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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 : equivalent_identifiers 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 : information_content 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
information_content:
Information content (IC) value for a term, primarily from Automats. 		0..1
Float		 NamedThing
equivalent_identifiers:
A set of identifiers that are considered equivalent to the primary identifier of the entity. This attribute is used to represent a collection of identifiers that are considered equivalent to the primary identifier of an entity. These equivalent identifiers may come from different databases, ontologies, or naming conventions, but they all refer to the same underlying concept or entity. This attribute is particularly useful in data integration and interoperability scenarios, where it is important to recognize and link different representations of the same entity across various sources. 		*
Uriorcurie		 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
GeneOrGeneProductOrGeneFamilyToBiologicalProcessOrActivityAssociation object range BiologicalProcessOrActivity
BiologicalProcessOrActivityToGeneOrGeneProductOrGeneFamilyAssociation subject range BiologicalProcessOrActivity
BiologicalProcessOrActivityToBiologicalProcessOrActivityAssociation subject range BiologicalProcessOrActivity
BiologicalProcessOrActivityToBiologicalProcessOrActivityAssociation object range BiologicalProcessOrActivity
BiologicalProcessOrActivityToAnatomicalEntityAssociation subject range 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