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Class: VariantDiseaseAssociation

Optional association for Variant -> Disease when variant-level evidence, clinical significance, inheritance, penetrance, or source assertions are needed. Materializes to variant_associated_with_disease.

URI: alskb:VariantDiseaseAssociation

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

      VariantDiseaseAssociation : association_id

      VariantDiseaseAssociation : association_label

      VariantDiseaseAssociation : association_type

      VariantDiseaseAssociation : clinical_significance

      VariantDiseaseAssociation : confidence

      VariantDiseaseAssociation : evidence_source

      VariantDiseaseAssociation : evidence_type

      VariantDiseaseAssociation : has_disease





        VariantDiseaseAssociation --> "1" Disease : has_disease
        click Disease href "../Disease/"



      VariantDiseaseAssociation : has_variant





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



      VariantDiseaseAssociation : ingest_date

      VariantDiseaseAssociation : inheritance_mode

      VariantDiseaseAssociation : last_updated

      VariantDiseaseAssociation : object

      VariantDiseaseAssociation : penetrance

      VariantDiseaseAssociation : predicate

      VariantDiseaseAssociation : source

      VariantDiseaseAssociation : source_version

      VariantDiseaseAssociation : subject

Inheritance

Slots

Name Cardinality and Range Description Inheritance
has_variant 1
Variant		 direct
has_disease 1
Disease		 direct
predicate 0..1
String		 direct
clinical_significance 0..1
String		 ClinVar/ACMG or ALS-specific clinical interpretation direct
inheritance_mode 0..1
String		 autosomal_dominant, autosomal_recessive, X_linked, mitochondrial, complex, or... direct
penetrance 0..1
String		 Complete, reduced, age-dependent, or unknown penetrance direct
association_type 0..1
String		 causal, risk_factor, modifier, protective, or uncertain 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:VariantDiseaseAssociation
native alskb:VariantDiseaseAssociation

LinkML Source

Direct

name: VariantDiseaseAssociation
description: Optional association for Variant -> Disease when variant-level evidence,
  clinical significance, inheritance, penetrance, or source assertions are needed.
  Materializes to variant_associated_with_disease.
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_disease:
    name: has_disease
    from_schema: https://cair2015.github.io/als-kg
    domain_of:
    - DiseasePhenotypeAssociation
    - GeneDiseaseAssociation
    - VariantDiseaseAssociation
    - DrugDiseaseTherapeuticAssociation
    - ExposureDiseaseAssociation
    range: Disease
    required: true
  predicate:
    name: predicate
    from_schema: https://cair2015.github.io/als-kg
    slot_uri: rdf:predicate
    ifabsent: alskb:variant_associated_with_disease
    domain_of:
    - Relationship
    - Association
    - DiseasePhenotypeAssociation
    - GeneDiseaseAssociation
    - VariantDiseaseAssociation
    - VariantProteinEffectAssociation
    - ProteinProteinInteractionAssociation
    - ProteinPathwayAssociation
    - DrugTargetAssociation
    - DrugDiseaseTherapeuticAssociation
    - ExposureDiseaseAssociation
    - TranscriptionFactorRegulationAssociation
    - GeneExpressionAssociation
    - DiseaseDiseaseAssociation
  clinical_significance:
    name: clinical_significance
    description: ClinVar/ACMG or ALS-specific clinical interpretation
    from_schema: https://cair2015.github.io/als-kg
    domain_of:
    - Variant
    - VariantDiseaseAssociation
  inheritance_mode:
    name: inheritance_mode
    description: autosomal_dominant, autosomal_recessive, X_linked, mitochondrial,
      complex, or unknown
    from_schema: https://cair2015.github.io/als-kg
    rank: 1000
    domain_of:
    - VariantDiseaseAssociation
  penetrance:
    name: penetrance
    description: Complete, reduced, age-dependent, or unknown penetrance
    from_schema: https://cair2015.github.io/als-kg
    rank: 1000
    domain_of:
    - VariantDiseaseAssociation
  association_type:
    name: association_type
    description: causal, risk_factor, modifier, protective, or uncertain
    from_schema: https://cair2015.github.io/als-kg
    domain_of:
    - GeneDiseaseAssociation
    - VariantDiseaseAssociation
    - ExposureDiseaseAssociation

Induced

name: VariantDiseaseAssociation
description: Optional association for Variant -> Disease when variant-level evidence,
  clinical significance, inheritance, penetrance, or source assertions are needed.
  Materializes to variant_associated_with_disease.
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: VariantDiseaseAssociation
    domain_of:
    - VariantDiseaseAssociation
    - VariantProteinEffectAssociation
    range: Variant
    required: true
  has_disease:
    name: has_disease
    from_schema: https://cair2015.github.io/als-kg
    alias: has_disease
    owner: VariantDiseaseAssociation
    domain_of:
    - DiseasePhenotypeAssociation
    - GeneDiseaseAssociation
    - VariantDiseaseAssociation
    - DrugDiseaseTherapeuticAssociation
    - ExposureDiseaseAssociation
    range: Disease
    required: true
  predicate:
    name: predicate
    from_schema: https://cair2015.github.io/als-kg
    slot_uri: rdf:predicate
    ifabsent: alskb:variant_associated_with_disease
    alias: predicate
    owner: VariantDiseaseAssociation
    domain_of:
    - Relationship
    - Association
    - DiseasePhenotypeAssociation
    - GeneDiseaseAssociation
    - VariantDiseaseAssociation
    - VariantProteinEffectAssociation
    - ProteinProteinInteractionAssociation
    - ProteinPathwayAssociation
    - DrugTargetAssociation
    - DrugDiseaseTherapeuticAssociation
    - ExposureDiseaseAssociation
    - TranscriptionFactorRegulationAssociation
    - GeneExpressionAssociation
    - DiseaseDiseaseAssociation
    range: string
  clinical_significance:
    name: clinical_significance
    description: ClinVar/ACMG or ALS-specific clinical interpretation
    from_schema: https://cair2015.github.io/als-kg
    alias: clinical_significance
    owner: VariantDiseaseAssociation
    domain_of:
    - Variant
    - VariantDiseaseAssociation
    range: string
  inheritance_mode:
    name: inheritance_mode
    description: autosomal_dominant, autosomal_recessive, X_linked, mitochondrial,
      complex, or unknown
    from_schema: https://cair2015.github.io/als-kg
    rank: 1000
    alias: inheritance_mode
    owner: VariantDiseaseAssociation
    domain_of:
    - VariantDiseaseAssociation
    range: string
  penetrance:
    name: penetrance
    description: Complete, reduced, age-dependent, or unknown penetrance
    from_schema: https://cair2015.github.io/als-kg
    rank: 1000
    alias: penetrance
    owner: VariantDiseaseAssociation
    domain_of:
    - VariantDiseaseAssociation
    range: string
  association_type:
    name: association_type
    description: causal, risk_factor, modifier, protective, or uncertain
    from_schema: https://cair2015.github.io/als-kg
    alias: association_type
    owner: VariantDiseaseAssociation
    domain_of:
    - GeneDiseaseAssociation
    - VariantDiseaseAssociation
    - ExposureDiseaseAssociation
    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: VariantDiseaseAssociation
    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: VariantDiseaseAssociation
    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: VariantDiseaseAssociation
    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: VariantDiseaseAssociation
    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: VariantDiseaseAssociation
    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: VariantDiseaseAssociation
    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: VariantDiseaseAssociation
    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: VariantDiseaseAssociation
    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: VariantDiseaseAssociation
    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: VariantDiseaseAssociation
    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: VariantDiseaseAssociation
    domain_of:
    - NamedEntity
    - Association
    range: string