Class: BiologicalProcess

One or more causally connected executions of molecular functions

URI: biolink:BiologicalProcess

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Identifier prefixes

• GO
• REACT
• metacyc.reaction
• KEGG.MODULE

Parents

• is_a: BiologicalProcessOrActivity - Either an individual molecular activity, or a collection of causally connected molecular activities in a biological system.

Uses Mixins

• mixin: Occurrent - A processual entity.
• mixin: OntologyClass - 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.

Children

• Behavior
• PathologicalProcess - A biologic function or a process having an abnormal or deleterious effect at the subcellular, cellular, multicellular, or organismal level.
• Pathway
• PhysiologicalProcess

Referenced by class

• GeneOrGeneProduct acts upstream of _0..* BiologicalProcess
• GeneOrGeneProduct acts upstream of negative effect _0..* BiologicalProcess
• GeneOrGeneProduct acts upstream of or within _0..* BiologicalProcess
• GeneOrGeneProduct acts upstream of or within negative effect _0..* BiologicalProcess
• GeneOrGeneProduct acts upstream of or within positive effect _0..* BiologicalProcess
• GeneOrGeneProduct acts upstream of positive effect _0..* BiologicalProcess
• MacromolecularMachineToBiologicalProcessAssociation macromolecular machine to biological process association➞object _1..1 BiologicalProcess

Attributes

Inherited from biological process or activity:

• enabled by _0..*
  • Description: holds between a process and a physical entity, where the physical entity executes the process
  • Range: PhysicalEntity
  • in subsets: (translator_minimal)

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}
  • Range: CategoryType
  • in subsets: (translator_minimal)
• type _0..1
  • Range: String
• description _0..1
  • Description: a human-readable description of an entity
  • Range: NarrativeText
  • in subsets: (translator_minimal)
• source _0..1
  • Description: a lightweight analog to the association class ‘has provider’ slot, which is the string name, or the authoritative (i.e. database) namespace, designating the origin of the entity to which the slot belongs.
  • Range: LabelType
  • in subsets: (translator_minimal)
• provided by _0..*
  • Description: connects an association to the agent (person, organization or group) that provided it
  • Range: Agent
• has attribute _0..*
  • Description: connects any entity to an attribute
  • Range: Attribute
  • in subsets: (samples)

Inherited from macromolecular machine mixin:

• macromolecular machine mixin➞name _0..1
  • Description: genes are typically designated by a short symbol and a full name. We map the symbol to the default display name and use an additional slot for full name
  • Range: SymbolType
  • in subsets: (translator_minimal,samples)

Inherited from named thing:

• named thing➞category _1..*
  • 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}
  • Range: NamedThing
  • in subsets: (translator_minimal)

Other properties