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bican_biolink.yaml
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id: https://w3id.org/biolink/bican-biolink-schema
name: bican-biolink-schema
title: BICAN Biolink Schema
description: The BICAN Biolink schema contains a subset of classes from the Biolink
Model that are frequently used in BICAN schemas. The Biolink model represents life-sciences
data and defines entities and association taxonomy classes.
version: 4.2.0-rc.2
imports:
- linkml:types
license: https://creativecommons.org/publicdomain/zero/1.0/
prefixes:
AGRKB:
prefix_prefix: AGRKB
prefix_reference: https://www.alliancegenome.org/
apollo:
prefix_prefix: apollo
prefix_reference: https://github.com/GMOD/Apollo
AspGD:
prefix_prefix: AspGD
prefix_reference: http://www.aspergillusgenome.org/cgi-bin/locus.pl?dbid=
biolink:
prefix_prefix: biolink
prefix_reference: https://w3id.org/biolink/vocab/
bioschemas:
prefix_prefix: bioschemas
prefix_reference: https://bioschemas.org/
linkml:
prefix_prefix: linkml
prefix_reference: https://w3id.org/linkml/
CAID:
prefix_prefix: CAID
prefix_reference: http://reg.clinicalgenome.org/redmine/projects/registry/genboree_registry/by_caid?caid=
CHADO:
prefix_prefix: CHADO
prefix_reference: http://gmod.org/wiki/Chado/
ChemBank:
prefix_prefix: ChemBank
prefix_reference: http://chembank.broadinstitute.org/chemistry/viewMolecule.htm?cbid=
CHEMBL.MECHANISM:
prefix_prefix: CHEMBL.MECHANISM
prefix_reference: https://www.ebi.ac.uk/chembl/mechanism/inspect/
CID:
prefix_prefix: CID
prefix_reference: http://pubchem.ncbi.nlm.nih.gov/compound/
CLINVAR:
prefix_prefix: CLINVAR
prefix_reference: http://identifiers.org/clinvar
COAR_RESOURCE:
prefix_prefix: COAR_RESOURCE
prefix_reference: http://purl.org/coar/resource_type/
COG:
prefix_prefix: COG
prefix_reference: https://www.ncbi.nlm.nih.gov/research/cog-project/
ComplexPortal:
prefix_prefix: ComplexPortal
prefix_reference: https://www.ebi.ac.uk/complexportal/complex/
CPT:
prefix_prefix: CPT
prefix_reference: https://www.ama-assn.org/practice-management/cpt/
CTD.CHEMICAL:
prefix_prefix: CTD.CHEMICAL
prefix_reference: http://ctdbase.org/detail.go?type=chem&acc=
CTD.DISEASE:
prefix_prefix: CTD.DISEASE
prefix_reference: http://ctdbase.org/detail.go?type=disease&db=MESH&acc=
CTD.GENE:
prefix_prefix: CTD.GENE
prefix_reference: http://ctdbase.org/detail.go?type=gene&acc=
CTD:
prefix_prefix: CTD
prefix_reference: http://ctdbase.org/
DGIdb:
prefix_prefix: DGIdb
prefix_reference: https://www.dgidb.org/interaction_types
dcat:
prefix_prefix: dcat
prefix_reference: http://www.w3.org/ns/dcat#
dct:
prefix_prefix: dct
prefix_reference: http://purl.org/dc/terms/
dcid:
prefix_prefix: dcid
prefix_reference: https://datacommons.org/browser/
doi:
prefix_prefix: doi
prefix_reference: https://doi.org/
DOID-PROPERTY:
prefix_prefix: DOID-PROPERTY
prefix_reference: http://purl.obolibrary.org/obo/doid#
DrugCentral:
prefix_prefix: DrugCentral
prefix_reference: http://drugcentral.org/drugcard/
ECTO:
prefix_prefix: ECTO
prefix_reference: http://purl.obolibrary.org/obo/ECTO_
EDAM-DATA:
prefix_prefix: EDAM-DATA
prefix_reference: http://edamontology.org/data_
EDAM-FORMAT:
prefix_prefix: EDAM-FORMAT
prefix_reference: http://edamontology.org/format_
EDAM-OPERATION:
prefix_prefix: EDAM-OPERATION
prefix_reference: http://edamontology.org/operation_
EDAM-TOPIC:
prefix_prefix: EDAM-TOPIC
prefix_reference: http://edamontology.org/topic_
EFO:
prefix_prefix: EFO
prefix_reference: http://www.ebi.ac.uk/efo/EFO_
ExO:
prefix_prefix: ExO
prefix_reference: http://purl.obolibrary.org/obo/ExO_
fabio:
prefix_prefix: fabio
prefix_reference: http://purl.org/spar/fabio/
foaf:
prefix_prefix: foaf
prefix_reference: http://xmlns.com/foaf/0.1/
foodb.compound:
prefix_prefix: foodb.compound
prefix_reference: http://foodb.ca/compounds/
foodb.food:
prefix_prefix: foodb.food
prefix_reference: http://foodb.ca/foods/
FYECO:
prefix_prefix: FYECO
prefix_reference: https://www.pombase.org/term/
FYPO:
prefix_prefix: FYPO
prefix_reference: http://purl.obolibrary.org/obo/FYPO_
gff3:
prefix_prefix: gff3
prefix_reference: https://github.com/The-Sequence-Ontology/Specifications/blob/master/gff3.md#
GOREL:
prefix_prefix: GOREL
prefix_reference: http://purl.obolibrary.org/obo/GOREL_
GOP:
prefix_prefix: GOP
prefix_reference: http://purl.obolibrary.org/obo/go#
gpi:
prefix_prefix: gpi
prefix_reference: https://github.com/geneontology/go-annotation/blob/master/specs/gpad-gpi-2-0.md#
GSID:
prefix_prefix: GSID
prefix_reference: https://scholar.google.com/citations?user=
GTEx:
prefix_prefix: GTEx
prefix_reference: https://www.gtexportal.org/home/gene/
GTOPDB:
prefix_prefix: GTOPDB
prefix_reference: https://www.guidetopharmacology.org/GRAC/LigandDisplayForward?ligandId=
gtpo:
prefix_prefix: gtpo
prefix_reference: https://rdf.guidetopharmacology.org/ns/gtpo#
HANCESTRO:
prefix_prefix: HANCESTRO
prefix_reference: http://www.ebi.ac.uk/ancestro/ancestro_
HCPCS:
prefix_prefix: HCPCS
prefix_reference: http://purl.bioontology.org/ontology/HCPCS/
HsapDv:
prefix_prefix: HsapDv
prefix_reference: http://purl.obolibrary.org/obo/HsapDv_
ICD10:
prefix_prefix: ICD10
prefix_reference: https://icd.codes/icd9cm/
ICD9:
prefix_prefix: ICD9
prefix_reference: http://translator.ncats.nih.gov/ICD9_
interpro:
prefix_prefix: interpro
prefix_reference: https://www.ebi.ac.uk/interpro/entry/
INO:
prefix_prefix: INO
prefix_reference: http://purl.obolibrary.org/obo/INO_
isbn:
prefix_prefix: isbn
prefix_reference: https://www.isbn-international.org/identifier/
isni:
prefix_prefix: isni
prefix_reference: https://isni.org/isni/
issn:
prefix_prefix: issn
prefix_reference: https://portal.issn.org/resource/ISSN/
ncats.drug:
prefix_prefix: ncats.drug
prefix_reference: https://drugs.ncats.io/drug/
KEGG.BRITE:
prefix_prefix: KEGG.BRITE
prefix_reference: 'https://bioregistry.io/kegg.brite:'
KEGG:
prefix_prefix: KEGG
prefix_reference: http://www.kegg.jp/entry/
KEGG.GENES:
prefix_prefix: KEGG.GENES
prefix_reference: 'https://bioregistry.io/kegg.genes:bsu:'
KEGG.PATHWAY:
prefix_prefix: KEGG.PATHWAY
prefix_reference: 'https://bioregistry.io/kegg.pathway:'
KEGG.RCLASS:
prefix_prefix: KEGG.RCLASS
prefix_reference: 'https://www.genome.jp/dbget-bin/www_bget?rc:'
LOINC:
prefix_prefix: LOINC
prefix_reference: http://loinc.org/rdf/
MAXO:
prefix_prefix: MAXO
prefix_reference: http://purl.obolibrary.org/obo/MAXO_
medgen:
prefix_prefix: medgen
prefix_reference: https://www.ncbi.nlm.nih.gov/medgen/
metacyc.reaction:
prefix_prefix: metacyc.reaction
prefix_reference: 'http://identifiers.org/metacyc.reaction:'
METANETX.REACTION:
prefix_prefix: METANETX.REACTION
prefix_reference: https://www.metanetx.org/equa_info/
MESH:
prefix_prefix: MESH
prefix_reference: http://id.nlm.nih.gov/mesh/
MI:
prefix_prefix: MI
prefix_reference: http://purl.obolibrary.org/obo/MI_
mirbase:
prefix_prefix: mirbase
prefix_reference: http://identifiers.org/mirbase
mmmp.biomaps:
prefix_prefix: mmmp.biomaps
prefix_reference: 'https://bioregistry.io/mmmp.biomaps:'
MmusDv:
prefix_prefix: MmusDv
prefix_reference: http://purl.obolibrary.org/obo/MMUSDV_
MSigDB:
prefix_prefix: MSigDB
prefix_reference: https://www.gsea-msigdb.org/gsea/msigdb/
NBO-PROPERTY:
prefix_prefix: NBO-PROPERTY
prefix_reference: http://purl.obolibrary.org/obo/nbo#
ncats.bioplanet:
prefix_prefix: ncats.bioplanet
prefix_reference: https://tripod.nih.gov/bioplanet/detail.jsp?pid=
NCBIGene:
prefix_prefix: NCBIGene
prefix_reference: http://identifiers.org/ncbigene/
NCIT-OBO:
prefix_prefix: NCIT-OBO
prefix_reference: http://purl.obolibrary.org/obo/ncit#
NDDF:
prefix_prefix: NDDF
prefix_reference: http://purl.bioontology.org/ontology/NDDF/
NLMID:
prefix_prefix: NLMID
prefix_reference: https://www.ncbi.nlm.nih.gov/nlmcatalog/?term=
OBAN:
prefix_prefix: OBAN
prefix_reference: http://purl.org/oban/
OMIM.PS:
prefix_prefix: OMIM.PS
prefix_reference: https://www.omim.org/phenotypicSeries/
ORCID:
prefix_prefix: ORCID
prefix_reference: https://orcid.org/
orphanet:
prefix_prefix: orphanet
prefix_reference: http://www.orpha.net/ORDO/Orphanet_
os:
prefix_prefix: os
prefix_reference: https://github.com/cmungall/owlstar/blob/master/owlstar.ttl
PANTHER.FAMILY:
prefix_prefix: PANTHER.FAMILY
prefix_reference: http://www.pantherdb.org/panther/family.do?clsAccession=
PathWhiz:
prefix_prefix: PathWhiz
prefix_reference: http://smpdb.ca/pathways/#
pav:
prefix_prefix: pav
prefix_reference: http://purl.org/pav/
PHARMGKB.CHEMICAL:
prefix_prefix: PHARMGKB.CHEMICAL
prefix_reference: https://www.pharmgkb.org/chemical/
PHARMGKB.DISEASE:
prefix_prefix: PHARMGKB.DISEASE
prefix_reference: https://www.pharmgkb.org/disease/
PHARMGKB.GENE:
prefix_prefix: PHARMGKB.GENE
prefix_reference: https://www.pharmgkb.org/gene/
PHARMGKB.PATHWAYS:
prefix_prefix: PHARMGKB.PATHWAYS
prefix_reference: https://www.pharmgkb.org/pathway/
PHARMGKB.VARIANT:
prefix_prefix: PHARMGKB.VARIANT
prefix_reference: https://www.pharmgkb.org/variant/
PHAROS:
prefix_prefix: PHAROS
prefix_reference: http://pharos.nih.gov
PomBase:
prefix_prefix: PomBase
prefix_reference: https://www.pombase.org/gene/
prov:
prefix_prefix: prov
prefix_reference: http://www.w3.org/ns/prov#
qud:
prefix_prefix: qud
prefix_reference: http://qudt.org/1.1/schema/qudt#
REPODB:
prefix_prefix: REPODB
prefix_reference: http://apps.chiragjpgroup.org/repoDB/
ResearchID:
prefix_prefix: ResearchID
prefix_reference: https://publons.com/researcher/
RO:
prefix_prefix: RO
prefix_reference: http://purl.obolibrary.org/obo/RO_
RXNORM:
prefix_prefix: RXNORM
prefix_reference: http://purl.bioontology.org/ontology/RXNORM/
RXCUI:
prefix_prefix: RXCUI
prefix_reference: https://mor.nlm.nih.gov/RxNav/search?searchBy=RXCUI&searchTerm=
schema:
prefix_prefix: schema
prefix_reference: http://schema.org/
ScopusID:
prefix_prefix: ScopusID
prefix_reference: https://www.scopus.com/authid/detail.uri?authorId=
SEED.REACTION:
prefix_prefix: SEED.REACTION
prefix_reference: https://modelseed.org/biochem/reactions/
SEMMEDDB:
prefix_prefix: SEMMEDDB
prefix_reference: https://skr3.nlm.nih.gov/SemMedDB
SIO:
prefix_prefix: SIO
prefix_reference: http://semanticscience.org/resource/SIO_
SNOMEDCT:
prefix_prefix: SNOMEDCT
prefix_reference: http://snomed.info/id/
SPDI:
prefix_prefix: SPDI
prefix_reference: https://api.ncbi.nlm.nih.gov/variation/v0/spdi/
UBERGRAPH:
prefix_prefix: UBERGRAPH
prefix_reference: http://translator.renci.org/ubergraph-axioms.ofn#
UBERON_CORE:
prefix_prefix: UBERON_CORE
prefix_reference: http://purl.obolibrary.org/obo/uberon/core#
UBERON_NONAMESPACE:
prefix_prefix: UBERON_NONAMESPACE
prefix_reference: http://purl.obolibrary.org/obo/core#
STY:
prefix_prefix: STY
prefix_reference: http://purl.bioontology.org/ontology/STY/
UMLSSG:
prefix_prefix: UMLSSG
prefix_reference: https://lhncbc.nlm.nih.gov/semanticnetwork/download/sg_archive/SemGroups-v04.txt
UniProtKB:
prefix_prefix: UniProtKB
prefix_reference: http://purl.uniprot.org/uniprot/
UNIPROT.ISOFORM:
prefix_prefix: UNIPROT.ISOFORM
prefix_reference: http://purl.uniprot.org/isoforms/
VANDF:
prefix_prefix: VANDF
prefix_reference: https://www.nlm.nih.gov/research/umls/sourcereleasedocs/current/VANDF/
UO-PROPERTY:
prefix_prefix: UO-PROPERTY
prefix_reference: http://purl.obolibrary.org/obo/uo#
VMC:
prefix_prefix: VMC
prefix_reference: https://github.com/ga4gh/vr-spec/
WBls:
prefix_prefix: WBls
prefix_reference: http://purl.obolibrary.org/obo/WBls_
WBbt:
prefix_prefix: WBbt
prefix_reference: http://purl.obolibrary.org/obo/WBbt_
WBVocab:
prefix_prefix: WBVocab
prefix_reference: http://bio2rdf.org/wormbase_vocabulary
WIKIDATA:
prefix_prefix: WIKIDATA
prefix_reference: https://www.wikidata.org/entity/
WIKIDATA_PROPERTY:
prefix_prefix: WIKIDATA_PROPERTY
prefix_reference: https://www.wikidata.org/prop/
wgs:
prefix_prefix: wgs
prefix_reference: http://www.w3.org/2003/01/geo/wgs84_pos
XPO:
prefix_prefix: XPO
prefix_reference: http://purl.obolibrary.org/obo/XPO_
Xenbase:
prefix_prefix: Xenbase
prefix_reference: http://www.xenbase.org/gene/showgene.do?method=display&geneId=
PMC:
prefix_prefix: PMC
prefix_reference: http://europepmc.org/articles/PMC
emit_prefixes:
- rdf
- rdfs
- xsd
- skos
- oboInOwl
- BIOGRID
- SO
default_curi_maps:
- obo_context
- idot_context
- monarch_context
- semweb_context
default_prefix: biolink
default_range: string
subsets:
model_organism_database:
name: model_organism_database
definition_uri: https://w3id.org/biolink/vocab/ModelOrganismDatabase
description: Subset that is relevant for a typical Model Organism Database (MOD)
from_schema: https://w3id.org/biolink/biolink-model
translator_minimal:
name: translator_minimal
definition_uri: https://w3id.org/biolink/vocab/TranslatorMinimal
description: Minimum subset of translator work
from_schema: https://w3id.org/biolink/biolink-model
samples:
name: samples
definition_uri: https://w3id.org/biolink/vocab/Samples
description: Sample/biosample datamodel
from_schema: https://w3id.org/biolink/biolink-model
testing:
name: testing
definition_uri: https://w3id.org/biolink/vocab/Testing
description: TBD
from_schema: https://w3id.org/biolink/biolink-model
types:
chemical formula value:
name: chemical formula value
definition_uri: https://w3id.org/biolink/vocab/ChemicalFormulaValue
description: A chemical formula
notes:
- Should be implemented as a stronger type
from_schema: https://w3id.org/biolink/biolink-model
base: str
uri: xsd:string
iri type:
name: iri type
definition_uri: https://w3id.org/biolink/vocab/IriType
description: An IRI
from_schema: https://w3id.org/biolink/biolink-model
typeof: uriorcurie
base: URIorCURIE
uri: xsd:anyURI
repr: str
label type:
name: label type
definition_uri: https://w3id.org/biolink/vocab/LabelType
description: A string that provides a human-readable name for an entity
from_schema: https://w3id.org/biolink/biolink-model
typeof: string
base: str
uri: xsd:string
predicate type:
name: predicate type
definition_uri: https://w3id.org/biolink/vocab/PredicateType
description: A CURIE from the biolink related_to hierarchy. For example, biolink:related_to,
biolink:causes, biolink:treats.
from_schema: https://w3id.org/biolink/biolink-model
typeof: uriorcurie
base: URIorCURIE
uri: xsd:anyURI
repr: str
narrative text:
name: narrative text
definition_uri: https://w3id.org/biolink/vocab/NarrativeText
description: A string that provides a human-readable description of something
from_schema: https://w3id.org/biolink/biolink-model
typeof: string
base: str
uri: xsd:string
symbol type:
name: symbol type
definition_uri: https://w3id.org/biolink/vocab/SymbolType
from_schema: https://w3id.org/biolink/biolink-model
typeof: string
base: str
uri: xsd:string
frequency value:
name: frequency value
definition_uri: https://w3id.org/biolink/vocab/FrequencyValue
from_schema: https://w3id.org/biolink/biolink-model
typeof: string
base: str
uri: UO:0000105
percentage frequency value:
name: percentage frequency value
definition_uri: https://w3id.org/biolink/vocab/PercentageFrequencyValue
from_schema: https://w3id.org/biolink/biolink-model
typeof: double
base: float
uri: UO:0000187
quotient:
name: quotient
definition_uri: https://w3id.org/biolink/vocab/Quotient
from_schema: https://w3id.org/biolink/biolink-model
aliases:
- ratio
typeof: double
base: float
uri: UO:0010006
unit:
name: unit
id_prefixes:
- UO
definition_uri: https://w3id.org/biolink/vocab/Unit
from_schema: https://w3id.org/biolink/biolink-model
exact_mappings:
- qud:Unit
typeof: string
base: str
uri: UO:0000000
time type:
name: time type
definition_uri: https://w3id.org/biolink/vocab/TimeType
from_schema: https://w3id.org/biolink/biolink-model
typeof: time
base: XSDTime
uri: xsd:time
repr: str
biological sequence:
name: biological sequence
definition_uri: https://w3id.org/biolink/vocab/BiologicalSequence
from_schema: https://w3id.org/biolink/biolink-model
typeof: string
base: str
uri: xsd:string
slots:
has attribute:
name: has attribute
definition_uri: https://w3id.org/biolink/vocab/has_attribute
description: connects any entity to an attribute
in_subset:
- samples
from_schema: https://w3id.org/biolink/biolink-model
exact_mappings:
- SIO:000008
close_mappings:
- OBI:0001927
narrow_mappings:
- OBAN:association_has_subject_property
- OBAN:association_has_object_property
- CPT:has_possibly_included_panel_element
- DRUGBANK:category
- EFO:is_executed_in
- HANCESTRO:0301
- LOINC:has_action_guidance
- LOINC:has_adjustment
- LOINC:has_aggregation_view
- LOINC:has_approach_guidance
- LOINC:has_divisor
- LOINC:has_exam
- LOINC:has_method
- LOINC:has_modality_subtype
- LOINC:has_object_guidance
- LOINC:has_scale
- LOINC:has_suffix
- LOINC:has_time_aspect
- LOINC:has_time_modifier
- LOINC:has_timing_of
- NCIT:R88
- NCIT:eo_disease_has_property_or_attribute
- NCIT:has_data_element
- NCIT:has_pharmaceutical_administration_method
- NCIT:has_pharmaceutical_basic_dose_form
- NCIT:has_pharmaceutical_intended_site
- NCIT:has_pharmaceutical_release_characteristics
- NCIT:has_pharmaceutical_state_of_matter
- NCIT:has_pharmaceutical_transformation
- NCIT:is_qualified_by
- NCIT:qualifier_applies_to
- NCIT:role_has_domain
- NCIT:role_has_range
- INO:0000154
- HANCESTRO:0308
- OMIM:has_inheritance_type
- orphanet:C016
- orphanet:C017
- RO:0000053
- RO:0000086
- RO:0000087
- SNOMED:has_access
- SNOMED:has_clinical_course
- SNOMED:has_count_of_base_of_active_ingredient
- SNOMED:has_dose_form_administration_method
- SNOMED:has_dose_form_release_characteristic
- SNOMED:has_dose_form_transformation
- SNOMED:has_finding_context
- SNOMED:has_finding_informer
- SNOMED:has_inherent_attribute
- SNOMED:has_intent
- SNOMED:has_interpretation
- SNOMED:has_laterality
- SNOMED:has_measurement_method
- SNOMED:has_method
- SNOMED:has_priority
- SNOMED:has_procedure_context
- SNOMED:has_process_duration
- SNOMED:has_property
- SNOMED:has_revision_status
- SNOMED:has_scale_type
- SNOMED:has_severity
- SNOMED:has_specimen
- SNOMED:has_state_of_matter
- SNOMED:has_subject_relationship_context
- SNOMED:has_surgical_approach
- SNOMED:has_technique
- SNOMED:has_temporal_context
- SNOMED:has_time_aspect
- SNOMED:has_units
- UMLS:has_structural_class
- UMLS:has_supported_concept_property
- UMLS:has_supported_concept_relationship
- UMLS:may_be_qualified_by
domain: entity
slot_uri: biolink:has_attribute
multivalued: true
owner: entity
domain_of:
- entity
range: attribute
has attribute type:
name: has attribute type
definition_uri: https://w3id.org/biolink/vocab/has_attribute_type
description: connects an attribute to a class that describes it
in_subset:
- samples
from_schema: https://w3id.org/biolink/biolink-model
narrow_mappings:
- LOINC:has_modality_type
- LOINC:has_view_type
domain: attribute
slot_uri: biolink:has_attribute_type
multivalued: false
owner: attribute
domain_of:
- attribute
range: ontology class
required: true
has qualitative value:
name: has qualitative value
definition_uri: https://w3id.org/biolink/vocab/has_qualitative_value
description: connects an attribute to a value
in_subset:
- samples
from_schema: https://w3id.org/biolink/biolink-model
domain: attribute
slot_uri: biolink:has_qualitative_value
multivalued: false
owner: attribute
domain_of:
- attribute
range: named thing
has quantitative value:
name: has quantitative value
definition_uri: https://w3id.org/biolink/vocab/has_quantitative_value
description: connects an attribute to a value
in_subset:
- samples
from_schema: https://w3id.org/biolink/biolink-model
exact_mappings:
- qud:quantityValue
narrow_mappings:
- SNOMED:has_concentration_strength_numerator_value
- SNOMED:has_presentation_strength_denominator_value
- SNOMED:has_presentation_strength_numerator_value
domain: attribute
slot_uri: biolink:has_quantitative_value
multivalued: true
owner: attribute
domain_of:
- attribute
range: quantity value
inlined: true
has numeric value:
name: has numeric value
definition_uri: https://w3id.org/biolink/vocab/has_numeric_value
description: connects a quantity value to a number
in_subset:
- samples
from_schema: https://w3id.org/biolink/biolink-model
exact_mappings:
- qud:quantityValue
domain: quantity value
slot_uri: biolink:has_numeric_value
multivalued: false
owner: quantity value
domain_of:
- quantity value
range: double
has unit:
name: has unit
definition_uri: https://w3id.org/biolink/vocab/has_unit
description: connects a quantity value to a unit
in_subset:
- samples
from_schema: https://w3id.org/biolink/biolink-model
exact_mappings:
- qud:unit
- IAO:0000039
close_mappings:
- EFO:0001697
- UO-PROPERTY:is_unit_of
narrow_mappings:
- SNOMED:has_concentration_strength_denominator_unit
- SNOMED:has_concentration_strength_numerator_unit
- SNOMED:has_presentation_strength_denominator_unit
- SNOMED:has_presentation_strength_numerator_unit
- SNOMED:has_unit_of_presentation
domain: quantity value
slot_uri: biolink:has_unit
multivalued: false
owner: quantity value
domain_of:
- quantity value
range: unit
node property:
name: node property
definition_uri: https://w3id.org/biolink/vocab/node_property
description: A grouping for any property that holds between a node and a value
from_schema: https://w3id.org/biolink/biolink-model
domain: named thing
slot_uri: biolink:node_property
owner: node property
range: string
id:
name: id
definition_uri: https://w3id.org/biolink/vocab/id
description: A unique identifier for an entity. Must be either a CURIE shorthand
for a URI or a complete URI
in_subset:
- translator_minimal
from_schema: https://w3id.org/biolink/biolink-model
exact_mappings:
- AGRKB:primaryId
- gff3:ID
- gpi:DB_Object_ID
domain: entity
slot_uri: biolink:id
identifier: true
owner: entity
domain_of:
- ontology class
- entity
range: string
required: true
iri:
name: iri
definition_uri: https://w3id.org/biolink/vocab/iri
description: An IRI for an entity. This is determined by the id using expansion
rules.
in_subset:
- translator_minimal
- samples
from_schema: https://w3id.org/biolink/biolink-model
exact_mappings:
- WIKIDATA_PROPERTY:P854
slot_uri: biolink:iri
owner: entity
domain_of:
- attribute
- entity
range: iri type
type:
name: type
definition_uri: https://w3id.org/biolink/vocab/type
from_schema: https://w3id.org/biolink/biolink-model
mappings:
- rdf:type
exact_mappings:
- gff3:type
- gpi:DB_Object_Type
domain: entity
slot_uri: rdf:type
multivalued: true
owner: entity
domain_of:
- entity
range: string
category:
name: category
definition_uri: https://w3id.org/biolink/vocab/category
description: 'Name of the high level ontology class in which this entity is categorized.
Corresponds to the label for the biolink entity type class. In a neo4j database
this MAY correspond to the neo4j label tag. In an RDF database it should be
a biolink model class URI. This field is multi-valued. It should include values
for ancestors of the biolink class; for example, a protein such as Shh would
have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`.
In an RDF database, nodes will typically have an rdf:type triples. This can
be to the most specific biolink class, or potentially to a class more specific
than something in biolink. For example, a sequence feature `f` may have a rdf:type
assertion to a SO class such as TF_binding_site, which is more specific than
anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity,
biolink:NamedThing}. NOTE: The category slot was modified to have a curie range
and a pattern for bican categories.'
in_subset:
- translator_minimal
from_schema: https://w3id.org/biolink/biolink-model
is_a: type
domain: entity
slot_uri: biolink:category
multivalued: true
designates_type: true
owner: entity
domain_of:
- entity
is_class_field: true
range: curie
pattern: ^bican:[A-Z][A-Za-z]+$
name:
name: name
definition_uri: https://w3id.org/biolink/vocab/name
description: A human-readable name for an attribute or entity.
in_subset:
- translator_minimal
- samples
from_schema: https://w3id.org/biolink/biolink-model
aliases:
- label
- display name
- title
mappings:
- rdfs:label
exact_mappings:
- gff3:Name
- gpi:DB_Object_Name
narrow_mappings:
- dct:title
- WIKIDATA_PROPERTY:P1476
domain: entity
slot_uri: rdfs:label
owner: macromolecular machine mixin
domain_of:
- attribute
- entity
- macromolecular machine mixin
range: label type
symbol:
name: symbol
definition_uri: https://w3id.org/biolink/vocab/symbol
description: Symbol for a particular thing
from_schema: https://w3id.org/biolink/biolink-model
exact_mappings:
- AGRKB:symbol
- gpi:DB_Object_Symbol
is_a: node property
domain: named thing
slot_uri: biolink:symbol
owner: symbol
domain_of:
- gene
range: string
synonym:
name: synonym
definition_uri: https://w3id.org/biolink/vocab/synonym
description: Alternate human-readable names for a thing
in_subset:
- translator_minimal
from_schema: https://w3id.org/biolink/biolink-model
aliases:
- alias
narrow_mappings:
- skos:altLabel
- gff3:Alias
- AGRKB:synonyms
- gpi:DB_Object_Synonyms
- HANCESTRO:0330
- IAO:0000136
- RXNORM:has_tradename
is_a: node property
domain: named thing
slot_uri: biolink:synonym
multivalued: true
owner: named thing
domain_of:
- named thing
range: label type
deprecated:
name: deprecated
definition_uri: https://w3id.org/biolink/vocab/deprecated
description: A boolean flag indicating that an entity is no longer considered
current or valid.
from_schema: https://w3id.org/biolink/biolink-model
exact_mappings:
- oboInOwl:ObsoleteClass
slot_uri: biolink:deprecated
owner: entity
domain_of:
- entity
range: boolean
xref:
name: xref
definition_uri: https://w3id.org/biolink/vocab/xref
description: A database cross reference or alternative identifier for a NamedThing
or edge between two NamedThings. This property should point to a database record
or webpage that supports the existence of the edge, or gives more detail about
the edge. This property can be used on a node or edge to provide multiple URIs
or CURIE cross references.
in_subset:
- translator_minimal
from_schema: https://w3id.org/biolink/biolink-model
aliases:
- dbxref
- Dbxref
- DbXref
- record_url
- source_record_urls
narrow_mappings:
- gff3:Dbxref
- gpi:DB_Xrefs
domain: named thing
slot_uri: biolink:xref
multivalued: true
owner: gene
domain_of:
- named thing
- gene
range: uriorcurie
full name:
name: full name
definition_uri: https://w3id.org/biolink/vocab/full_name
description: a long-form human readable name for a thing
from_schema: https://w3id.org/biolink/biolink-model
is_a: node property
domain: named thing
slot_uri: biolink:full_name
owner: named thing
domain_of:
- named thing
range: label type
description:
name: description
definition_uri: https://w3id.org/biolink/vocab/description
description: a human-readable description of an entity
in_subset:
- translator_minimal
from_schema: https://w3id.org/biolink/biolink-model
aliases:
- definition
mappings:
- dct:description
exact_mappings:
- IAO:0000115
- skos:definitions
narrow_mappings:
- gff3:Description
slot_uri: dct:description
owner: entity
domain_of:
- entity
range: narrative text
creation date:
name: creation date
definition_uri: https://w3id.org/biolink/vocab/creation_date
description: date on which an entity was created. This can be applied to nodes
or edges
from_schema: https://w3id.org/biolink/biolink-model
aliases:
- publication date
exact_mappings:
- dct:createdOn
- WIKIDATA_PROPERTY:P577
is_a: node property
domain: named thing
slot_uri: biolink:creation_date
owner: information content entity
domain_of:
- information content entity
range: date
has taxonomic rank:
name: has taxonomic rank
definition_uri: https://w3id.org/biolink/vocab/has_taxonomic_rank
from_schema: https://w3id.org/biolink/biolink-model
mappings:
- WIKIDATA:P105
is_a: node property
domain: named thing
slot_uri: biolink:has_taxonomic_rank
multivalued: false
owner: organism taxon
domain_of:
- organism taxon
range: taxonomic rank
version:
name: version
definition_uri: https://w3id.org/biolink/vocab/version
from_schema: https://w3id.org/biolink/biolink-model
broad_mappings:
- pav:version
- owl:versionInfo
is_a: node property
domain: dataset