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Class: ProteinPathwayAssociation

Optional association for Protein -> Pathway when Reactome evidence code, source release, pathway hierarchy, species, or annotation provenance are needed. Materializes to protein_participates_in_pathway.

URI: alskb:ProteinPathwayAssociation

 classDiagram
    class ProteinPathwayAssociation
    click ProteinPathwayAssociation href "../ProteinPathwayAssociation/"
      Association <|-- ProteinPathwayAssociation
        click Association href "../Association/"

      ProteinPathwayAssociation : association_id

      ProteinPathwayAssociation : association_label

      ProteinPathwayAssociation : confidence

      ProteinPathwayAssociation : evidence_source

      ProteinPathwayAssociation : evidence_type

      ProteinPathwayAssociation : has_pathway





        ProteinPathwayAssociation --> "1" Pathway : has_pathway
        click Pathway href "../Pathway/"



      ProteinPathwayAssociation : has_protein





        ProteinPathwayAssociation --> "1" Protein : has_protein
        click Protein href "../Protein/"



      ProteinPathwayAssociation : ingest_date

      ProteinPathwayAssociation : last_updated

      ProteinPathwayAssociation : object

      ProteinPathwayAssociation : pathway_role

      ProteinPathwayAssociation : predicate

      ProteinPathwayAssociation : reactome_evidence_code

      ProteinPathwayAssociation : source

      ProteinPathwayAssociation : source_version

      ProteinPathwayAssociation : species

      ProteinPathwayAssociation : subject

Inheritance

Slots

Name Cardinality and Range Description Inheritance
has_protein 1
Protein		 direct
has_pathway 1
Pathway		 direct
predicate 0..1
String		 direct
reactome_evidence_code 0..1
String		 Reactome evidence code or inferred/electronic/manual annotation category when... direct
pathway_role 0..1
String		 participant, catalyst, regulator, input, output, or member, when this detail ... direct
species 0..1
String		 Species context for the Reactome protein-pathway annotation direct
association_id 0..1
Uriorcurie		 Stable identifier for the association record Association
association_label 0..1
String		 Human-readable summary of the association Association
subject 1
String		 Subject entity IRI or CURIE used to materialize a direct edge Association, Relationship
object 1
String		 Object entity IRI or CURIE used to materialize a direct edge Association, Relationship
source 0..1
String		 Data source for this association Association, Relationship
source_version 0..1
String		 Data source version or release date Association
evidence_type 0..1
String		 Type of supporting evidence Association, Relationship
evidence_source 0..1
String		 Publication, study, database record, or extraction artifact supporting the as... Association, Relationship
confidence 0..1
String		 Normalized confidence score from 0 to 1 Association, Relationship
ingest_date 0..1
String		 Date this association was ingested Association, Relationship
last_updated 0..1
String		 Date this association was last modified Association

Identifier and Mapping Information

Schema Source

  • from schema: https://cair2015.github.io/als-kg

Mappings

Mapping Type Mapped Value
self alskb:ProteinPathwayAssociation
native alskb:ProteinPathwayAssociation

LinkML Source

Direct

name: ProteinPathwayAssociation
description: Optional association for Protein -> Pathway when Reactome evidence code,
  source release, pathway hierarchy, species, or annotation provenance are needed.
  Materializes to protein_participates_in_pathway.
from_schema: https://cair2015.github.io/als-kg
is_a: Association
attributes:
  has_protein:
    name: has_protein
    from_schema: https://cair2015.github.io/als-kg
    domain_of:
    - VariantProteinEffectAssociation
    - ProteinPathwayAssociation
    range: Protein
    required: true
  has_pathway:
    name: has_pathway
    from_schema: https://cair2015.github.io/als-kg
    domain_of:
    - ProteinPathwayAssociation
    range: Pathway
    required: true
  predicate:
    name: predicate
    from_schema: https://cair2015.github.io/als-kg
    slot_uri: rdf:predicate
    ifabsent: alskb:protein_participates_in_pathway
    domain_of:
    - Relationship
    - Association
    - DiseasePhenotypeAssociation
    - GeneDiseaseAssociation
    - VariantDiseaseAssociation
    - VariantProteinEffectAssociation
    - ProteinProteinInteractionAssociation
    - ProteinPathwayAssociation
    - DrugTargetAssociation
    - DrugDiseaseTherapeuticAssociation
    - ExposureDiseaseAssociation
    - TranscriptionFactorRegulationAssociation
    - GeneExpressionAssociation
    - DiseaseDiseaseAssociation
  reactome_evidence_code:
    name: reactome_evidence_code
    description: Reactome evidence code or inferred/electronic/manual annotation category
      when available
    from_schema: https://cair2015.github.io/als-kg
    rank: 1000
    domain_of:
    - ProteinPathwayAssociation
  pathway_role:
    name: pathway_role
    description: participant, catalyst, regulator, input, output, or member, when
      this detail is available
    from_schema: https://cair2015.github.io/als-kg
    rank: 1000
    domain_of:
    - ProteinPathwayAssociation
  species:
    name: species
    description: Species context for the Reactome protein-pathway annotation
    from_schema: https://cair2015.github.io/als-kg
    domain_of:
    - Pathway
    - ProteinPathwayAssociation

Induced

name: ProteinPathwayAssociation
description: Optional association for Protein -> Pathway when Reactome evidence code,
  source release, pathway hierarchy, species, or annotation provenance are needed.
  Materializes to protein_participates_in_pathway.
from_schema: https://cair2015.github.io/als-kg
is_a: Association
attributes:
  has_protein:
    name: has_protein
    from_schema: https://cair2015.github.io/als-kg
    alias: has_protein
    owner: ProteinPathwayAssociation
    domain_of:
    - VariantProteinEffectAssociation
    - ProteinPathwayAssociation
    range: Protein
    required: true
  has_pathway:
    name: has_pathway
    from_schema: https://cair2015.github.io/als-kg
    alias: has_pathway
    owner: ProteinPathwayAssociation
    domain_of:
    - ProteinPathwayAssociation
    range: Pathway
    required: true
  predicate:
    name: predicate
    from_schema: https://cair2015.github.io/als-kg
    slot_uri: rdf:predicate
    ifabsent: alskb:protein_participates_in_pathway
    alias: predicate
    owner: ProteinPathwayAssociation
    domain_of:
    - Relationship
    - Association
    - DiseasePhenotypeAssociation
    - GeneDiseaseAssociation
    - VariantDiseaseAssociation
    - VariantProteinEffectAssociation
    - ProteinProteinInteractionAssociation
    - ProteinPathwayAssociation
    - DrugTargetAssociation
    - DrugDiseaseTherapeuticAssociation
    - ExposureDiseaseAssociation
    - TranscriptionFactorRegulationAssociation
    - GeneExpressionAssociation
    - DiseaseDiseaseAssociation
    range: string
  reactome_evidence_code:
    name: reactome_evidence_code
    description: Reactome evidence code or inferred/electronic/manual annotation category
      when available
    from_schema: https://cair2015.github.io/als-kg
    rank: 1000
    alias: reactome_evidence_code
    owner: ProteinPathwayAssociation
    domain_of:
    - ProteinPathwayAssociation
    range: string
  pathway_role:
    name: pathway_role
    description: participant, catalyst, regulator, input, output, or member, when
      this detail is available
    from_schema: https://cair2015.github.io/als-kg
    rank: 1000
    alias: pathway_role
    owner: ProteinPathwayAssociation
    domain_of:
    - ProteinPathwayAssociation
    range: string
  species:
    name: species
    description: Species context for the Reactome protein-pathway annotation
    from_schema: https://cair2015.github.io/als-kg
    alias: species
    owner: ProteinPathwayAssociation
    domain_of:
    - Pathway
    - ProteinPathwayAssociation
    range: string
  association_id:
    name: association_id
    description: Stable identifier for the association record
    from_schema: https://cair2015.github.io/als-kg
    rank: 1000
    slot_uri: schema:identifier
    alias: association_id
    owner: ProteinPathwayAssociation
    domain_of:
    - Association
    range: uriorcurie
  association_label:
    name: association_label
    description: Human-readable summary of the association
    from_schema: https://cair2015.github.io/als-kg
    rank: 1000
    slot_uri: rdfs:label
    alias: association_label
    owner: ProteinPathwayAssociation
    domain_of:
    - Association
    range: string
  subject:
    name: subject
    description: Subject entity IRI or CURIE used to materialize a direct edge
    from_schema: https://cair2015.github.io/als-kg
    slot_uri: rdf:subject
    alias: subject
    owner: ProteinPathwayAssociation
    domain_of:
    - Relationship
    - Association
    range: string
    required: true
  object:
    name: object
    description: Object entity IRI or CURIE used to materialize a direct edge
    from_schema: https://cair2015.github.io/als-kg
    slot_uri: rdf:object
    alias: object
    owner: ProteinPathwayAssociation
    domain_of:
    - Relationship
    - Association
    range: string
    required: true
  source:
    name: source
    description: Data source for this association
    from_schema: https://cair2015.github.io/als-kg
    slot_uri: dcterms:source
    alias: source
    owner: ProteinPathwayAssociation
    domain_of:
    - NamedEntity
    - Relationship
    - Association
    range: string
  source_version:
    name: source_version
    description: Data source version or release date
    from_schema: https://cair2015.github.io/als-kg
    slot_uri: dcterms:hasVersion
    alias: source_version
    owner: ProteinPathwayAssociation
    domain_of:
    - OntologyClass
    - Association
    range: string
  evidence_type:
    name: evidence_type
    description: Type of supporting evidence
    from_schema: https://cair2015.github.io/als-kg
    slot_uri: ECO:0000000
    alias: evidence_type
    owner: ProteinPathwayAssociation
    domain_of:
    - Relationship
    - Association
    range: string
  evidence_source:
    name: evidence_source
    description: Publication, study, database record, or extraction artifact supporting
      the association
    from_schema: https://cair2015.github.io/als-kg
    alias: evidence_source
    owner: ProteinPathwayAssociation
    domain_of:
    - Relationship
    - Association
    range: string
  confidence:
    name: confidence
    description: Normalized confidence score from 0 to 1
    from_schema: https://cair2015.github.io/als-kg
    alias: confidence
    owner: ProteinPathwayAssociation
    domain_of:
    - Relationship
    - Association
    range: string
  ingest_date:
    name: ingest_date
    description: Date this association was ingested
    from_schema: https://cair2015.github.io/als-kg
    alias: ingest_date
    owner: ProteinPathwayAssociation
    domain_of:
    - OntologyClass
    - Relationship
    - Association
    range: string
  last_updated:
    name: last_updated
    description: Date this association was last modified
    from_schema: https://cair2015.github.io/als-kg
    slot_uri: dcterms:modified
    alias: last_updated
    owner: ProteinPathwayAssociation
    domain_of:
    - NamedEntity
    - Association
    range: string