Skip to content

Class: OntologyClass

Description: a concept or class in an ontology, vocabulary or thesaurus. Note that nodes in a biolink compatible KG can be considered both instances of biolink classes, and OWL classes in their own right. In general you should not need to use this class directly. Instead, use the appropriate biolink class. For example, for the GO concept of endocytosis (GO:0006897), use bl:BiologicalProcess as the type.
classDiagram class OntologyClass OntologyClass <|-- Attribute OntologyClass <|-- RelationshipType OntologyClass <|-- TaxonomicRank OntologyClass <|-- NucleicAcidEntity OntologyClass <|-- RegulatoryRegion OntologyClass <|-- AccessibleDnaRegion OntologyClass <|-- TranscriptionFactorBindingSite OntologyClass <|-- BiologicalProcessOrActivity OntologyClass <|-- MolecularActivity OntologyClass <|-- BiologicalProcess OntologyClass <|-- Pathway OntologyClass <|-- PhysiologicalProcess OntologyClass <|-- Behavior OntologyClass <|-- Drug OntologyClass <|-- Gene OntologyClass <|-- Genome OntologyClass <|-- Genotype OntologyClass <|-- Haplotype OntologyClass <|-- SequenceVariant OntologyClass <|-- ReagentTargetedGene OntologyClass <|-- ExposureEvent OntologyClass <|-- GenomicBackgroundExposure OntologyClass : id

Inheritance

Slots

Name Cardinality and Range Inheritance Examples
id:
A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI
1
String
direct

Mixin Usage

mixed into description
Attribute A property or characteristic of an entity. For example, an apple may have properties such as color, shape, age, crispiness. An environmental sample may have attributes such as depth, lat, long, material.
NucleicAcidEntity A nucleic acid entity is a molecular entity characterized by availability in gene databases of nucleotide-based sequence representations of its precise sequence; for convenience of representation, partial sequences of various kinds are included.
RegulatoryRegion A region (or regions) of the genome that contains known or putative regulatory elements that act in cis- or trans- to affect the transcription of gene
AccessibleDnaRegion A region (or regions) of a chromatinized genome that has been measured to be more accessible to an enzyme such as DNase-I or Tn5 Transpose
TranscriptionFactorBindingSite A region (or regions) of the genome that contains a region of DNA known or predicted to bind a protein that modulates gene transcription
BiologicalProcessOrActivity Either an individual molecular activity, or a collection of causally connected molecular activities in a biological system.
MolecularActivity An execution of a molecular function carried out by a gene product or macromolecular complex.
BiologicalProcess One or more causally connected executions of molecular functions
Pathway None
PhysiologicalProcess None
Behavior None
Drug A substance intended for use in the diagnosis, cure, mitigation, treatment, or prevention of disease
Gene A region (or regions) that includes all of the sequence elements necessary to encode a functional transcript. A gene locus may include regulatory regions, transcribed regions and/or other functional sequence regions.
Genome A genome is the sum of genetic material within a cell or virion.
Genotype An information content entity that describes a genome by specifying the total variation in genomic sequence and/or gene expression, relative to some established background
Haplotype A set of zero or more Alleles on a single instance of a Sequence[VMC]
SequenceVariant A sequence_variant is a non exact copy of a sequence_feature or genome exhibiting one or more sequence_alteration.
ReagentTargetedGene A gene altered in its expression level in the context of some experiment as a result of being targeted by gene-knockdown reagent(s) such as a morpholino or RNAi.
GenomicBackgroundExposure A genomic background exposure is where an individual's specific genomic background of genes, sequence variants or other pre-existing genomic conditions constitute a kind of 'exposure' to the organism, leading to or influencing an outcome.

Usages

used by used in type used
Attribute has_attribute_type range OntologyClass
ChemicalRole has_attribute_type range OntologyClass
BiologicalSex has_attribute_type range OntologyClass
PhenotypicSex has_attribute_type range OntologyClass
GenotypicSex has_attribute_type range OntologyClass
SeverityValue has_attribute_type range OntologyClass
OrganismAttribute has_attribute_type range OntologyClass
PhenotypicQuality has_attribute_type range OntologyClass
Zygosity has_attribute_type range OntologyClass
ClinicalAttribute has_attribute_type range OntologyClass
ClinicalMeasurement has_attribute_type range OntologyClass
ClinicalModifier has_attribute_type range OntologyClass
ClinicalCourse has_attribute_type range OntologyClass
Onset has_attribute_type range OntologyClass
SocioeconomicAttribute has_attribute_type range OntologyClass
GenomicBackgroundExposure has_attribute_type range OntologyClass
PathologicalProcessExposure has_attribute_type range OntologyClass
PathologicalAnatomicalExposure has_attribute_type range OntologyClass
DiseaseOrPhenotypicFeatureExposure has_attribute_type range OntologyClass
ChemicalExposure has_attribute_type range OntologyClass
ComplexChemicalExposure has_attribute_type range OntologyClass
DrugExposure has_attribute_type range OntologyClass
DrugToGeneInteractionExposure has_attribute_type range OntologyClass
BioticExposure has_attribute_type range OntologyClass
GeographicExposure has_attribute_type range OntologyClass
EnvironmentalExposure has_attribute_type range OntologyClass
BehavioralExposure has_attribute_type range OntologyClass
SocioeconomicExposure has_attribute_type range OntologyClass
Association qualifiers range OntologyClass
Association subject_category range OntologyClass
Association object_category range OntologyClass
Association subject_category_closure range OntologyClass
Association object_category_closure range OntologyClass
ChemicalEntityAssessesNamedThingAssociation qualifiers range OntologyClass
ChemicalEntityAssessesNamedThingAssociation subject_category range OntologyClass
ChemicalEntityAssessesNamedThingAssociation object_category range OntologyClass
ChemicalEntityAssessesNamedThingAssociation subject_category_closure range OntologyClass
ChemicalEntityAssessesNamedThingAssociation object_category_closure range OntologyClass
ContributorAssociation qualifiers range OntologyClass
ContributorAssociation subject_category range OntologyClass
ContributorAssociation object_category range OntologyClass
ContributorAssociation subject_category_closure range OntologyClass
ContributorAssociation object_category_closure range OntologyClass
GenotypeToGenotypePartAssociation qualifiers range OntologyClass
GenotypeToGenotypePartAssociation subject_category range OntologyClass
GenotypeToGenotypePartAssociation object_category range OntologyClass
GenotypeToGenotypePartAssociation subject_category_closure range OntologyClass
GenotypeToGenotypePartAssociation object_category_closure range OntologyClass
GenotypeToGeneAssociation qualifiers range OntologyClass
GenotypeToGeneAssociation subject_category range OntologyClass
GenotypeToGeneAssociation object_category range OntologyClass
GenotypeToGeneAssociation subject_category_closure range OntologyClass
GenotypeToGeneAssociation object_category_closure range OntologyClass
GenotypeToVariantAssociation qualifiers range OntologyClass
GenotypeToVariantAssociation subject_category range OntologyClass
GenotypeToVariantAssociation object_category range OntologyClass
GenotypeToVariantAssociation subject_category_closure range OntologyClass
GenotypeToVariantAssociation object_category_closure range OntologyClass
GeneToGeneAssociation qualifiers range OntologyClass
GeneToGeneAssociation subject_category range OntologyClass
GeneToGeneAssociation object_category range OntologyClass
GeneToGeneAssociation subject_category_closure range OntologyClass
GeneToGeneAssociation object_category_closure range OntologyClass
GeneToGeneHomologyAssociation qualifiers range OntologyClass
GeneToGeneHomologyAssociation subject_category range OntologyClass
GeneToGeneHomologyAssociation object_category range OntologyClass
GeneToGeneHomologyAssociation subject_category_closure range OntologyClass
GeneToGeneHomologyAssociation object_category_closure range OntologyClass
GeneToGeneFamilyAssociation qualifiers range OntologyClass
GeneToGeneFamilyAssociation subject_category range OntologyClass
GeneToGeneFamilyAssociation object_category range OntologyClass
GeneToGeneFamilyAssociation subject_category_closure range OntologyClass
GeneToGeneFamilyAssociation object_category_closure range OntologyClass
GeneExpressionMixin quantifier_qualifier range OntologyClass
GeneToGeneCoexpressionAssociation quantifier_qualifier range OntologyClass
GeneToGeneCoexpressionAssociation qualifiers range OntologyClass
GeneToGeneCoexpressionAssociation subject_category range OntologyClass
GeneToGeneCoexpressionAssociation object_category range OntologyClass
GeneToGeneCoexpressionAssociation subject_category_closure range OntologyClass
GeneToGeneCoexpressionAssociation object_category_closure range OntologyClass
PairwiseGeneToGeneInteraction qualifiers range OntologyClass
PairwiseGeneToGeneInteraction subject_category range OntologyClass
PairwiseGeneToGeneInteraction object_category range OntologyClass
PairwiseGeneToGeneInteraction subject_category_closure range OntologyClass
PairwiseGeneToGeneInteraction object_category_closure range OntologyClass
PairwiseMolecularInteraction interacting_molecules_category range OntologyClass
PairwiseMolecularInteraction qualifiers range OntologyClass
PairwiseMolecularInteraction subject_category range OntologyClass
PairwiseMolecularInteraction object_category range OntologyClass
PairwiseMolecularInteraction subject_category_closure range OntologyClass
PairwiseMolecularInteraction object_category_closure range OntologyClass
CellLineToDiseaseOrPhenotypicFeatureAssociation qualifiers range OntologyClass
CellLineToDiseaseOrPhenotypicFeatureAssociation subject_category range OntologyClass
CellLineToDiseaseOrPhenotypicFeatureAssociation object_category range OntologyClass
CellLineToDiseaseOrPhenotypicFeatureAssociation subject_category_closure range OntologyClass
CellLineToDiseaseOrPhenotypicFeatureAssociation object_category_closure range OntologyClass
ChemicalToChemicalAssociation qualifiers range OntologyClass
ChemicalToChemicalAssociation subject_category range OntologyClass
ChemicalToChemicalAssociation object_category range OntologyClass
ChemicalToChemicalAssociation subject_category_closure range OntologyClass
ChemicalToChemicalAssociation object_category_closure range OntologyClass
ReactionToParticipantAssociation qualifiers range OntologyClass
ReactionToParticipantAssociation subject_category range OntologyClass
ReactionToParticipantAssociation object_category range OntologyClass
ReactionToParticipantAssociation subject_category_closure range OntologyClass
ReactionToParticipantAssociation object_category_closure range OntologyClass
ReactionToCatalystAssociation qualifiers range OntologyClass
ReactionToCatalystAssociation subject_category range OntologyClass
ReactionToCatalystAssociation object_category range OntologyClass
ReactionToCatalystAssociation subject_category_closure range OntologyClass
ReactionToCatalystAssociation object_category_closure range OntologyClass
ChemicalToChemicalDerivationAssociation qualifiers range OntologyClass
ChemicalToChemicalDerivationAssociation subject_category range OntologyClass
ChemicalToChemicalDerivationAssociation object_category range OntologyClass
ChemicalToChemicalDerivationAssociation subject_category_closure range OntologyClass
ChemicalToChemicalDerivationAssociation object_category_closure range OntologyClass
ChemicalToDiseaseOrPhenotypicFeatureAssociation qualifiers range OntologyClass
ChemicalToDiseaseOrPhenotypicFeatureAssociation subject_category range OntologyClass
ChemicalToDiseaseOrPhenotypicFeatureAssociation object_category range OntologyClass
ChemicalToDiseaseOrPhenotypicFeatureAssociation subject_category_closure range OntologyClass
ChemicalToDiseaseOrPhenotypicFeatureAssociation object_category_closure range OntologyClass
ChemicalOrDrugOrTreatmentToDiseaseOrPhenotypicFeatureAssociation qualifiers range OntologyClass
ChemicalOrDrugOrTreatmentToDiseaseOrPhenotypicFeatureAssociation subject_category range OntologyClass
ChemicalOrDrugOrTreatmentToDiseaseOrPhenotypicFeatureAssociation object_category range OntologyClass
ChemicalOrDrugOrTreatmentToDiseaseOrPhenotypicFeatureAssociation subject_category_closure range OntologyClass
ChemicalOrDrugOrTreatmentToDiseaseOrPhenotypicFeatureAssociation object_category_closure range OntologyClass
ChemicalOrDrugOrTreatmentSideEffectDiseaseOrPhenotypicFeatureAssociation qualifiers range OntologyClass
ChemicalOrDrugOrTreatmentSideEffectDiseaseOrPhenotypicFeatureAssociation subject_category range OntologyClass
ChemicalOrDrugOrTreatmentSideEffectDiseaseOrPhenotypicFeatureAssociation object_category range OntologyClass
ChemicalOrDrugOrTreatmentSideEffectDiseaseOrPhenotypicFeatureAssociation subject_category_closure range OntologyClass
ChemicalOrDrugOrTreatmentSideEffectDiseaseOrPhenotypicFeatureAssociation object_category_closure range OntologyClass
GeneToPathwayAssociation qualifiers range OntologyClass
GeneToPathwayAssociation subject_category range OntologyClass
GeneToPathwayAssociation object_category range OntologyClass
GeneToPathwayAssociation subject_category_closure range OntologyClass
GeneToPathwayAssociation object_category_closure range OntologyClass
MolecularActivityToPathwayAssociation qualifiers range OntologyClass
MolecularActivityToPathwayAssociation subject_category range OntologyClass
MolecularActivityToPathwayAssociation object_category range OntologyClass
MolecularActivityToPathwayAssociation subject_category_closure range OntologyClass
MolecularActivityToPathwayAssociation object_category_closure range OntologyClass
ChemicalToPathwayAssociation qualifiers range OntologyClass
ChemicalToPathwayAssociation subject_category range OntologyClass
ChemicalToPathwayAssociation object_category range OntologyClass
ChemicalToPathwayAssociation subject_category_closure range OntologyClass
ChemicalToPathwayAssociation object_category_closure range OntologyClass
NamedThingAssociatedWithLikelihoodOfNamedThingAssociation subject_context_qualifier range OntologyClass
NamedThingAssociatedWithLikelihoodOfNamedThingAssociation object_context_qualifier range OntologyClass
NamedThingAssociatedWithLikelihoodOfNamedThingAssociation qualifiers range OntologyClass
NamedThingAssociatedWithLikelihoodOfNamedThingAssociation subject_category range OntologyClass
NamedThingAssociatedWithLikelihoodOfNamedThingAssociation object_category range OntologyClass
NamedThingAssociatedWithLikelihoodOfNamedThingAssociation subject_category_closure range OntologyClass
NamedThingAssociatedWithLikelihoodOfNamedThingAssociation object_category_closure range OntologyClass
ChemicalGeneInteractionAssociation qualifiers range OntologyClass
ChemicalGeneInteractionAssociation subject_category range OntologyClass
ChemicalGeneInteractionAssociation object_category range OntologyClass
ChemicalGeneInteractionAssociation subject_category_closure range OntologyClass
ChemicalGeneInteractionAssociation object_category_closure range OntologyClass
GeneRegulatesGeneAssociation qualifiers range OntologyClass
GeneRegulatesGeneAssociation subject_category range OntologyClass
GeneRegulatesGeneAssociation object_category range OntologyClass
GeneRegulatesGeneAssociation subject_category_closure range OntologyClass
GeneRegulatesGeneAssociation object_category_closure range OntologyClass
ProcessRegulatesProcessAssociation qualifiers range OntologyClass
ProcessRegulatesProcessAssociation subject_category range OntologyClass
ProcessRegulatesProcessAssociation object_category range OntologyClass
ProcessRegulatesProcessAssociation subject_category_closure range OntologyClass
ProcessRegulatesProcessAssociation object_category_closure range OntologyClass
ChemicalAffectsGeneAssociation qualifiers range OntologyClass
ChemicalAffectsGeneAssociation subject_category range OntologyClass
ChemicalAffectsGeneAssociation object_category range OntologyClass
ChemicalAffectsGeneAssociation subject_category_closure range OntologyClass
ChemicalAffectsGeneAssociation object_category_closure range OntologyClass
GeneAffectsChemicalAssociation qualifiers range OntologyClass
GeneAffectsChemicalAssociation subject_category range OntologyClass
GeneAffectsChemicalAssociation object_category range OntologyClass
GeneAffectsChemicalAssociation subject_category_closure range OntologyClass
GeneAffectsChemicalAssociation object_category_closure range OntologyClass
DrugToGeneAssociation qualifiers range OntologyClass
DrugToGeneAssociation subject_category range OntologyClass
DrugToGeneAssociation object_category range OntologyClass
DrugToGeneAssociation subject_category_closure range OntologyClass
DrugToGeneAssociation object_category_closure range OntologyClass
MaterialSampleDerivationAssociation qualifiers range OntologyClass
MaterialSampleDerivationAssociation subject_category range OntologyClass
MaterialSampleDerivationAssociation object_category range OntologyClass
MaterialSampleDerivationAssociation subject_category_closure range OntologyClass
MaterialSampleDerivationAssociation object_category_closure range OntologyClass
MaterialSampleToDiseaseOrPhenotypicFeatureAssociation qualifiers range OntologyClass
MaterialSampleToDiseaseOrPhenotypicFeatureAssociation subject_category range OntologyClass
MaterialSampleToDiseaseOrPhenotypicFeatureAssociation object_category range OntologyClass
MaterialSampleToDiseaseOrPhenotypicFeatureAssociation subject_category_closure range OntologyClass
MaterialSampleToDiseaseOrPhenotypicFeatureAssociation object_category_closure range OntologyClass
DiseaseToExposureEventAssociation qualifiers range OntologyClass
DiseaseToExposureEventAssociation subject_category range OntologyClass
DiseaseToExposureEventAssociation object_category range OntologyClass
DiseaseToExposureEventAssociation subject_category_closure range OntologyClass
DiseaseToExposureEventAssociation object_category_closure range OntologyClass
ExposureEventToOutcomeAssociation qualifiers range OntologyClass
ExposureEventToOutcomeAssociation subject_category range OntologyClass
ExposureEventToOutcomeAssociation object_category range OntologyClass
ExposureEventToOutcomeAssociation subject_category_closure range OntologyClass
ExposureEventToOutcomeAssociation object_category_closure range OntologyClass
PhenotypicFeatureToPhenotypicFeatureAssociation qualifiers range OntologyClass
PhenotypicFeatureToPhenotypicFeatureAssociation subject_category range OntologyClass
PhenotypicFeatureToPhenotypicFeatureAssociation object_category range OntologyClass
PhenotypicFeatureToPhenotypicFeatureAssociation subject_category_closure range OntologyClass
PhenotypicFeatureToPhenotypicFeatureAssociation object_category_closure range OntologyClass
InformationContentEntityToNamedThingAssociation qualifiers range OntologyClass
InformationContentEntityToNamedThingAssociation subject_category range OntologyClass
InformationContentEntityToNamedThingAssociation object_category range OntologyClass
InformationContentEntityToNamedThingAssociation subject_category_closure range OntologyClass
InformationContentEntityToNamedThingAssociation object_category_closure range OntologyClass
DiseaseOrPhenotypicFeatureToLocationAssociation qualifiers range OntologyClass
DiseaseOrPhenotypicFeatureToLocationAssociation subject_category range OntologyClass
DiseaseOrPhenotypicFeatureToLocationAssociation object_category range OntologyClass
DiseaseOrPhenotypicFeatureToLocationAssociation subject_category_closure range OntologyClass
DiseaseOrPhenotypicFeatureToLocationAssociation object_category_closure range OntologyClass
DiseaseOrPhenotypicFeatureToGeneticInheritanceAssociation qualifiers range OntologyClass
DiseaseOrPhenotypicFeatureToGeneticInheritanceAssociation subject_category range OntologyClass
DiseaseOrPhenotypicFeatureToGeneticInheritanceAssociation object_category range OntologyClass
DiseaseOrPhenotypicFeatureToGeneticInheritanceAssociation subject_category_closure range OntologyClass
DiseaseOrPhenotypicFeatureToGeneticInheritanceAssociation object_category_closure range OntologyClass
GenotypeToPhenotypicFeatureAssociation qualifiers range OntologyClass
GenotypeToPhenotypicFeatureAssociation subject_category range OntologyClass
GenotypeToPhenotypicFeatureAssociation object_category range OntologyClass
GenotypeToPhenotypicFeatureAssociation subject_category_closure range OntologyClass
GenotypeToPhenotypicFeatureAssociation object_category_closure range OntologyClass
ExposureEventToPhenotypicFeatureAssociation qualifiers range OntologyClass
ExposureEventToPhenotypicFeatureAssociation subject_category range OntologyClass
ExposureEventToPhenotypicFeatureAssociation object_category range OntologyClass
ExposureEventToPhenotypicFeatureAssociation subject_category_closure range OntologyClass
ExposureEventToPhenotypicFeatureAssociation object_category_closure range OntologyClass
DiseaseToPhenotypicFeatureAssociation qualifiers range OntologyClass
DiseaseToPhenotypicFeatureAssociation subject_category range OntologyClass
DiseaseToPhenotypicFeatureAssociation object_category range OntologyClass
DiseaseToPhenotypicFeatureAssociation subject_category_closure range OntologyClass
DiseaseToPhenotypicFeatureAssociation object_category_closure range OntologyClass
CaseToPhenotypicFeatureAssociation qualifiers range OntologyClass
CaseToPhenotypicFeatureAssociation subject_category range OntologyClass
CaseToPhenotypicFeatureAssociation object_category range OntologyClass
CaseToPhenotypicFeatureAssociation subject_category_closure range OntologyClass
CaseToPhenotypicFeatureAssociation object_category_closure range OntologyClass
BehaviorToBehavioralFeatureAssociation qualifiers range OntologyClass
BehaviorToBehavioralFeatureAssociation subject_category range OntologyClass
BehaviorToBehavioralFeatureAssociation object_category range OntologyClass
BehaviorToBehavioralFeatureAssociation subject_category_closure range OntologyClass
BehaviorToBehavioralFeatureAssociation object_category_closure range OntologyClass
GeneToDiseaseOrPhenotypicFeatureAssociation qualifiers range OntologyClass
GeneToDiseaseOrPhenotypicFeatureAssociation subject_category range OntologyClass
GeneToDiseaseOrPhenotypicFeatureAssociation object_category range OntologyClass
GeneToDiseaseOrPhenotypicFeatureAssociation subject_category_closure range OntologyClass
GeneToDiseaseOrPhenotypicFeatureAssociation object_category_closure range OntologyClass
GeneToPhenotypicFeatureAssociation qualifiers range OntologyClass
GeneToPhenotypicFeatureAssociation subject_category range OntologyClass
GeneToPhenotypicFeatureAssociation object_category range OntologyClass
GeneToPhenotypicFeatureAssociation subject_category_closure range OntologyClass
GeneToPhenotypicFeatureAssociation object_category_closure range OntologyClass
GeneToDiseaseAssociation qualifiers range OntologyClass
GeneToDiseaseAssociation subject_category range OntologyClass
GeneToDiseaseAssociation object_category range OntologyClass
GeneToDiseaseAssociation subject_category_closure range OntologyClass
GeneToDiseaseAssociation object_category_closure range OntologyClass
CausalGeneToDiseaseAssociation qualifiers range OntologyClass
CausalGeneToDiseaseAssociation subject_category range OntologyClass
CausalGeneToDiseaseAssociation object_category range OntologyClass
CausalGeneToDiseaseAssociation subject_category_closure range OntologyClass
CausalGeneToDiseaseAssociation object_category_closure range OntologyClass
CorrelatedGeneToDiseaseAssociation qualifiers range OntologyClass
CorrelatedGeneToDiseaseAssociation subject_category range OntologyClass
CorrelatedGeneToDiseaseAssociation object_category range OntologyClass
CorrelatedGeneToDiseaseAssociation subject_category_closure range OntologyClass
CorrelatedGeneToDiseaseAssociation object_category_closure range OntologyClass
DruggableGeneToDiseaseAssociation qualifiers range OntologyClass
DruggableGeneToDiseaseAssociation subject_category range OntologyClass
DruggableGeneToDiseaseAssociation object_category range OntologyClass
DruggableGeneToDiseaseAssociation subject_category_closure range OntologyClass
DruggableGeneToDiseaseAssociation object_category_closure range OntologyClass
PhenotypicFeatureToDiseaseAssociation qualifiers range OntologyClass
PhenotypicFeatureToDiseaseAssociation subject_category range OntologyClass
PhenotypicFeatureToDiseaseAssociation object_category range OntologyClass
PhenotypicFeatureToDiseaseAssociation subject_category_closure range OntologyClass
PhenotypicFeatureToDiseaseAssociation object_category_closure range OntologyClass
VariantToGeneAssociation qualifiers range OntologyClass
VariantToGeneAssociation subject_category range OntologyClass
VariantToGeneAssociation object_category range OntologyClass
VariantToGeneAssociation subject_category_closure range OntologyClass
VariantToGeneAssociation object_category_closure range OntologyClass
VariantToGeneExpressionAssociation quantifier_qualifier range OntologyClass
VariantToGeneExpressionAssociation qualifiers range OntologyClass
VariantToGeneExpressionAssociation subject_category range OntologyClass
VariantToGeneExpressionAssociation object_category range OntologyClass
VariantToGeneExpressionAssociation subject_category_closure range OntologyClass
VariantToGeneExpressionAssociation object_category_closure range OntologyClass
VariantToPopulationAssociation qualifiers range OntologyClass
VariantToPopulationAssociation subject_category range OntologyClass
VariantToPopulationAssociation object_category range OntologyClass
VariantToPopulationAssociation subject_category_closure range OntologyClass
VariantToPopulationAssociation object_category_closure range OntologyClass
PopulationToPopulationAssociation qualifiers range OntologyClass
PopulationToPopulationAssociation subject_category range OntologyClass
PopulationToPopulationAssociation object_category range OntologyClass
PopulationToPopulationAssociation subject_category_closure range OntologyClass
PopulationToPopulationAssociation object_category_closure range OntologyClass
VariantToPhenotypicFeatureAssociation qualifiers range OntologyClass
VariantToPhenotypicFeatureAssociation subject_category range OntologyClass
VariantToPhenotypicFeatureAssociation object_category range OntologyClass
VariantToPhenotypicFeatureAssociation subject_category_closure range OntologyClass
VariantToPhenotypicFeatureAssociation object_category_closure range OntologyClass
VariantToDiseaseAssociation qualifiers range OntologyClass
VariantToDiseaseAssociation subject_category range OntologyClass
VariantToDiseaseAssociation object_category range OntologyClass
VariantToDiseaseAssociation subject_category_closure range OntologyClass
VariantToDiseaseAssociation object_category_closure range OntologyClass
GenotypeToDiseaseAssociation qualifiers range OntologyClass
GenotypeToDiseaseAssociation subject_category range OntologyClass
GenotypeToDiseaseAssociation object_category range OntologyClass
GenotypeToDiseaseAssociation subject_category_closure range OntologyClass
GenotypeToDiseaseAssociation object_category_closure range OntologyClass
GeneAsAModelOfDiseaseAssociation qualifiers range OntologyClass
GeneAsAModelOfDiseaseAssociation subject_category range OntologyClass
GeneAsAModelOfDiseaseAssociation object_category range OntologyClass
GeneAsAModelOfDiseaseAssociation subject_category_closure range OntologyClass
GeneAsAModelOfDiseaseAssociation object_category_closure range OntologyClass
VariantAsAModelOfDiseaseAssociation qualifiers range OntologyClass
VariantAsAModelOfDiseaseAssociation subject_category range OntologyClass
VariantAsAModelOfDiseaseAssociation object_category range OntologyClass
VariantAsAModelOfDiseaseAssociation subject_category_closure range OntologyClass
VariantAsAModelOfDiseaseAssociation object_category_closure range OntologyClass
GenotypeAsAModelOfDiseaseAssociation qualifiers range OntologyClass
GenotypeAsAModelOfDiseaseAssociation subject_category range OntologyClass
GenotypeAsAModelOfDiseaseAssociation object_category range OntologyClass
GenotypeAsAModelOfDiseaseAssociation subject_category_closure range OntologyClass
GenotypeAsAModelOfDiseaseAssociation object_category_closure range OntologyClass
CellLineAsAModelOfDiseaseAssociation qualifiers range OntologyClass
CellLineAsAModelOfDiseaseAssociation subject_category range OntologyClass
CellLineAsAModelOfDiseaseAssociation object_category range OntologyClass
CellLineAsAModelOfDiseaseAssociation subject_category_closure range OntologyClass
CellLineAsAModelOfDiseaseAssociation object_category_closure range OntologyClass
OrganismalEntityAsAModelOfDiseaseAssociation qualifiers range OntologyClass
OrganismalEntityAsAModelOfDiseaseAssociation subject_category range OntologyClass
OrganismalEntityAsAModelOfDiseaseAssociation object_category range OntologyClass
OrganismalEntityAsAModelOfDiseaseAssociation subject_category_closure range OntologyClass
OrganismalEntityAsAModelOfDiseaseAssociation object_category_closure range OntologyClass
OrganismToOrganismAssociation qualifiers range OntologyClass
OrganismToOrganismAssociation subject_category range OntologyClass
OrganismToOrganismAssociation object_category range OntologyClass
OrganismToOrganismAssociation subject_category_closure range OntologyClass
OrganismToOrganismAssociation object_category_closure range OntologyClass
TaxonToTaxonAssociation qualifiers range OntologyClass
TaxonToTaxonAssociation subject_category range OntologyClass
TaxonToTaxonAssociation object_category range OntologyClass
TaxonToTaxonAssociation subject_category_closure range OntologyClass
TaxonToTaxonAssociation object_category_closure range OntologyClass
GeneHasVariantThatContributesToDiseaseAssociation qualifiers range OntologyClass
GeneHasVariantThatContributesToDiseaseAssociation subject_category range OntologyClass
GeneHasVariantThatContributesToDiseaseAssociation object_category range OntologyClass
GeneHasVariantThatContributesToDiseaseAssociation subject_category_closure range OntologyClass
GeneHasVariantThatContributesToDiseaseAssociation object_category_closure range OntologyClass
GeneToExpressionSiteAssociation quantifier_qualifier range OntologyClass
GeneToExpressionSiteAssociation qualifiers range OntologyClass
GeneToExpressionSiteAssociation subject_category range OntologyClass
GeneToExpressionSiteAssociation object_category range OntologyClass
GeneToExpressionSiteAssociation subject_category_closure range OntologyClass
GeneToExpressionSiteAssociation object_category_closure range OntologyClass
SequenceVariantModulatesTreatmentAssociation qualifiers range OntologyClass
SequenceVariantModulatesTreatmentAssociation subject_category range OntologyClass
SequenceVariantModulatesTreatmentAssociation object_category range OntologyClass
SequenceVariantModulatesTreatmentAssociation subject_category_closure range OntologyClass
SequenceVariantModulatesTreatmentAssociation object_category_closure range OntologyClass
FunctionalAssociation object range OntologyClass
FunctionalAssociation qualifiers range OntologyClass
FunctionalAssociation subject_category range OntologyClass
FunctionalAssociation object_category range OntologyClass
FunctionalAssociation subject_category_closure range OntologyClass
FunctionalAssociation object_category_closure range OntologyClass
MacromolecularMachineToMolecularActivityAssociation qualifiers range OntologyClass
MacromolecularMachineToMolecularActivityAssociation subject_category range OntologyClass
MacromolecularMachineToMolecularActivityAssociation object_category range OntologyClass
MacromolecularMachineToMolecularActivityAssociation subject_category_closure range OntologyClass
MacromolecularMachineToMolecularActivityAssociation object_category_closure range OntologyClass
MacromolecularMachineToBiologicalProcessAssociation qualifiers range OntologyClass
MacromolecularMachineToBiologicalProcessAssociation subject_category range OntologyClass
MacromolecularMachineToBiologicalProcessAssociation object_category range OntologyClass
MacromolecularMachineToBiologicalProcessAssociation subject_category_closure range OntologyClass
MacromolecularMachineToBiologicalProcessAssociation object_category_closure range OntologyClass
MacromolecularMachineToCellularComponentAssociation qualifiers range OntologyClass
MacromolecularMachineToCellularComponentAssociation subject_category range OntologyClass
MacromolecularMachineToCellularComponentAssociation object_category range OntologyClass
MacromolecularMachineToCellularComponentAssociation subject_category_closure range OntologyClass
MacromolecularMachineToCellularComponentAssociation object_category_closure range OntologyClass
MolecularActivityToChemicalEntityAssociation qualifiers range OntologyClass
MolecularActivityToChemicalEntityAssociation subject_category range OntologyClass
MolecularActivityToChemicalEntityAssociation object_category range OntologyClass
MolecularActivityToChemicalEntityAssociation subject_category_closure range OntologyClass
MolecularActivityToChemicalEntityAssociation object_category_closure range OntologyClass
MolecularActivityToMolecularActivityAssociation qualifiers range OntologyClass
MolecularActivityToMolecularActivityAssociation subject_category range OntologyClass
MolecularActivityToMolecularActivityAssociation object_category range OntologyClass
MolecularActivityToMolecularActivityAssociation subject_category_closure range OntologyClass
MolecularActivityToMolecularActivityAssociation object_category_closure range OntologyClass
GeneToGoTermAssociation object range OntologyClass
GeneToGoTermAssociation qualifiers range OntologyClass
GeneToGoTermAssociation subject_category range OntologyClass
GeneToGoTermAssociation object_category range OntologyClass
GeneToGoTermAssociation subject_category_closure range OntologyClass
GeneToGoTermAssociation object_category_closure range OntologyClass
EntityToDiseaseAssociation qualifiers range OntologyClass
EntityToDiseaseAssociation subject_category range OntologyClass
EntityToDiseaseAssociation object_category range OntologyClass
EntityToDiseaseAssociation subject_category_closure range OntologyClass
EntityToDiseaseAssociation object_category_closure range OntologyClass
EntityToPhenotypicFeatureAssociation qualifiers range OntologyClass
EntityToPhenotypicFeatureAssociation subject_category range OntologyClass
EntityToPhenotypicFeatureAssociation object_category range OntologyClass
EntityToPhenotypicFeatureAssociation subject_category_closure range OntologyClass
EntityToPhenotypicFeatureAssociation object_category_closure range OntologyClass
SequenceAssociation qualifiers range OntologyClass
SequenceAssociation subject_category range OntologyClass
SequenceAssociation object_category range OntologyClass
SequenceAssociation subject_category_closure range OntologyClass
SequenceAssociation object_category_closure range OntologyClass
GenomicSequenceLocalization qualifiers range OntologyClass
GenomicSequenceLocalization subject_category range OntologyClass
GenomicSequenceLocalization object_category range OntologyClass
GenomicSequenceLocalization subject_category_closure range OntologyClass
GenomicSequenceLocalization object_category_closure range OntologyClass
SequenceFeatureRelationship qualifiers range OntologyClass
SequenceFeatureRelationship subject_category range OntologyClass
SequenceFeatureRelationship object_category range OntologyClass
SequenceFeatureRelationship subject_category_closure range OntologyClass
SequenceFeatureRelationship object_category_closure range OntologyClass
TranscriptToGeneRelationship qualifiers range OntologyClass
TranscriptToGeneRelationship subject_category range OntologyClass
TranscriptToGeneRelationship object_category range OntologyClass
TranscriptToGeneRelationship subject_category_closure range OntologyClass
TranscriptToGeneRelationship object_category_closure range OntologyClass
GeneToGeneProductRelationship qualifiers range OntologyClass
GeneToGeneProductRelationship subject_category range OntologyClass
GeneToGeneProductRelationship object_category range OntologyClass
GeneToGeneProductRelationship subject_category_closure range OntologyClass
GeneToGeneProductRelationship object_category_closure range OntologyClass
ExonToTranscriptRelationship qualifiers range OntologyClass
ExonToTranscriptRelationship subject_category range OntologyClass
ExonToTranscriptRelationship object_category range OntologyClass
ExonToTranscriptRelationship subject_category_closure range OntologyClass
ExonToTranscriptRelationship object_category_closure range OntologyClass
ChemicalEntityOrGeneOrGeneProductRegulatesGeneAssociation qualifiers range OntologyClass
ChemicalEntityOrGeneOrGeneProductRegulatesGeneAssociation subject_category range OntologyClass
ChemicalEntityOrGeneOrGeneProductRegulatesGeneAssociation object_category range OntologyClass
ChemicalEntityOrGeneOrGeneProductRegulatesGeneAssociation subject_category_closure range OntologyClass
ChemicalEntityOrGeneOrGeneProductRegulatesGeneAssociation object_category_closure range OntologyClass
AnatomicalEntityToAnatomicalEntityAssociation qualifiers range OntologyClass
AnatomicalEntityToAnatomicalEntityAssociation subject_category range OntologyClass
AnatomicalEntityToAnatomicalEntityAssociation object_category range OntologyClass
AnatomicalEntityToAnatomicalEntityAssociation subject_category_closure range OntologyClass
AnatomicalEntityToAnatomicalEntityAssociation object_category_closure range OntologyClass
AnatomicalEntityToAnatomicalEntityPartOfAssociation qualifiers range OntologyClass
AnatomicalEntityToAnatomicalEntityPartOfAssociation subject_category range OntologyClass
AnatomicalEntityToAnatomicalEntityPartOfAssociation object_category range OntologyClass
AnatomicalEntityToAnatomicalEntityPartOfAssociation subject_category_closure range OntologyClass
AnatomicalEntityToAnatomicalEntityPartOfAssociation object_category_closure range OntologyClass
AnatomicalEntityToAnatomicalEntityOntogenicAssociation qualifiers range OntologyClass
AnatomicalEntityToAnatomicalEntityOntogenicAssociation subject_category range OntologyClass
AnatomicalEntityToAnatomicalEntityOntogenicAssociation object_category range OntologyClass
AnatomicalEntityToAnatomicalEntityOntogenicAssociation subject_category_closure range OntologyClass
AnatomicalEntityToAnatomicalEntityOntogenicAssociation object_category_closure range OntologyClass
OrganismTaxonToOrganismTaxonAssociation qualifiers range OntologyClass
OrganismTaxonToOrganismTaxonAssociation subject_category range OntologyClass
OrganismTaxonToOrganismTaxonAssociation object_category range OntologyClass
OrganismTaxonToOrganismTaxonAssociation subject_category_closure range OntologyClass
OrganismTaxonToOrganismTaxonAssociation object_category_closure range OntologyClass
OrganismTaxonToOrganismTaxonSpecialization qualifiers range OntologyClass
OrganismTaxonToOrganismTaxonSpecialization subject_category range OntologyClass
OrganismTaxonToOrganismTaxonSpecialization object_category range OntologyClass
OrganismTaxonToOrganismTaxonSpecialization subject_category_closure range OntologyClass
OrganismTaxonToOrganismTaxonSpecialization object_category_closure range OntologyClass
OrganismTaxonToOrganismTaxonInteraction qualifiers range OntologyClass
OrganismTaxonToOrganismTaxonInteraction subject_category range OntologyClass
OrganismTaxonToOrganismTaxonInteraction object_category range OntologyClass
OrganismTaxonToOrganismTaxonInteraction subject_category_closure range OntologyClass
OrganismTaxonToOrganismTaxonInteraction object_category_closure range OntologyClass
OrganismTaxonToEnvironmentAssociation qualifiers range OntologyClass
OrganismTaxonToEnvironmentAssociation subject_category range OntologyClass
OrganismTaxonToEnvironmentAssociation object_category range OntologyClass
OrganismTaxonToEnvironmentAssociation subject_category_closure range OntologyClass
OrganismTaxonToEnvironmentAssociation object_category_closure range OntologyClass

Valid ID Prefixes

Instances of this class should have identifiers with one of the following prefixes, ordered with the most preferred first:

ID Prefix Usage
MESH OntologyClass
OrganismTaxon
MolecularEntity
ChemicalEntity
SmallMolecule
ChemicalMixture
NucleicAcidEntity
MolecularMixture
ComplexMolecularMixture
ProcessedMaterial
Drug
EnvironmentalFoodContaminant
FoodAdditive
Food
Disease
PhenotypicFeature
AnatomicalEntity
CellularComponent
Cell
GrossAnatomicalStructure
Protein
UMLS OntologyClass
OrganismTaxon
MolecularEntity
ChemicalEntity
SmallMolecule
ChemicalMixture
NucleicAcidEntity
MolecularMixture
ComplexMolecularMixture
MolecularActivity
ProcessedMaterial
Drug
EnvironmentalFoodContaminant
FoodAdditive
Food
Disease
PhenotypicFeature
AnatomicalEntity
CellularComponent
Cell
GrossAnatomicalStructure
Gene
Polypeptide
Protein
KEGG.BRITE OntologyClass

Example values

Slot Name Value
OntologyClass UBERON:0000955

LinkML Source

name: ontology class
id_prefixes:
- MESH
- UMLS
- KEGG.BRITE
description: a concept or class in an ontology, vocabulary or thesaurus. Note that
  nodes in a biolink compatible KG can be considered both instances of biolink classes,
  and OWL classes in their own right. In general you should not need to use this class
  directly. Instead, use the appropriate biolink class. For example, for the GO concept
  of endocytosis (GO:0006897), use bl:BiologicalProcess as the type.
comments:
- This is modeled as a mixin. 'ontology class' should not be the primary type of a
  node in the KG. Instead you should use an informative bioloink category, such as
  AnatomicalEntity (for Uberon classes), ChemicalSubstance (for CHEBI or CHEMBL),
  etc
- Note that formally this is a metaclass. Instances of this class are instances in
  the graph, but can be the object of 'type' edges. For example, if we had a node
  in the graph representing a specific brain of a specific patient (e.g brain001),
  this could have a category of bl:Sample, and by typed more specifically with an
  ontology class UBERON:nnn, which has as category bl:AnatomicalEntity
examples:
- value: UBERON:0000955
  description: the class 'brain' from the Uberon anatomy ontology
from_schema: https://w3id.org/biolink/biolink-model
see_also:
- https://github.com/biolink/biolink-model/issues/486
exact_mappings:
- owl:Class
- schema:Class
mixin: true
slots:
- id