Class: OrganismalEntity
A named entity that is either a part of an organism, a whole organism, population or clade of organisms, excluding chemical entities
URI: biolink:OrganismalEntity
:label_type%20%3F;provided_by(i):string%20%2A;xref(i):uriorcurie%20%2A;full_name(i):label_type%20%3F;synonym(i):label_type%20%2A;category(i):category_type%20%2B;id(i):string;iri(i):iri_type%20%3F;type(i):string%20%2A;name(i):label_type%20%3F;description(i):narrative_text%20%3F],[OrganismalEntityAsAModelOfDiseaseAssociation]-%20subject%201..1%3E[OrganismalEntity],[OrganismalEntity]uses%20-.-%3E[SubjectOfInvestigation],[OrganismalEntity]%5E-[Virus],[OrganismalEntity]%5E-[PopulationOfIndividualOrganisms],[OrganismalEntity]%5E-[LifeStage],[OrganismalEntity]%5E-[IndividualOrganism],[OrganismalEntity]%5E-[CellularOrganism],[OrganismalEntity]%5E-[CellLine],[OrganismalEntity]%5E-[Bacterium],[OrganismalEntity]%5E-[AnatomicalEntity],[BiologicalEntity]%5E-[OrganismalEntity],[OrganismTaxon],[LifeStage],[IndividualOrganism],[ExposureEvent],[CellularOrganism],[CellLine],[BiologicalEntity],[Bacterium],[Attribute],[AnatomicalEntity])
Parents
Uses Mixins
- mixin: SubjectOfInvestigation - An entity that has the role of being studied in an investigation, study, or experiment
Children
- AnatomicalEntity - A subcellular location, cell type or gross anatomical part
- Bacterium - A member of a group of unicellular microorganisms lacking a nuclear membrane, that reproduce by binary fission and are often motile.
- CellLine
- CellularOrganism
- IndividualOrganism - An instance of an organism. For example, Richard Nixon, Charles Darwin, my pet cat. Example ID: ORCID:0000-0002-5355-2576
- LifeStage - A stage of development or growth of an organism, including post-natal adult stages
- PopulationOfIndividualOrganisms - A collection of individuals from the same taxonomic class distinguished by one or more characteristics. Characteristics can include, but are not limited to, shared geographic location, genetics, phenotypes.
- Virus - A virus is a microorganism that replicates itself as a microRNA and infects the host cell.
Referenced by class
Attributes
Own
Inherited from entity:
- id 1..1
- Description: A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI
- Range: String
- in subsets: (translator_minimal)
- iri 0..1
- Description: An IRI for an entity. This is determined by the id using expansion rules.
- Range: IriType
- in subsets: (translator_minimal,samples)
- category 0..*
- 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}
- type 0..*
- description 0..1
- Description: a human-readable description of an entity
- Range: NarrativeText
- in subsets: (translator_minimal)
- has attribute 0..*
- Description: connects any entity to an attribute
- Range: Attribute
- in subsets: (samples)
Inherited from gene product mixin:
- synonym 0..*
- Description: Alternate human-readable names for a thing
- Range: LabelType
- in subsets: (translator_minimal)
- xref 0..*
- 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.
- Range: Uriorcurie
- in subsets: (translator_minimal)
Inherited from macromolecular machine mixin:
- name 0..1
- Description: A human-readable name for an attribute or entity.
- Range: LabelType
- in subsets: (translator_minimal,samples)
Inherited from named thing:
- provided by 0..*
- Description: The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.
- Range: String
- full name 0..1
- Description: a long-form human readable name for a thing
- Range: LabelType
- category 0..*
- 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}
Inherited from thing with taxon:
- in taxon 0..*
- Description: connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see ‘thing with taxon’
- Range: OrganismTaxon
- in subsets: (translator_minimal)
- in taxon label 0..1
- Description: The human readable scientific name for the taxon of the entity.
- Range: LabelType
- in subsets: (translator_minimal)
Domain for slot:
Other properties
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Exact Mappings: |
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WIKIDATA:Q7239 |
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UMLSSG:LIVB |
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CARO:0001010 |
Narrow Mappings: |
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STY:T008 |