kempersc/glam
1
0
Fork 0
Code Issues Pull requests Projects Releases Packages Wiki Activity Actions
glam/frontend/public/schemas/20251121/linkml/modules/classes/BiologicalObject.yaml
kempersc f9f3cc8e74 fix: resolve YAML import indentation and add missing slot descriptions 
Schema Improvements:
- Fix YAML import indentation across 800+ class files (sed: '^- ../' → '  - ../')
- Add descriptions to 26 inline slots missing them (lint warnings)
- Fix malformed imports in BirthPlace.yaml and CustodianObservation.yaml

Validation Results:
- linkml-lint: 4 warnings (intentional SCREAMING_CASE tier names)
- gen-owl: SUCCESS (164,069 lines generated)
- gen-json-schema: SUCCESS (9.4MB generated)

Files affected: 1,034 files, +23,908 -15,200 lines
2026-01-16 00:09:28 +01:00

536 lines
20 KiB
YAML
Raw Blame History

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
# REMOVED 2026-01-15: ../slots/wikidata_id - inherits has_or_had_identifier from ExhibitedObject (Rule 53)
- ./WikiDataIdentifier
# associated_taxa REMOVED - migrated to is_or_was_associated_with (Rule 53)
- ../slots/is_or_was_associated_with
- ./Taxon
# bold_id REMOVED - migrated to has_or_had_identifier with BOLDIdentifier class (Rule 53)
- ../slots/has_or_had_identifier
- ./BOLDIdentifier
- ../slots/cites_appendix
- ../slots/collection_date
- ../slots/collection_locality_text
- ../slots/collection_location
- ../slots/collector
- ../slots/common_name
- ../slots/common_name_language
- ../slots/has_or_had_custodian_type
- ../slots/date_identified
- ../slots/field_number
- ../slots/gbif_id
- ../slots/genbank_accession
- ../slots/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
# REMOVED 2026-01-14: ../slots/taxon_name - migrated to has_or_had_label with TaxonName (Rule 53)
- ../slots/has_or_had_label
- ./TaxonName
- ../slots/has_or_had_comment # was: taxon_remark - migrated per Rule 53
- ../slots/taxonomic_authority
- ../slots/taxonomic_rank
- ../slots/template_specificity
# REMOVED 2026-01-14: ../slots/type_status - migrated to has_or_had_status with TypeStatus
- ../slots/has_or_had_status
- ./TypeStatus
- ./SpecificityAnnotation
- ./TemplateSpecificityScores
- ../slots/has_associated_taxon
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- `taxon_name` → dwc:scientificName\n- `collection_date`\
\ → dwc:eventDate\n- `collector` → dwc:recordedBy\n- `preservation_method` → dwc:preparations\n- `gbif_id` → dwc:occurrenceID\
\ (GBIF)\n\n**Taxonomic Data Model**:\n\n```\nBiologicalObject\n │\n ├── taxon_name (scientific name: \"Raphus\
\ cucullatus\")\n │ │\n │ ├── common_name (\"Dodo\")\n │ ├── taxonomic_rank (SPECIES)\n \
\ │ ├── taxonomic_authority (\"Linnaeus, 1758\")\n │ └── higher_classification (Aves → Columbiformes\
\ → Columbidae)\n │\n ├── specimen_data\n │ │\n │ ├── specimen_type (HOLOTYPE, PARATYPE, etc.)\n\
\ │ ├── is_type_specimen (boolean)\n │ ├── sex (MALE, FEMALE, UNKNOWN)\n │ ├── life_stage\
\ (ADULT, JUVENILE, LARVA, etc.)\n │ └── part_type (SKELETON, SKIN, SHELL, etc.)\n │\n ├── preservation\n\
\ │ │\n │ ├── preservation_method (PreservationMethodEnum)\n │ └── preservative_details (specific\
\ chemicals, methods)\n │\n └── collection_event\n │\n ├── collection_date (when collected)\n\
\ ├── collection_location (where collected)\n ├── collector (who collected)\n └── 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_taxa REMOVED - migrated to is_or_was_associated_with (Rule 53)
- is_or_was_associated_with
# bold_id REMOVED - migrated to has_or_had_identifier with BOLDIdentifier (Rule 53)
- has_or_had_identifier
- cites_appendix
- collection_date
- collection_locality_text
- collection_location
- collector
- common_name
- common_name_language
- has_or_had_custodian_type
- date_identified
- field_number
- gbif_id
- genbank_accession
- 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
# REMOVED 2026-01-14: taxon_name - migrated to has_or_had_label with TaxonName (Rule 53)
- has_or_had_label # was: taxon_name - migrated per Rule 53
- has_or_had_comment # was: taxon_remark - migrated per Rule 53
- taxonomic_authority
- taxonomic_rank
- template_specificity
# REMOVED 2026-01-14: type_status - migrated to has_or_had_status with TypeStatus
- 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: >-
MIGRATED from bold_id (Rule 53).
BOLD (Barcode of Life Data System) identifier for DNA barcode records.
Range narrowed to BOLDIdentifier class.
range: BOLDIdentifier
multivalued: true
inlined_as_list: true
examples:
- value:
id: https://nde.nl/ontology/hc/bold-id/NLNAT001-21
identifier_value: NLNAT001-21
description: BOLD identifier for specimen
# DEPRECATED: taxon_name - migrated to has_or_had_label (2026-01-14, Rule 53)
# taxon_name:
# required: true
# range: string
# examples:
# - value: Raphus cucullatus (Linnaeus, 1758)
# description: Dodo with nomenclatural authority
# - value: Panthera leo
# description: Lion (authority omitted)
has_or_had_label: # was: taxon_name - migrated per Rule 53
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)
common_name:
required: false
range: string
multivalued: true
examples:
- value: Dodo
- value: Lion
- value: Coast Redwood
common_name_language:
required: false
range: string
multivalued: true
examples:
- value: en
- value: nl
taxonomic_rank:
required: false
range: string
examples:
- value: SPECIES
- value: SUBSPECIES
- value: GENUS
description: When only identified to genus level
taxonomic_authority:
required: false
range: string
examples:
- value: Linnaeus, 1758
- value: (Gray, 1821)
description: Parentheses indicate original genus differs
higher_classification:
required: false
range: string
examples:
- value: Animalia|Chordata|Aves|Columbiformes|Columbidae|Raphus
description: Dodo classification
has_or_had_comment: # was: taxon_remark - migrated per Rule 53
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
date_identified:
required: false
range: date
examples:
- value: '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
# REMOVED 2026-01-14: type_status - migrated to has_or_had_status with TypeStatus
# type_status:
# required: false
# range: string
# examples:
# - value: Holotype of Raphus cucullatus Linnaeus, 1758
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:
status_value: "Holotype of Raphus cucullatus Linnaeus, 1758"
status_type: "nomenclatural"
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°C
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
collection_date:
required: false
range: string
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
examples:
- value:
place_name: Mauritius
country: MU
latitude: -20.2
longitude: 57.5
collection_locality_text:
required: false
range: string
examples:
- value: Mauritius, near Port Louis, in forest
- value: 'Indonesia: Java: Mt. Gede, 1500m'
collector:
required: false
range: string
multivalued: true
examples:
- value: Alfred Russel Wallace
- value: Charles Darwin
field_number:
required: false
range: string
examples:
- value: ARW-1234
- value: CD-HMS Beagle-567
habitat:
required: false
range: string
examples:
- value: Tropical rainforest, understory
- value: Coral reef, depth 15m
has_associated_taxon:
required: false
range: string
multivalued: true
examples:
- value: host:Quercus robur
description: Insect collected from oak tree
- value: parasite of:Cervus elaphus
iucn_status:
required: false
range: string
examples:
- value: EX
description: Extinct (e.g., Dodo)
- value: CR
description: Critically Endangered
cites_appendix:
required: false
range: string
examples:
- value: APPENDIX_I
description: Most endangered, trade prohibited
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
bold_id:
required: false
range: string
examples:
- value: BOLD:AAA0001
genbank_accession:
required: false
range: string
multivalued: true
examples:
- value: MW123456
- value: MN987654
has_or_had_custodian_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"
# taxon_name: Raphus cucullatus (Linnaeus, 1758) - MIGRATED to has_or_had_label (2026-01-14)
has_or_had_label:
scientific_name: "Raphus cucullatus (Linnaeus, 1758)"
authorship: "Linnaeus, 1758"
taxonomic_rank: SPECIES
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
# MIGRATED 2026-01-15: wikidata_id → has_or_had_identifier (Rule 53)
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.
'
# taxon_name: Megatherium americanum Cuvier, 1796 - MIGRATED to has_or_had_label (2026-01-14)
has_or_had_label:
scientific_name: "Megatherium americanum Cuvier, 1796"
authorship: "Cuvier, 1796"
taxonomic_rank: SPECIES
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. - MIGRATED to has_or_had_label (2026-01-14)
has_or_had_label:
scientific_name: "Quercus robur L."
authorship: "L."
taxonomic_rank: SPECIES
common_name:
- English Oak
- Pedunculate Oak
taxonomic_rank: SPECIES
taxonomic_authority: Linnaeus, 1753
specimen_type: LECTOTYPE
is_type_specimen: true
has_or_had_status: # was: type_status
status_value: Lectotype of Quercus robur L., designated by Schwarz (1936)
status_type: nomenclatural
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
Reference in a new issue View git blame Copy permalink