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 : 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 : iri
MolecularActivity : name
MolecularActivity : provided_by
MolecularActivity : synonym
MolecularActivity : type
MolecularActivity : xref
Inheritance
- Entity
- NamedThing
- BiologicalEntity [ ThingWithTaxon]
- BiologicalProcessOrActivity [ Occurrent OntologyClass]
- MolecularActivity [ Occurrent OntologyClass]
- BiologicalProcessOrActivity [ Occurrent OntologyClass]
- BiologicalEntity [ ThingWithTaxon]
- NamedThing
Slots
| Name | Cardinality and Range | Inheritance | Examples |
|---|---|---|---|
| id: A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI |
1..1 String |
OntologyClass, Entity | |
| has_input: A chemical entity that is the input for the reaction |
0..* MolecularEntity |
BiologicalProcessOrActivity | |
| has_output: A chemical entity that is the output for the reaction |
0..* MolecularEntity |
BiologicalProcessOrActivity | |
| enabled_by: The gene product, gene, or complex that catalyzes the reaction |
0..* MacromolecularMachineMixin |
BiologicalProcessOrActivity | |
| in_taxon: connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon' |
0..* 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. |
0..* 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. |
0..* 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 |
0..* 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 |
0..* 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 |
0..* Attribute |
Entity | |
| deprecated: A boolean flag indicating that an entity is no longer considered current or valid. |
0..1 Boolean |
Entity |
Usages
Valid ID Prefixes
Instances of this class should have identifiers with one of the following prefixes, ordered with the most preferred first:
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
domain_of:
- biological process or activity
range: molecular entity
has output:
name: has output
description: A chemical entity that is the output for the reaction
domain_of:
- biological process or activity
range: molecular entity
enabled by:
name: enabled by
description: The gene product, gene, or complex that catalyzes the reaction
domain_of:
- biological process or activity
range: macromolecular machine mixin