glam/schemas/20251121/linkml/modules/classes/BiologicalObject.yaml
2026-01-02 02:11:04 +01:00

875 lines
27 KiB
YAML

# BiologicalObject Class
# Models biological specimens in natural history collections
#
# Created January 2026 to support:
# - Natural history museums with zoological/botanical collections
# - Botanical gardens with herbarium specimens
# - Zoos with specimen archives
# - Research centers with biological reference collections
#
# Key relationships:
# BiologicalObject --is_a--> ExhibitedObject (inherits base object properties)
# BiologicalObject --has_preservation--> PreservationMethodEnum
# BiologicalObject --collected_at--> CustodianPlace
# BiologicalObject --collected_by--> Person/collector
# BiologicalObject --part_of--> Collection
#
# CIDOC-CRM: E20_Biological_Object - "Physical objects that have been produced by
# biological processes... includes organisms, parts of organisms, and biological
# products."
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
- ../slots/wikidata_id
default_prefix: hc
classes:
BiologicalObject:
class_uri: crm:E20_Biological_Object
annotations:
custodian_types: '["B", "M", "R"]'
custodian_types_rationale: |
BiologicalObject is primarily relevant to:
- Botanical gardens/zoos (B): Living collections, herbaria, specimen archives
- Museums (M): Natural history museums with zoological/botanical collections
- Research centers (R): Biological reference collections, type specimens
description: |
A biological specimen or natural history object held in a heritage collection.
Models organisms, parts of organisms, or biological products preserved for
scientific study, education, or display.
**CIDOC-CRM Alignment**:
E20_Biological_Object - "Physical objects that have been produced by
biological processes and include organisms, parts of organisms, and
biological products."
**Key Distinction from ExhibitedObject**:
| Concept | Class | Example |
|---------|-------|---------|
| General museum object | ExhibitedObject | "Girl with a Pearl Earring" |
| **Biological specimen** | **BiologicalObject** | **Dodo skeleton** |
| Archaeological find | ExhibitedObject | Roman pottery |
**When to Use BiologicalObject**:
Use for specimens that are primarily biological in nature:
- Taxidermy mounts (mammals, birds, fish)
- Study skins and skeletal material
- Herbarium specimens (pressed plants)
- Wet specimens (fluid-preserved animals)
- Fossils of organisms
- Entomological collections (pinned insects)
- Paleontological specimens
- Living collection records (botanical gardens, zoos)
**Darwin Core Integration**:
BiologicalObject aligns with Darwin Core (TDWG) occurrence/specimen standards:
- `taxon_name` → dwc:scientificName
- `collection_date` → dwc:eventDate
- `collector` → dwc:recordedBy
- `preservation_method` → dwc:preparations
- `gbif_id` → dwc:occurrenceID (GBIF)
**Taxonomic Data Model**:
```
BiologicalObject
├── taxon_name (scientific name: "Raphus cucullatus")
│ │
│ ├── common_name ("Dodo")
│ ├── taxonomic_rank (SPECIES)
│ ├── taxonomic_authority ("Linnaeus, 1758")
│ └── higher_classification (Aves → Columbiformes → Columbidae)
├── specimen_data
│ │
│ ├── specimen_type (HOLOTYPE, PARATYPE, etc.)
│ ├── is_type_specimen (boolean)
│ ├── sex (MALE, FEMALE, UNKNOWN)
│ ├── life_stage (ADULT, JUVENILE, LARVA, etc.)
│ └── part_type (SKELETON, SKIN, SHELL, etc.)
├── preservation
│ │
│ ├── preservation_method (PreservationMethodEnum)
│ └── preservative_details (specific chemicals, methods)
└── collection_event
├── collection_date (when collected)
├── collection_location (where collected)
├── collector (who collected)
└── field_number (collector's field ID)
```
**Conservation Status Integration**:
For specimens of conservation-sensitive species, BiologicalObject supports:
- IUCN Red List status tracking
- CITES appendix listing
- Provenance documentation for legal compliance
**Example**:
Oxford Dodo specimen at Oxford University Museum of Natural History:
- taxon_name: "Raphus cucullatus"
- common_name: "Dodo"
- specimen_type: Historical specimen
- preservation_method: SKELETON (partial)
- significance: Last reliably dated dodo remains
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:
# Taxonomic identification
- taxon_name
- common_name
- common_name_language
- taxonomic_rank
- taxonomic_authority
- higher_classification
- taxon_remarks
- identification_qualifier
- identified_by
- date_identified
# Specimen characterization
- specimen_type
- is_type_specimen
- type_status
- sex
- life_stage
- part_type
- specimen_count
# Preservation
- preservation_method
- preservative_details
- preparation_date
- prepared_by
# Collection event
- collection_date
- collection_location
- collection_locality_text
- collector
- field_number
- habitat
- associated_taxa
# Conservation/Legal
- iucn_status
- cites_appendix
- legal_provenance_notes
# External identifiers
- gbif_id
- bold_id
- genbank_accessions
slot_usage:
taxon_name:
required: true
range: string
slot_uri: dwc:scientificName
description: |
Scientific name (Linnean binomial or trinomial).
Include author and year for formal nomenclature.
**Format**: "Genus species (Author, Year)"
**Examples**:
- "Raphus cucullatus (Linnaeus, 1758)"
- "Tyrannosaurus rex Osborn, 1905"
- "Quercus robur L."
examples:
- value: "Raphus cucullatus (Linnaeus, 1758)"
description: "Dodo with nomenclatural authority"
- value: "Panthera leo"
description: "Lion (authority omitted)"
common_name:
required: false
range: string
multivalued: true
slot_uri: dwc:vernacularName
description: |
Common/vernacular name(s) in one or more languages.
Use common_name_language to specify language.
examples:
- value: "Dodo"
- value: "Lion"
- value: "Coast Redwood"
common_name_language:
required: false
range: string
multivalued: true
slot_uri: dcterms:language
description: |
Language code(s) for common names (ISO 639-1 or 639-3).
Corresponds to common_name list by position.
examples:
- value: "en"
- value: "nl"
taxonomic_rank:
required: false
range: string
slot_uri: dwc:taxonRank
description: |
Taxonomic rank of the identification.
**Values**: KINGDOM, PHYLUM, CLASS, ORDER, FAMILY, GENUS, SPECIES,
SUBSPECIES, VARIETY, FORM
examples:
- value: "SPECIES"
- value: "SUBSPECIES"
- value: "GENUS"
description: "When only identified to genus level"
taxonomic_authority:
required: false
range: string
slot_uri: dwc:scientificNameAuthorship
description: |
The authorship information for the scientific name.
**Format**: "Author, Year" or "(Author, Year)" for recombinations
examples:
- value: "Linnaeus, 1758"
- value: "(Gray, 1821)"
description: "Parentheses indicate original genus differs"
higher_classification:
required: false
range: string
slot_uri: dwc:higherClassification
description: |
Full taxonomic hierarchy from kingdom to genus.
**Format**: Pipe-separated: "Kingdom|Phylum|Class|Order|Family|Genus"
examples:
- value: "Animalia|Chordata|Aves|Columbiformes|Columbidae|Raphus"
description: "Dodo classification"
taxon_remarks:
required: false
range: string
slot_uri: dwc:taxonRemarks
description: |
Notes about taxonomic identification, uncertainties, or changes.
examples:
- value: "Previously classified as Didus ineptus"
identification_qualifier:
required: false
range: string
slot_uri: dwc:identificationQualifier
description: |
Qualifier for uncertain identifications.
**Values**: "cf." (compare with), "aff." (affinity with), "?" (uncertain)
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
slot_uri: dwc:identifiedBy
description: |
Person(s) who made the taxonomic identification.
examples:
- value: "Dr. Jane Smith"
date_identified:
required: false
range: date
slot_uri: dwc:dateIdentified
description: |
Date when the current identification was made.
examples:
- value: "2020-03-15"
specimen_type:
required: false
range: string
slot_uri: dwc:typeStatus
description: |
Nomenclatural type status if applicable.
**Values**: HOLOTYPE, PARATYPE, SYNTYPE, LECTOTYPE, NEOTYPE,
TOPOTYPE, ISOTYPE (plants), TYPE (informal)
examples:
- value: "HOLOTYPE"
- value: "PARATYPE"
is_type_specimen:
required: false
range: boolean
description: |
Whether this is a nomenclatural type specimen.
True if specimen has any type status (holotype, paratype, etc.)
examples:
- value: true
description: "Type specimen"
type_status:
required: false
range: string
slot_uri: dwc:typeStatus
description: |
Full type status statement including taxon name.
**Format**: "Type status of Taxon Name Author, Year"
examples:
- value: "Holotype of Raphus cucullatus Linnaeus, 1758"
sex:
required: false
range: string
slot_uri: dwc:sex
description: |
Sex of the organism.
**Values**: MALE, FEMALE, HERMAPHRODITE, UNKNOWN, NOT_APPLICABLE
examples:
- value: "MALE"
- value: "FEMALE"
- value: "UNKNOWN"
life_stage:
required: false
range: string
slot_uri: dwc:lifeStage
description: |
Life stage of the organism when collected/preserved.
**Values vary by taxon**:
- Vertebrates: ADULT, JUVENILE, SUBADULT, NEONATE
- Insects: ADULT, LARVA, PUPA, NYMPH, EGG
- Plants: FLOWERING, FRUITING, VEGETATIVE, SEED
examples:
- value: "ADULT"
- value: "LARVA"
- value: "FLOWERING"
part_type:
required: false
range: string
multivalued: true
slot_uri: dwc:preparations
description: |
Part(s) of organism represented in this specimen.
**Values**: WHOLE_ORGANISM, SKELETON, SKULL, SKIN, SHELL,
WING, LEG, FEATHER, TISSUE, DNA, LEAF, FLOWER, ROOT, SEED
examples:
- value: "SKELETON"
- value: "SKULL"
- value: "SKIN"
specimen_count:
required: false
range: integer
slot_uri: dwc:individualCount
description: |
Number of individuals represented by this specimen record.
Default is 1 for most specimens.
examples:
- value: 1
- value: 50
description: "Lot of 50 insects on one pin/slide"
preservation_method:
required: false
range: PreservationMethodEnum
slot_uri: dwc:preparations
description: |
Primary preservation method used for this specimen.
See PreservationMethodEnum for full list of values.
examples:
- value: TAXIDERMY_MOUNT
- value: FLUID_ETHANOL
- value: DRIED_PRESSED
- value: FROZEN_TISSUE
preservative_details:
required: false
range: string
description: |
Specific details about preservation (concentrations, solutions, etc.).
examples:
- value: "70% ethanol"
- value: "Formalin-fixed, ethanol-transferred"
- value: "Silica gel dried, stored at -20°C"
preparation_date:
required: false
range: date
description: |
Date when specimen was prepared/preserved.
May differ from collection date.
examples:
- value: "2020-06-15"
prepared_by:
required: false
range: string
slot_uri: crm:P14_carried_out_by
description: |
Person or institution who prepared the specimen.
examples:
- value: "Natural History Museum Preparation Lab"
- value: "J. van der Berg"
collection_date:
required: false
range: string
slot_uri: dwc:eventDate
description: |
Date when specimen was collected in the field.
**Format**: ISO 8601 (YYYY-MM-DD) or range (YYYY-MM-DD/YYYY-MM-DD)
Can also use text for historical specimens with approximate dates.
examples:
- value: "2020-06-15"
- value: "2020-06/2020-07"
description: "Collected sometime in June-July 2020"
- value: "1870s"
description: "Historical specimen with approximate date"
collection_location:
required: false
range: CustodianPlace
inlined: true
slot_uri: dwc:locality
description: |
Structured location where specimen was collected.
Use for geocoded locations with coordinates.
examples:
- value:
place_name: "Mauritius"
country: "MU"
latitude: -20.2
longitude: 57.5
collection_locality_text:
required: false
range: string
slot_uri: dwc:verbatimLocality
description: |
Verbatim locality description as recorded on label.
Preserves original text for historical specimens.
examples:
- value: "Mauritius, near Port Louis, in forest"
- value: "Indonesia: Java: Mt. Gede, 1500m"
collector:
required: false
range: string
multivalued: true
slot_uri: dwc:recordedBy
description: |
Person(s) who collected the specimen.
examples:
- value: "Alfred Russel Wallace"
- value: "Charles Darwin"
field_number:
required: false
range: string
slot_uri: dwc:fieldNumber
description: |
Collector's original field number or catalog number.
examples:
- value: "ARW-1234"
- value: "CD-HMS Beagle-567"
habitat:
required: false
range: string
slot_uri: dwc:habitat
description: |
Description of habitat where specimen was found.
examples:
- value: "Tropical rainforest, understory"
- value: "Coral reef, depth 15m"
associated_taxa:
required: false
range: string
multivalued: true
slot_uri: dwc:associatedTaxa
description: |
Other taxa associated with this specimen (host, parasite, symbiont).
**Format**: "relationship:Taxon name"
examples:
- value: "host:Quercus robur"
description: "Insect collected from oak tree"
- value: "parasite of:Cervus elaphus"
iucn_status:
required: false
range: string
description: |
IUCN Red List conservation status.
**Values**: EX (Extinct), EW (Extinct in Wild), CR (Critically Endangered),
EN (Endangered), VU (Vulnerable), NT (Near Threatened), LC (Least Concern),
DD (Data Deficient), NE (Not Evaluated)
examples:
- value: "EX"
description: "Extinct (e.g., Dodo)"
- value: "CR"
description: "Critically Endangered"
cites_appendix:
required: false
range: string
description: |
CITES (Convention on International Trade in Endangered Species) listing.
**Values**: APPENDIX_I, APPENDIX_II, APPENDIX_III, NOT_LISTED
Important for legal compliance in specimen transfers.
examples:
- value: "APPENDIX_I"
description: "Most endangered, trade prohibited"
legal_provenance_notes:
required: false
range: string
description: |
Notes on legal status and provenance for conservation-sensitive specimens.
Document pre-CITES collection, permits, legal transfers.
examples:
- value: "Collected pre-CITES (1975). Import permit #12345."
gbif_id:
required: false
range: string
slot_uri: dwc:occurrenceID
description: |
Global Biodiversity Information Facility occurrence ID.
Links specimen to GBIF occurrence record.
examples:
- value: "https://www.gbif.org/occurrence/1234567890"
bold_id:
required: false
range: string
description: |
Barcode of Life Data System (BOLD) record ID.
Links to DNA barcode data.
examples:
- value: "BOLD:AAA0001"
genbank_accessions:
required: false
range: string
multivalued: true
description: |
NCBI GenBank accession numbers for sequences from this specimen.
examples:
- value: "MW123456"
- value: "MN987654"
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
feathers, plus associated foot. The most complete dodo specimen known.
Donated by Elias Ashmole in 1683.
taxon_name: "Raphus cucullatus (Linnaeus, 1758)"
common_name:
- "Dodo"
- "Dronte"
taxonomic_rank: "SPECIES"
higher_classification: "Animalia|Chordata|Aves|Columbiformes|Columbidae|Raphus"
part_type:
- "HEAD"
- "FOOT"
preservation_method: DRIED_WHOLE
collection_date: "pre-1662"
collection_location:
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"
wikidata_id: "Q193493"
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.
taxon_name: "Megatherium americanum Cuvier, 1796"
common_name:
- "Giant Ground Sloth"
taxonomic_rank: "SPECIES"
part_type:
- "SKELETON"
preservation_method: FOSSIL_PREPARED
collection_locality_text: "Argentina, Buenos Aires Province"
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.
taxon_name: "Quercus robur L."
common_name:
- "English Oak"
- "Pedunculate Oak"
taxonomic_rank: "SPECIES"
taxonomic_authority: "Linnaeus, 1753"
specimen_type: "LECTOTYPE"
is_type_specimen: true
type_status: "Lectotype of Quercus robur L., designated by Schwarz (1936)"
part_type:
- "LEAF"
- "FLOWER"
preservation_method: DRIED_PRESSED
collection_date: "1750s"
collector:
- "Carl Linnaeus"
current_keeper: "https://nde.nl/ontology/hc/custodian/uk/royal-botanic-gardens-kew"
description: "Oak type specimen at Royal Botanic Gardens, Kew"
# Slot definitions (not inherited from ExhibitedObject)
slots:
taxon_name:
description: Scientific name (Linnean binomial)
range: string
slot_uri: dwc:scientificName
common_name:
description: Common/vernacular name(s)
range: string
multivalued: true
slot_uri: dwc:vernacularName
common_name_language:
description: Language code for common names
range: string
multivalued: true
slot_uri: dcterms:language
taxonomic_rank:
description: Taxonomic rank (SPECIES, GENUS, etc.)
range: string
slot_uri: dwc:taxonRank
taxonomic_authority:
description: Author and year of scientific name
range: string
slot_uri: dwc:scientificNameAuthorship
higher_classification:
description: Full taxonomic hierarchy
range: string
slot_uri: dwc:higherClassification
taxon_remarks:
description: Notes about taxonomic identification
range: string
slot_uri: dwc:taxonRemarks
identification_qualifier:
description: Qualifier for uncertain identifications (cf., aff.)
range: string
slot_uri: dwc:identificationQualifier
identified_by:
description: Person who made the identification
range: string
multivalued: true
slot_uri: dwc:identifiedBy
date_identified:
description: Date of current identification
range: date
slot_uri: dwc:dateIdentified
specimen_type:
description: Nomenclatural type status
range: string
slot_uri: dwc:typeStatus
is_type_specimen:
description: Whether this is a type specimen
range: boolean
type_status:
description: Full type status statement
range: string
slot_uri: dwc:typeStatus
sex:
description: Sex of organism
range: string
slot_uri: dwc:sex
life_stage:
description: Life stage when collected
range: string
slot_uri: dwc:lifeStage
part_type:
description: Part(s) of organism represented
range: string
multivalued: true
slot_uri: dwc:preparations
specimen_count:
description: Number of individuals in specimen
range: integer
slot_uri: dwc:individualCount
preservation_method:
description: Primary preservation method
range: PreservationMethodEnum
slot_uri: dwc:preparations
preservative_details:
description: Specific preservation details
range: string
preparation_date:
description: Date specimen was prepared
range: date
prepared_by:
description: Person/institution that prepared specimen
range: string
slot_uri: crm:P14_carried_out_by
collection_date:
description: Date specimen was collected
range: string
slot_uri: dwc:eventDate
collection_location:
description: Structured collection location
range: CustodianPlace
slot_uri: dwc:locality
collection_locality_text:
description: Verbatim locality description
range: string
slot_uri: dwc:verbatimLocality
collector:
description: Person(s) who collected specimen
range: string
multivalued: true
slot_uri: dwc:recordedBy
field_number:
description: Collector's field number
range: string
slot_uri: dwc:fieldNumber
habitat:
description: Habitat description
range: string
slot_uri: dwc:habitat
associated_taxa:
description: Associated taxa (host, parasite, etc.)
range: string
multivalued: true
slot_uri: dwc:associatedTaxa
iucn_status:
description: IUCN Red List status
range: string
cites_appendix:
description: CITES appendix listing
range: string
legal_provenance_notes:
description: Notes on legal status for CITES species
range: string
gbif_id:
description: GBIF occurrence ID
range: string
slot_uri: dwc:occurrenceID
bold_id:
description: BOLD barcode record ID
range: string
genbank_accessions:
description: GenBank accession numbers
range: string
multivalued: true