurspecimen predicate: EXACT_SYNONYM in_language: nl - literal_form: biologisches Objekt predicate: EXACT_SYNONYM in_language: de - literal_form: Naturkundliches Exemplar predicate: EXACT_SYNONYM in_language: de - literal_form: objet biologique predicate: EXACT_SYNONYM in_language: fr - literal_form: spécimen d'histoire naturelle predicate: EXACT_SYNONYM in_language: fr - literal_form: objeto biológico predicate: EXACT_SYNONYM in_language: es - literal_form: espécimen de historia natural predicate: EXACT_SYNONYM in_language: es - literal_form: كائن بيولوجي predicate: EXACT_SYNONYM in_language: ar - literal_form: عينة تاريخ طبيعي predicate: EXACT_SYNONYM in_language: ar - literal_form: objek biologis predicate: EXACT_SYNONYM in_language: id - literal_form: spesimen sejarah alam predicate: EXACT_SYNONYM in_language: id - literal_form: 生物对象 predicate: EXACT_SYNONYM in_language: zh - literal_form: 自然史标本 predicate: EXACT_SYNONYM in_language: zh - literal_form: biological specimen predicate: EXACT_SYNONYM in_language: zh - literal_form: natural history predicate: EXACT_SYNONYM in_language: zh - literal_form: taxonomic identification predicate: EXACT_SYNONYM in_language: zh - literal_form: preserved specimen predicate: EXACT_SYNONYM in_language: zh - literal_form: organism predicate: EXACT_SYNONYM in_language: zh - literal_form: crm:E20_Biological_Object predicate: EXACT_SYNONYM in_language: zh - literal_form: dwc:Occurrence predicate: EXACT_SYNONYM in_language: zh - literal_form: dwc:Organism predicate: EXACT_SYNONYM in_language: zh - literal_form: schema:Taxon predicate: EXACT_SYNONYM in_language: zh - literal_form: crm:E19_Physical_Object predicate: EXACT_SYNONYM in_language: zh - literal_form: crm:E22_Human-Made_Object predicate: EXACT_SYNONYM in_language: zh - literal_form: gbif:Specimen predicate: EXACT_SYNONYM in_language: zh - literal_form: associated_with predicate: EXACT_SYNONYM in_language: zh - literal_form: identified_by predicate: EXACT_SYNONYM in_language: zh - literal_form: listed_in predicate: EXACT_SYNONYM in_language: zh - literal_form: acquired_through predicate: EXACT_SYNONYM in_language: zh - literal_form: describe predicate: EXACT_SYNONYM in_language: zh - literal_form: in_place predicate: EXACT_SYNONYM in_language: zh - literal_form: has_hypernym predicate: EXACT_SYNONYM in_language: zh - literal_form: acquired_by predicate: EXACT_SYNONYM in_language: zh - literal_form: has_name predicate: EXACT_SYNONYM in_language: zh - literal_form: has_type predicate: EXACT_SYNONYM in_language: zh - literal_form: identified_through predicate: EXACT_SYNONYM in_language: zh - literal_form: has_habitat predicate: EXACT_SYNONYM in_language: zh - literal_form: symbolize predicate: EXACT_SYNONYM in_language: zh - literal_form: has_status predicate: EXACT_SYNONYM in_language: zh - literal_form: has_provenance predicate: EXACT_SYNONYM in_language: zh - literal_form: has_stage predicate: EXACT_SYNONYM in_language: zh - literal_form: contain predicate: EXACT_SYNONYM in_language: zh - literal_form: prepared_on predicate: EXACT_SYNONYM in_language: zh - literal_form: prepared_by predicate: EXACT_SYNONYM in_language: zh - literal_form: has_method predicate: EXACT_SYNONYM in_language: zh - literal_form: has_detail predicate: EXACT_SYNONYM in_language: zh - literal_form: has_gender predicate: EXACT_SYNONYM in_language: zh - literal_form: has_quantity predicate: EXACT_SYNONYM in_language: zh - literal_form: has_specimen predicate: EXACT_SYNONYM in_language: zh - literal_form: has_label predicate: EXACT_SYNONYM in_language: zh - literal_form: commented_on predicate: EXACT_SYNONYM in_language: zh - literal_form: has_authority predicate: EXACT_SYNONYM in_language: zh - literal_form: has_rank predicate: EXACT_SYNONYM in_language: zh - literal_form: has_score predicate: EXACT_SYNONYM in_language: zh broad_mappings: - crm:E20_Biological_Object close_mappings: - dwc:Occurrence - gbif:Specimen related_mappings: - crm:E19_Physical_Object - crm:E22_Human-Made_Object - schema:Taxon slots: - identified_by - has_label - has_name - has_rank - has_authority - commented_on - identified_through - has_specimen - symbolize - has_status - has_gender - has_stage - contain - has_quantity - has_method - has_detail - prepared_on - prepared_by - acquired_through - in_place - describe - acquired_by - has_habitat - has_hypernym - listed_in - has_provenance - has_type slot_usage: identified_by: 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' has_specimen: required: false # range: string examples: - value: HOLOTYPE - value: PARATYPE symbolize: required: false range: boolean examples: - value: true has_status: required: false range: TypeStatus inlined: true examples: - value: "TypeStatus:\n status_value: \"Holotype of Raphus cucullatus Linnaeus, 1758\"\n status_type: \"nomenclatural\"\n" - value: EX - value: CR has_gender: required: false examples: - value: MALE - value: FEMALE - value: UNKNOWN has_stage: required: false # range: string examples: - value: ADULT - value: LARVA - value: FLOWERING contain: required: false # range: string multivalued: true examples: - value: SKELETON - value: SKULL - value: SKIN has_quantity: required: false range: integer examples: - value: 1 - value: 50 has_method: required: false range: PreservationMethodEnum examples: - value: TAXIDERMY_MOUNT - value: FLUID_ETHANOL - value: DRIED_PRESSED - value: FROZEN_TISSUE has_detail: required: false # range: string examples: - value: 70% ethanol - value: Formalin-fixed, ethanol-transferred - value: "Silica gel dried, stored at -20\xB0C" prepared_on: 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 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" in_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 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 has_provenance: required: false # range: string examples: - value: 'Collected pre-CITES (1975). Import permit #12345.' has_type: any_of: - equals_string: hc:BioCustodianType - equals_string: hc:MuseumType - equals_string: 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 contain: - HEAD - FOOT preservation_method: DRIED_WHOLE 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 contain: - 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) contain: - LEAF - FLOWER preservation_method: DRIED_PRESSED 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: "['*']" modeling_notes: | Use for biologically derived specimens such as taxidermy, herbarium, wet collections, and paleontological material, rather than general exhibited objects. Supports Darwin Core-aligned biodiversity documentation, including scientific naming, specimen typing, collection events, and preservation method records.