Class: Pathway
classDiagram
class Pathway
OntologyClass <|-- Pathway
BiologicalProcess <|-- Pathway
Pathway : category
Pathway : deprecated
Pathway : description
Pathway : enabled_by
Pathway --|> PhysicalEntity : enabled_by
Pathway : full_name
Pathway : has_attribute
Pathway --|> Attribute : has_attribute
Pathway : has_input
Pathway --|> NamedThing : has_input
Pathway : has_output
Pathway --|> NamedThing : has_output
Pathway : id
Pathway : in_taxon
Pathway --|> OrganismTaxon : 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 | Inheritance | Examples |
|---|---|---|---|
| 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: holds between a process and a continuant, where the continuant is an input into the process |
* NamedThing |
BiologicalProcessOrActivity | |
| has_output: holds between a process and a continuant, where the continuant is an output of the process |
* NamedThing |
BiologicalProcessOrActivity | |
| enabled_by: holds between a process and a physical entity, where the physical entity executes the process |
* PhysicalEntity |
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 | |
| 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 |
|---|---|---|---|
| GeneToPathwayAssociation | object | range | Pathway |
| MolecularActivityToPathwayAssociation | object | range | Pathway |
| ChemicalToPathwayAssociation | object | range | Pathway |
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: 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