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Class: BiologicalEntity

URI: biolink:BiologicalEntity


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Parents

  • is_a: NamedThing - a databased entity or concept/class

Uses Mixins

  • mixin: ThingWithTaxon - A mixin that can be used on any entity that can be taxonomically classified. This includes individual organisms; genes, their products and other molecular entities; body parts; biological processes

Children

  • BiologicalProcessOrActivity - Either an individual molecular activity, or a collection of causally connected molecular activities in a biological system.
  • DiseaseOrPhenotypicFeature - Either one of a disease or an individual phenotypic feature. Some knowledge resources such as Monarch treat these as distinct, others such as MESH conflate.
  • 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.
  • GeneFamily - any grouping of multiple genes or gene products related by common descent
  • 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]
  • NucleicAcidSequenceMotif - A linear nucleotide sequence pattern that is widespread and has, or is conjectured to have, a biological significance. e.g. the TATA box promoter motif, transcription factor binding consensus sequences.
  • OrganismalEntity - A named entity that is either a part of an organism, a whole organism, population or clade of organisms, excluding chemical entities
  • Polypeptide - A polypeptide is a molecular entity characterized by availability in protein databases of amino-acid-based sequence representations of its precise primary structure; for convenience of representation, partial sequences of various kinds are included, even if they do not represent a physical molecule.
  • ProteinDomain - A conserved part of protein sequence and (tertiary) structure that can evolve, function, and exist independently of the rest of the protein chain. Protein domains maintain their structure and function independently of the proteins in which they are found. e.g. an SH3 domain.
  • ProteinFamily
  • 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.
  • SequenceVariant - An allele that varies in its sequence from what is considered the reference allele at that locus.

Referenced by class

Attributes

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..1
  • description 0..1
    • Description: a human-readable description of an entity
    • Range: NarrativeText
    • in subsets: (translator_minimal)
  • source 0..1
  • has attribute 0..*
    • Description: connects any entity to an attribute
    • Range: Attribute
    • in subsets: (samples)

Inherited from gene product mixin:

  • xref 0..*
    • Description: Alternate CURIEs for a thing
    • 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
  • 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)

Other properties

     
Aliases:   bioentity
Narrow Mappings:   WIKIDATA:Q28845870
    STY:T050
    SIO:010046