Class: BiologicalProcess

Description: One or more causally connected executions of molecular functions

classDiagram class BiologicalProcess Occurrent <|-- BiologicalProcess OntologyClass <|-- BiologicalProcess BiologicalProcessOrActivity <|-- BiologicalProcess BiologicalProcess <|-- Pathway BiologicalProcess <|-- PhysiologicalProcess BiologicalProcess <|-- Behavior BiologicalProcess <|-- PathologicalProcess BiologicalProcess : category BiologicalProcess : deprecated BiologicalProcess : description BiologicalProcess : enabled_by BiologicalProcess --|> PhysicalEntity : enabled_by BiologicalProcess : full_name BiologicalProcess : has_attribute BiologicalProcess --|> Attribute : has_attribute BiologicalProcess : has_input BiologicalProcess --|> NamedThing : has_input BiologicalProcess : has_output BiologicalProcess --|> NamedThing : has_output BiologicalProcess : id BiologicalProcess : in_taxon BiologicalProcess --|> OrganismTaxon : in_taxon BiologicalProcess : in_taxon_label BiologicalProcess : iri BiologicalProcess : name BiologicalProcess : provided_by BiologicalProcess : synonym BiologicalProcess : type BiologicalProcess : xref

Inheritance

Entity
- NamedThing
  - BiologicalEntity [ ThingWithTaxon]
    - BiologicalProcessOrActivity [ Occurrent OntologyClass]
      - BiologicalProcess [ Occurrent OntologyClass]
        
        Pathway [ OntologyClass]
        
        PhysiologicalProcess [ OntologyClass]
        
        Behavior [ OntologyClass ActivityAndBehavior]
        
        PathologicalProcess [ PathologicalEntityMixin]

Slots

Name	Cardinality and Range	Inheritance
id: A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI	1 String	OntologyClass, Entity
has_input: holds between a process and a continuant, where the continuant is an input into the process	* NamedThing	BiologicalProcessOrActivity
has_output: holds between a process and a continuant, where the continuant is an output of the process	* NamedThing	BiologicalProcessOrActivity
enabled_by: holds between a process and a physical entity, where the physical entity executes the process	* PhysicalEntity	BiologicalProcessOrActivity
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
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: connects any entity to an 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
ProcessRegulatesProcessAssociation	subject	range	BiologicalProcess
ProcessRegulatesProcessAssociation	object	range	BiologicalProcess
MacromolecularMachineToBiologicalProcessAssociation	object	range	BiologicalProcess

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
GO	BiologicalProcessOrActivity MolecularActivity BiologicalProcess Pathway PhysiologicalProcess AnatomicalEntity CellularComponent MacromolecularComplex
REACT	BiologicalProcessOrActivity MolecularActivity BiologicalProcess Pathway PhysiologicalProcess MacromolecularComplex
metacyc.reaction	MolecularActivity BiologicalProcess
KEGG.MODULE	BiologicalProcess
KEGG	MolecularEntity ChemicalEntity SmallMolecule ChemicalMixture NucleicAcidEntity MolecularMixture ComplexMolecularMixture MolecularActivity BiologicalProcess Pathway ProcessedMaterial Drug EnvironmentalFoodContaminant FoodAdditive Food

LinkML Source

name: biological process
id_prefixes:
- GO
- REACT
- metacyc.reaction
- KEGG.MODULE
- KEGG
description: One or more causally connected executions of molecular functions
from_schema: https://w3id.org/biolink/biolink-model
exact_mappings:
- GO:0008150
- SIO:000006
- WIKIDATA:Q2996394
broad_mappings:
- WIKIDATA:P682
is_a: biological process or activity
mixins:
- occurrent
- ontology class