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Class: Pathway

URI: biolink:Pathway

classDiagram class Pathway OntologyClass <|-- Pathway BiologicalProcess <|-- Pathway Pathway : category Pathway : description Pathway : enabled_by Pathway --|> physical entity : enabled_by Pathway : full_name Pathway : has_attribute Pathway --|> attribute : has_attribute Pathway : has_input Pathway --|> named thing : has_input Pathway : has_output Pathway --|> named thing : has_output Pathway : id Pathway : in_taxon Pathway --|> organism taxon : in_taxon Pathway : in_taxon_label Pathway : iri Pathway : name Pathway : provided_by Pathway : synonym Pathway : type Pathway : xref

Inheritance

Slots

Name Cardinality and Range Description Inheritance
id 1..1
String		 A unique identifier for an entity Entity, OntologyClass
has_input 0..*
NamedThing		 holds between a process and a continuant, where the continuant is an input in... BiologicalProcessOrActivity
has_output 0..*
NamedThing		 holds between a process and a continuant, where the continuant is an output o... BiologicalProcessOrActivity
enabled_by 0..*
PhysicalEntity		 holds between a process and a physical entity, where the physical entity exec... BiologicalProcessOrActivity
in_taxon 0..*
OrganismTaxon		 connects an entity to its taxonomic classification ThingWithTaxon
in_taxon_label 0..1
LabelType		 The human readable scientific name for the taxon of the entity ThingWithTaxon
provided_by 0..*
String		 The value in this node property represents the knowledge provider that create... NamedThing
xref 0..*
Uriorcurie		 A database cross reference or alternative identifier for a NamedThing or edge... NamedThing
full_name 0..1
LabelType		 a long-form human readable name for a thing NamedThing
synonym 0..*
LabelType		 Alternate human-readable names for a thing NamedThing
iri 0..1
IriType		 An IRI for an entity Entity
category 1..*
CategoryType		 Name of the high level ontology class in which this entity is categorized Entity
type 0..*
String		 Entity
name 0..1
LabelType		 A human-readable name for an attribute or entity Entity
description 0..1
NarrativeText		 a human-readable description of an entity Entity
has_attribute 0..*
Attribute		 connects any entity to an attribute Entity

Usages

used by used in type used
GeneToPathwayAssociation object range Pathway
MolecularActivityToPathwayAssociation object range Pathway
ChemicalToPathwayAssociation object range Pathway

Identifier and Mapping Information

Valid ID Prefixes

Instances of this class should have identifiers with one of the following prefixes:

  • GO

  • REACT

  • KEGG

  • SMPDB

  • MSigDB

  • PHARMGKB.PATHWAYS

  • WIKIPATHWAYS

  • FB

  • PANTHER.PATHWAY

  • KEGG.PATHWAY

  • ncats.bioplanet

Schema Source

  • from schema: https://w3id.org/biolink/biolink-model

Mappings

Mapping Type Mapped Value
self biolink:Pathway
native biolink:Pathway
exact PW:0000001, WIKIDATA:Q4915012
narrow SIO:010526, GO:0007165

LinkML Source

Direct

name: pathway
id_prefixes:
- GO
- REACT
- KEGG
- SMPDB
- MSigDB
- PHARMGKB.PATHWAYS
- WIKIPATHWAYS
- FB
- PANTHER.PATHWAY
- KEGG.PATHWAY
- ncats.bioplanet
from_schema: https://w3id.org/biolink/biolink-model
exact_mappings:
- PW:0000001
- WIKIDATA:Q4915012
narrow_mappings:
- SIO:010526
- GO:0007165
is_a: biological process
mixins:
- ontology class