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 b34a8ac777 Update LinkML manifest generation timestamp and enhance MappingExplorer with schema validation 
- Updated the generated timestamp in the LinkML manifest file.
- Added new CSS styles for schema status and warning indicators in MappingExplorer.
- Implemented schema validation logic in MappingExplorer to check field validity against the loaded LinkML schema.
- Enhanced the UI to display schema status and warnings for invalid fields in the mapping interface.
- Refactored field details panel to show schema validity messages for target classes and slots.
- Updated various target classes and slots in custodian data mappings for consistency and accuracy.
2026-02-18 18:44:03 +01:00

788 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:
- ./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.
Reference in a new issue View git blame Copy permalink