Skip to content

Class: BiologicalProcessOrActivity

Description: Either an individual molecular activity, or a collection of causally connected molecular activities in a biological system.
classDiagram class BiologicalProcessOrActivity Occurrent <|-- BiologicalProcessOrActivity OntologyClass <|-- BiologicalProcessOrActivity BiologicalEntity <|-- BiologicalProcessOrActivity BiologicalProcessOrActivity <|-- MolecularActivity BiologicalProcessOrActivity <|-- BiologicalProcess BiologicalProcessOrActivity : category BiologicalProcessOrActivity : deprecated BiologicalProcessOrActivity : description BiologicalProcessOrActivity : enabled_by BiologicalProcessOrActivity --|> PhysicalEntity : enabled_by BiologicalProcessOrActivity : full_name BiologicalProcessOrActivity : has_attribute BiologicalProcessOrActivity --|> Attribute : has_attribute BiologicalProcessOrActivity : has_input BiologicalProcessOrActivity --|> NamedThing : has_input BiologicalProcessOrActivity : has_output BiologicalProcessOrActivity --|> NamedThing : has_output BiologicalProcessOrActivity : id BiologicalProcessOrActivity : in_taxon BiologicalProcessOrActivity --|> OrganismTaxon : in_taxon BiologicalProcessOrActivity : in_taxon_label BiologicalProcessOrActivity : iri BiologicalProcessOrActivity : name BiologicalProcessOrActivity : provided_by BiologicalProcessOrActivity : synonym BiologicalProcessOrActivity : type BiologicalProcessOrActivity : xref

Inheritance

Slots

Name Cardinality and Range Inheritance Examples
has_input:
holds between a process and a continuant, where the continuant is an input into the process
*
NamedThing		 direct
has_output:
holds between a process and a continuant, where the continuant is an output of the process 		*
NamedThing		 direct
enabled_by:
holds between a process and a physical entity, where the physical entity executes the process 		*
PhysicalEntity		 direct
id:
A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI 		1
String		 OntologyClass, Entity
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
BiologicalProcessOrActivity has_input domain BiologicalProcessOrActivity
BiologicalProcessOrActivity has_output domain BiologicalProcessOrActivity
BiologicalProcessOrActivity enabled_by domain BiologicalProcessOrActivity
MolecularActivity has_input domain BiologicalProcessOrActivity
MolecularActivity has_output domain BiologicalProcessOrActivity
MolecularActivity enabled_by domain BiologicalProcessOrActivity
BiologicalProcess has_input domain BiologicalProcessOrActivity
BiologicalProcess has_output domain BiologicalProcessOrActivity
BiologicalProcess enabled_by domain BiologicalProcessOrActivity
Pathway has_input domain BiologicalProcessOrActivity
Pathway has_output domain BiologicalProcessOrActivity
Pathway enabled_by domain BiologicalProcessOrActivity
PhysiologicalProcess has_input domain BiologicalProcessOrActivity
PhysiologicalProcess has_output domain BiologicalProcessOrActivity
PhysiologicalProcess enabled_by domain BiologicalProcessOrActivity
Behavior has_input domain BiologicalProcessOrActivity
Behavior has_output domain BiologicalProcessOrActivity
Behavior enabled_by domain BiologicalProcessOrActivity
PathologicalProcess has_input domain BiologicalProcessOrActivity
PathologicalProcess has_output domain BiologicalProcessOrActivity
PathologicalProcess enabled_by domain BiologicalProcessOrActivity

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

LinkML Source

name: biological process or activity
id_prefixes:
- GO
- REACT
description: Either an individual molecular activity, or a collection of causally
  connected molecular activities in a biological system.
from_schema: https://w3id.org/biolink/biolink-model
is_a: biological entity
mixins:
- occurrent
- ontology class
slots:
- has input
- has output
- enabled by