Class: MolecularActivity

Description: An execution of a molecular function carried out by a gene product or macromolecular complex.

Aliases: molecular function, molecular event, reaction

classDiagram class MolecularActivity Occurrent <|-- MolecularActivity OntologyClass <|-- MolecularActivity BiologicalProcessOrActivity <|-- MolecularActivity MolecularActivity : category MolecularActivity : deprecated MolecularActivity : description MolecularActivity : enabled_by MolecularActivity --|> MacromolecularMachineMixin : enabled_by MolecularActivity : equivalent_identifiers MolecularActivity : full_name MolecularActivity : has_attribute MolecularActivity --|> Attribute : has_attribute MolecularActivity : has_input MolecularActivity --|> MolecularEntity : has_input MolecularActivity : has_output MolecularActivity --|> MolecularEntity : has_output MolecularActivity : id MolecularActivity : in_taxon MolecularActivity --|> OrganismTaxon : in_taxon MolecularActivity : in_taxon_label MolecularActivity : information_content MolecularActivity : iri MolecularActivity : name MolecularActivity : provided_by MolecularActivity : synonym MolecularActivity : type MolecularActivity : xref

Inheritance

Entity
- NamedThing
  - BiologicalEntity [ ThingWithTaxon]
    - BiologicalProcessOrActivity [ Occurrent OntologyClass]
      - MolecularActivity [ Occurrent OntologyClass]

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: A chemical entity that is the input for the reaction	* MolecularEntity	BiologicalProcessOrActivity
has_output: A chemical entity that is the output for the reaction	* MolecularEntity	BiologicalProcessOrActivity
enabled_by: The gene product, gene, or complex that catalyzes the reaction	* MacromolecularMachineMixin	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
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
MolecularActivityToPathwayAssociation	subject	range	MolecularActivity
MacromolecularMachineToMolecularActivityAssociation	object	range	MolecularActivity
MolecularActivityToChemicalEntityAssociation	subject	range	MolecularActivity
MolecularActivityToMolecularActivityAssociation	subject	range	MolecularActivity
MolecularActivityToMolecularActivityAssociation	object	range	MolecularActivity

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
RHEA	MolecularActivity
metacyc.reaction	MolecularActivity BiologicalProcess
EC	MolecularActivity
TCDB	MolecularActivity
KEGG.REACTION	MolecularActivity
KEGG	MolecularEntity ChemicalEntity SmallMolecule ChemicalMixture NucleicAcidEntity MolecularMixture ComplexMolecularMixture MolecularActivity BiologicalProcess Pathway ProcessedMaterial Drug EnvironmentalFoodContaminant FoodAdditive Food
KEGG.ORTHOLOGY	MolecularActivity GeneFamily
UMLS	OntologyClass OrganismTaxon MolecularEntity ChemicalEntity SmallMolecule ChemicalMixture NucleicAcidEntity MolecularMixture ComplexMolecularMixture MolecularActivity BiologicalProcess ProcessedMaterial Drug EnvironmentalFoodContaminant FoodAdditive Food Disease PhenotypicFeature AnatomicalEntity CellularComponent Cell GrossAnatomicalStructure Gene Polypeptide Protein
BIGG.REACTION	MolecularActivity
SEED.REACTION	MolecularActivity
METANETX.REACTION	MolecularActivity

LinkML Source

name: molecular activity
id_prefixes:
- GO
- REACT
- RHEA
- metacyc.reaction
- EC
- TCDB
- KEGG.REACTION
- KEGG
- KEGG.ORTHOLOGY
- UMLS
- BIGG.REACTION
- SEED.REACTION
- METANETX.REACTION
description: An execution of a molecular function carried out by a gene product or
  macromolecular complex.
from_schema: https://w3id.org/biolink/biolink-model
aliases:
- molecular function
- molecular event
- reaction
exact_mappings:
- GO:0003674
- STY:T044
broad_mappings:
- STY:T045
is_a: biological process or activity
mixins:
- occurrent
- ontology class
slot_usage:
  has input:
    name: has input
    description: A chemical entity that is the input for the reaction
    range: molecular entity
  has output:
    name: has output
    description: A chemical entity that is the output for the reaction
    range: molecular entity
  enabled by:
    name: enabled by
    description: The gene product, gene, or complex that catalyzes the reaction
    range: macromolecular machine mixin