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Class: VariantProteinEffectAssociation

Optional association for Variant -> Protein when protein consequence, predicted effect, assay result, or functional evidence is needed. Materializes to variant_affects_protein.

URI: alskb:VariantProteinEffectAssociation

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

      VariantProteinEffectAssociation : assay

      VariantProteinEffectAssociation : association_id

      VariantProteinEffectAssociation : association_label

      VariantProteinEffectAssociation : confidence

      VariantProteinEffectAssociation : evidence_source

      VariantProteinEffectAssociation : evidence_type

      VariantProteinEffectAssociation : functional_consequence

      VariantProteinEffectAssociation : has_protein





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



      VariantProteinEffectAssociation : has_variant





        VariantProteinEffectAssociation --> "1" Variant : has_variant
        click Variant href "../Variant/"



      VariantProteinEffectAssociation : ingest_date

      VariantProteinEffectAssociation : last_updated

      VariantProteinEffectAssociation : object

      VariantProteinEffectAssociation : predicate

      VariantProteinEffectAssociation : predicted_effect

      VariantProteinEffectAssociation : source

      VariantProteinEffectAssociation : source_version

      VariantProteinEffectAssociation : subject

Inheritance

Slots

Name Cardinality and Range Description Inheritance
has_variant 1
Variant		 direct
has_protein 1
Protein		 direct
predicate 0..1
String		 direct
functional_consequence 0..1
String		 missense, frameshift, nonsense, splice_site, synonymous, repeat_expansion, or... direct
predicted_effect 0..1
String		 loss_of_function, gain_of_function, dominant_negative, aggregation_prone, no_... direct
assay 0..1
String		 Functional assay or computational method supporting the effect 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:VariantProteinEffectAssociation
native alskb:VariantProteinEffectAssociation

LinkML Source

Direct

name: VariantProteinEffectAssociation
description: Optional association for Variant -> Protein when protein consequence,
  predicted effect, assay result, or functional evidence is needed. Materializes to
  variant_affects_protein.
from_schema: https://cair2015.github.io/als-kg
is_a: Association
attributes:
  has_variant:
    name: has_variant
    from_schema: https://cair2015.github.io/als-kg
    domain_of:
    - VariantDiseaseAssociation
    - VariantProteinEffectAssociation
    range: Variant
    required: true
  has_protein:
    name: has_protein
    from_schema: https://cair2015.github.io/als-kg
    domain_of:
    - VariantProteinEffectAssociation
    - ProteinPathwayAssociation
    range: Protein
    required: true
  predicate:
    name: predicate
    from_schema: https://cair2015.github.io/als-kg
    slot_uri: rdf:predicate
    ifabsent: alskb:variant_affects_protein
    domain_of:
    - Relationship
    - Association
    - DiseasePhenotypeAssociation
    - GeneDiseaseAssociation
    - VariantDiseaseAssociation
    - VariantProteinEffectAssociation
    - ProteinProteinInteractionAssociation
    - ProteinPathwayAssociation
    - DrugTargetAssociation
    - DrugDiseaseTherapeuticAssociation
    - ExposureDiseaseAssociation
    - TranscriptionFactorRegulationAssociation
    - GeneExpressionAssociation
    - DiseaseDiseaseAssociation
  functional_consequence:
    name: functional_consequence
    description: missense, frameshift, nonsense, splice_site, synonymous, repeat_expansion,
      or structural
    from_schema: https://cair2015.github.io/als-kg
    rank: 1000
    domain_of:
    - VariantProteinEffectAssociation
  predicted_effect:
    name: predicted_effect
    description: loss_of_function, gain_of_function, dominant_negative, aggregation_prone,
      no_change, or unknown
    from_schema: https://cair2015.github.io/als-kg
    rank: 1000
    domain_of:
    - VariantProteinEffectAssociation
  assay:
    name: assay
    description: Functional assay or computational method supporting the effect
    from_schema: https://cair2015.github.io/als-kg
    rank: 1000
    domain_of:
    - VariantProteinEffectAssociation
    - ProteinProteinInteractionAssociation

Induced

name: VariantProteinEffectAssociation
description: Optional association for Variant -> Protein when protein consequence,
  predicted effect, assay result, or functional evidence is needed. Materializes to
  variant_affects_protein.
from_schema: https://cair2015.github.io/als-kg
is_a: Association
attributes:
  has_variant:
    name: has_variant
    from_schema: https://cair2015.github.io/als-kg
    alias: has_variant
    owner: VariantProteinEffectAssociation
    domain_of:
    - VariantDiseaseAssociation
    - VariantProteinEffectAssociation
    range: Variant
    required: true
  has_protein:
    name: has_protein
    from_schema: https://cair2015.github.io/als-kg
    alias: has_protein
    owner: VariantProteinEffectAssociation
    domain_of:
    - VariantProteinEffectAssociation
    - ProteinPathwayAssociation
    range: Protein
    required: true
  predicate:
    name: predicate
    from_schema: https://cair2015.github.io/als-kg
    slot_uri: rdf:predicate
    ifabsent: alskb:variant_affects_protein
    alias: predicate
    owner: VariantProteinEffectAssociation
    domain_of:
    - Relationship
    - Association
    - DiseasePhenotypeAssociation
    - GeneDiseaseAssociation
    - VariantDiseaseAssociation
    - VariantProteinEffectAssociation
    - ProteinProteinInteractionAssociation
    - ProteinPathwayAssociation
    - DrugTargetAssociation
    - DrugDiseaseTherapeuticAssociation
    - ExposureDiseaseAssociation
    - TranscriptionFactorRegulationAssociation
    - GeneExpressionAssociation
    - DiseaseDiseaseAssociation
    range: string
  functional_consequence:
    name: functional_consequence
    description: missense, frameshift, nonsense, splice_site, synonymous, repeat_expansion,
      or structural
    from_schema: https://cair2015.github.io/als-kg
    rank: 1000
    alias: functional_consequence
    owner: VariantProteinEffectAssociation
    domain_of:
    - VariantProteinEffectAssociation
    range: string
  predicted_effect:
    name: predicted_effect
    description: loss_of_function, gain_of_function, dominant_negative, aggregation_prone,
      no_change, or unknown
    from_schema: https://cair2015.github.io/als-kg
    rank: 1000
    alias: predicted_effect
    owner: VariantProteinEffectAssociation
    domain_of:
    - VariantProteinEffectAssociation
    range: string
  assay:
    name: assay
    description: Functional assay or computational method supporting the effect
    from_schema: https://cair2015.github.io/als-kg
    rank: 1000
    alias: assay
    owner: VariantProteinEffectAssociation
    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: VariantProteinEffectAssociation
    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: VariantProteinEffectAssociation
    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: VariantProteinEffectAssociation
    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: VariantProteinEffectAssociation
    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: VariantProteinEffectAssociation
    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: VariantProteinEffectAssociation
    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: VariantProteinEffectAssociation
    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: VariantProteinEffectAssociation
    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: VariantProteinEffectAssociation
    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: VariantProteinEffectAssociation
    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: VariantProteinEffectAssociation
    domain_of:
    - NamedEntity
    - Association
    range: string