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Class: ProteinProteinInteractionAssociation

Optional association for Protein -> Protein when interaction score, interaction type, database evidence, or assay metadata are needed. Materializes to protein_interacts_with_protein.

URI: alskb:ProteinProteinInteractionAssociation

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

      ProteinProteinInteractionAssociation : assay

      ProteinProteinInteractionAssociation : association_id

      ProteinProteinInteractionAssociation : association_label

      ProteinProteinInteractionAssociation : confidence

      ProteinProteinInteractionAssociation : evidence_source

      ProteinProteinInteractionAssociation : evidence_type

      ProteinProteinInteractionAssociation : ingest_date

      ProteinProteinInteractionAssociation : interaction_score

      ProteinProteinInteractionAssociation : interaction_type

      ProteinProteinInteractionAssociation : last_updated

      ProteinProteinInteractionAssociation : object

      ProteinProteinInteractionAssociation : predicate

      ProteinProteinInteractionAssociation : protein_1





        ProteinProteinInteractionAssociation --> "1" Protein : protein_1
        click Protein href "../Protein/"



      ProteinProteinInteractionAssociation : protein_2





        ProteinProteinInteractionAssociation --> "1" Protein : protein_2
        click Protein href "../Protein/"



      ProteinProteinInteractionAssociation : source

      ProteinProteinInteractionAssociation : source_version

      ProteinProteinInteractionAssociation : subject

Inheritance

Slots

Name Cardinality and Range Description Inheritance
protein_1 1
Protein		 direct
protein_2 1
Protein		 direct
predicate 0..1
String		 direct
interaction_score 0..1
Float		 Source-specific confidence score such as STRING combined score direct
interaction_type 0..1
String		 direct, indirect, physical, genetic, colocalization, pathway, or predicted direct
assay 0..1
String		 Assay or method supporting the interaction 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:ProteinProteinInteractionAssociation
native alskb:ProteinProteinInteractionAssociation

LinkML Source

Direct

name: ProteinProteinInteractionAssociation
description: Optional association for Protein -> Protein when interaction score, interaction
  type, database evidence, or assay metadata are needed. Materializes to protein_interacts_with_protein.
from_schema: https://cair2015.github.io/als-kg
is_a: Association
attributes:
  protein_1:
    name: protein_1
    from_schema: https://cair2015.github.io/als-kg
    rank: 1000
    domain_of:
    - ProteinProteinInteractionAssociation
    range: Protein
    required: true
  protein_2:
    name: protein_2
    from_schema: https://cair2015.github.io/als-kg
    rank: 1000
    domain_of:
    - ProteinProteinInteractionAssociation
    range: Protein
    required: true
  predicate:
    name: predicate
    from_schema: https://cair2015.github.io/als-kg
    slot_uri: rdf:predicate
    ifabsent: alskb:protein_interacts_with_protein
    domain_of:
    - Relationship
    - Association
    - DiseasePhenotypeAssociation
    - GeneDiseaseAssociation
    - VariantDiseaseAssociation
    - VariantProteinEffectAssociation
    - ProteinProteinInteractionAssociation
    - ProteinPathwayAssociation
    - DrugTargetAssociation
    - DrugDiseaseTherapeuticAssociation
    - ExposureDiseaseAssociation
    - TranscriptionFactorRegulationAssociation
    - GeneExpressionAssociation
    - DiseaseDiseaseAssociation
  interaction_score:
    name: interaction_score
    description: Source-specific confidence score such as STRING combined score
    from_schema: https://cair2015.github.io/als-kg
    rank: 1000
    domain_of:
    - ProteinProteinInteractionAssociation
    range: float
  interaction_type:
    name: interaction_type
    description: direct, indirect, physical, genetic, colocalization, pathway, or
      predicted
    from_schema: https://cair2015.github.io/als-kg
    rank: 1000
    domain_of:
    - ProteinProteinInteractionAssociation
  assay:
    name: assay
    description: Assay or method supporting the interaction
    from_schema: https://cair2015.github.io/als-kg
    domain_of:
    - VariantProteinEffectAssociation
    - ProteinProteinInteractionAssociation

Induced

name: ProteinProteinInteractionAssociation
description: Optional association for Protein -> Protein when interaction score, interaction
  type, database evidence, or assay metadata are needed. Materializes to protein_interacts_with_protein.
from_schema: https://cair2015.github.io/als-kg
is_a: Association
attributes:
  protein_1:
    name: protein_1
    from_schema: https://cair2015.github.io/als-kg
    rank: 1000
    alias: protein_1
    owner: ProteinProteinInteractionAssociation
    domain_of:
    - ProteinProteinInteractionAssociation
    range: Protein
    required: true
  protein_2:
    name: protein_2
    from_schema: https://cair2015.github.io/als-kg
    rank: 1000
    alias: protein_2
    owner: ProteinProteinInteractionAssociation
    domain_of:
    - ProteinProteinInteractionAssociation
    range: Protein
    required: true
  predicate:
    name: predicate
    from_schema: https://cair2015.github.io/als-kg
    slot_uri: rdf:predicate
    ifabsent: alskb:protein_interacts_with_protein
    alias: predicate
    owner: ProteinProteinInteractionAssociation
    domain_of:
    - Relationship
    - Association
    - DiseasePhenotypeAssociation
    - GeneDiseaseAssociation
    - VariantDiseaseAssociation
    - VariantProteinEffectAssociation
    - ProteinProteinInteractionAssociation
    - ProteinPathwayAssociation
    - DrugTargetAssociation
    - DrugDiseaseTherapeuticAssociation
    - ExposureDiseaseAssociation
    - TranscriptionFactorRegulationAssociation
    - GeneExpressionAssociation
    - DiseaseDiseaseAssociation
    range: string
  interaction_score:
    name: interaction_score
    description: Source-specific confidence score such as STRING combined score
    from_schema: https://cair2015.github.io/als-kg
    rank: 1000
    alias: interaction_score
    owner: ProteinProteinInteractionAssociation
    domain_of:
    - ProteinProteinInteractionAssociation
    range: float
  interaction_type:
    name: interaction_type
    description: direct, indirect, physical, genetic, colocalization, pathway, or
      predicted
    from_schema: https://cair2015.github.io/als-kg
    rank: 1000
    alias: interaction_type
    owner: ProteinProteinInteractionAssociation
    domain_of:
    - ProteinProteinInteractionAssociation
    range: string
  assay:
    name: assay
    description: Assay or method supporting the interaction
    from_schema: https://cair2015.github.io/als-kg
    alias: assay
    owner: ProteinProteinInteractionAssociation
    domain_of:
    - VariantProteinEffectAssociation
    - ProteinProteinInteractionAssociation
    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: ProteinProteinInteractionAssociation
    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: ProteinProteinInteractionAssociation
    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: ProteinProteinInteractionAssociation
    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: ProteinProteinInteractionAssociation
    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: ProteinProteinInteractionAssociation
    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: ProteinProteinInteractionAssociation
    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: ProteinProteinInteractionAssociation
    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: ProteinProteinInteractionAssociation
    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: ProteinProteinInteractionAssociation
    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: ProteinProteinInteractionAssociation
    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: ProteinProteinInteractionAssociation
    domain_of:
    - NamedEntity
    - Association
    range: string