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Class: IndividualOrganism

Description: An instance of an organism. For example, Richard Nixon, Charles Darwin, my pet cat. Example ID: ORCID:0000-0002-5355-2576

Aliases: organism

classDiagram class IndividualOrganism SubjectOfInvestigation <|-- IndividualOrganism OrganismalEntity <|-- IndividualOrganism IndividualOrganism <|-- Case IndividualOrganism : category IndividualOrganism : deprecated IndividualOrganism : description IndividualOrganism : full_name IndividualOrganism : has_attribute IndividualOrganism --|> Attribute : has_attribute IndividualOrganism : id IndividualOrganism : in_taxon IndividualOrganism --|> OrganismTaxon : in_taxon IndividualOrganism : in_taxon_label IndividualOrganism : iri IndividualOrganism : name IndividualOrganism : provided_by IndividualOrganism : synonym IndividualOrganism : type IndividualOrganism : xref

Inheritance

Slots

Name Cardinality and Range Inheritance Examples
in_taxon:
connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'
*
OrganismTaxon		 ThingWithTaxon
in_taxon_label:
The human readable scientific name for the taxon of the entity. 		0..1
LabelType		 ThingWithTaxon
provided_by:
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. 		*
String		 NamedThing
xref:
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. 		*
Uriorcurie		 NamedThing
full_name:
a long-form human readable name for a thing 		0..1
LabelType		 NamedThing
synonym:
Alternate human-readable names for a thing 		*
LabelType		 NamedThing
id:
A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI 		1
String		 Entity
iri:
An IRI for an entity. This is determined by the id using expansion rules. 		0..1
IriType		 Entity
category:
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} 		1..*
Uriorcurie		 Entity
type:
None 		*
String		 Entity
name:
A human-readable name for an attribute or entity. 		0..1
LabelType		 Entity
description:
a human-readable description of an entity 		0..1
NarrativeText		 Entity
has_attribute:
may often be an organism attribute 		*
Attribute		 Entity
deprecated:
A boolean flag indicating that an entity is no longer considered current or valid. 		0..1
Boolean		 Entity

Usages

used by used in type used
OrganismToOrganismAssociation subject range IndividualOrganism
OrganismToOrganismAssociation object range IndividualOrganism

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
ORCID Agent
IndividualOrganism

LinkML Source

name: individual organism
id_prefixes:
- ORCID
description: 'An instance of an organism. For example, Richard Nixon, Charles Darwin,
  my pet cat. Example ID: ORCID:0000-0002-5355-2576'
from_schema: https://w3id.org/biolink/biolink-model
aliases:
- organism
exact_mappings:
- SIO:010000
- STY:T001
narrow_mappings:
- WIKIDATA:Q795052
- foaf:Person
is_a: organismal entity
mixins:
- subject of investigation