Class: GeneDiseaseAssociation

Optional association for Gene -> Disease when causal/risk/protective or correlative gene-disease edges need evidence, scores, statistics, or source-specific qualifiers. Materializes to gene_associated_with_disease.

URI: alskb:GeneDiseaseAssociation

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

      GeneDiseaseAssociation : association_id

      GeneDiseaseAssociation : association_label

      GeneDiseaseAssociation : association_score

      GeneDiseaseAssociation : association_type

      GeneDiseaseAssociation : confidence

      GeneDiseaseAssociation : effect_direction

      GeneDiseaseAssociation : evidence_count

      GeneDiseaseAssociation : evidence_source

      GeneDiseaseAssociation : evidence_type

      GeneDiseaseAssociation : has_disease





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



      GeneDiseaseAssociation : has_gene





        GeneDiseaseAssociation --> "1" Gene : has_gene
        click Gene href "../Gene/"



      GeneDiseaseAssociation : ingest_date

      GeneDiseaseAssociation : last_updated

      GeneDiseaseAssociation : object

      GeneDiseaseAssociation : odds_ratio

      GeneDiseaseAssociation : p_value

      GeneDiseaseAssociation : predicate

      GeneDiseaseAssociation : source

      GeneDiseaseAssociation : source_version

      GeneDiseaseAssociation : subject

Inheritance

Relationship
- Association
  - GeneDiseaseAssociation

Slots

Name	Cardinality and Range	Description	Inheritance
has_gene	1 Gene		direct
has_disease	1 Disease		direct
predicate	0..1 String		direct
association_type	0..1 String	causal, risk_factor, protective, modifier, biomarker, or correlative	direct
association_score	0..1 Float	Source-specific gene-disease association score	direct
p_value	0..1 Float	Statistical significance when available	direct
odds_ratio	0..1 Float	Genetic association odds ratio when available	direct
effect_direction	0..1 String	increased_risk, decreased_risk, protective, upregulated, downregulated, or un...	direct
evidence_count	0..1 Integer	Number of supporting studies or records	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:GeneDiseaseAssociation
native	alskb:GeneDiseaseAssociation

LinkML Source

Direct

name: GeneDiseaseAssociation
description: Optional association for Gene -> Disease when causal/risk/protective
  or correlative gene-disease edges need evidence, scores, statistics, or source-specific
  qualifiers. Materializes to gene_associated_with_disease.
from_schema: https://cair2015.github.io/als-kg
is_a: Association
attributes:
  has_gene:
    name: has_gene
    from_schema: https://cair2015.github.io/als-kg
    domain_of:
    - GeneDiseaseAssociation
    - GeneExpressionAssociation
    range: Gene
    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:gene_associated_with_disease
    domain_of:
    - Relationship
    - Association
    - DiseasePhenotypeAssociation
    - GeneDiseaseAssociation
    - VariantDiseaseAssociation
    - VariantProteinEffectAssociation
    - ProteinProteinInteractionAssociation
    - ProteinPathwayAssociation
    - DrugTargetAssociation
    - DrugDiseaseTherapeuticAssociation
    - ExposureDiseaseAssociation
    - TranscriptionFactorRegulationAssociation
    - GeneExpressionAssociation
    - DiseaseDiseaseAssociation
  association_type:
    name: association_type
    description: causal, risk_factor, protective, modifier, biomarker, or correlative
    from_schema: https://cair2015.github.io/als-kg
    rank: 1000
    domain_of:
    - GeneDiseaseAssociation
    - VariantDiseaseAssociation
    - ExposureDiseaseAssociation
  association_score:
    name: association_score
    description: Source-specific gene-disease association score
    from_schema: https://cair2015.github.io/als-kg
    rank: 1000
    domain_of:
    - GeneDiseaseAssociation
    range: float
  p_value:
    name: p_value
    description: Statistical significance when available
    from_schema: https://cair2015.github.io/als-kg
    rank: 1000
    domain_of:
    - GeneDiseaseAssociation
    range: float
  odds_ratio:
    name: odds_ratio
    description: Genetic association odds ratio when available
    from_schema: https://cair2015.github.io/als-kg
    rank: 1000
    domain_of:
    - GeneDiseaseAssociation
    - ExposureDiseaseAssociation
    range: float
  effect_direction:
    name: effect_direction
    description: increased_risk, decreased_risk, protective, upregulated, downregulated,
      or unknown
    from_schema: https://cair2015.github.io/als-kg
    rank: 1000
    domain_of:
    - GeneDiseaseAssociation
  evidence_count:
    name: evidence_count
    description: Number of supporting studies or records
    from_schema: https://cair2015.github.io/als-kg
    rank: 1000
    domain_of:
    - GeneDiseaseAssociation
    range: integer

Induced

name: GeneDiseaseAssociation
description: Optional association for Gene -> Disease when causal/risk/protective
  or correlative gene-disease edges need evidence, scores, statistics, or source-specific
  qualifiers. Materializes to gene_associated_with_disease.
from_schema: https://cair2015.github.io/als-kg
is_a: Association
attributes:
  has_gene:
    name: has_gene
    from_schema: https://cair2015.github.io/als-kg
    alias: has_gene
    owner: GeneDiseaseAssociation
    domain_of:
    - GeneDiseaseAssociation
    - GeneExpressionAssociation
    range: Gene
    required: true
  has_disease:
    name: has_disease
    from_schema: https://cair2015.github.io/als-kg
    alias: has_disease
    owner: GeneDiseaseAssociation
    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:gene_associated_with_disease
    alias: predicate
    owner: GeneDiseaseAssociation
    domain_of:
    - Relationship
    - Association
    - DiseasePhenotypeAssociation
    - GeneDiseaseAssociation
    - VariantDiseaseAssociation
    - VariantProteinEffectAssociation
    - ProteinProteinInteractionAssociation
    - ProteinPathwayAssociation
    - DrugTargetAssociation
    - DrugDiseaseTherapeuticAssociation
    - ExposureDiseaseAssociation
    - TranscriptionFactorRegulationAssociation
    - GeneExpressionAssociation
    - DiseaseDiseaseAssociation
    range: string
  association_type:
    name: association_type
    description: causal, risk_factor, protective, modifier, biomarker, or correlative
    from_schema: https://cair2015.github.io/als-kg
    rank: 1000
    alias: association_type
    owner: GeneDiseaseAssociation
    domain_of:
    - GeneDiseaseAssociation
    - VariantDiseaseAssociation
    - ExposureDiseaseAssociation
    range: string
  association_score:
    name: association_score
    description: Source-specific gene-disease association score
    from_schema: https://cair2015.github.io/als-kg
    rank: 1000
    alias: association_score
    owner: GeneDiseaseAssociation
    domain_of:
    - GeneDiseaseAssociation
    range: float
  p_value:
    name: p_value
    description: Statistical significance when available
    from_schema: https://cair2015.github.io/als-kg
    rank: 1000
    alias: p_value
    owner: GeneDiseaseAssociation
    domain_of:
    - GeneDiseaseAssociation
    range: float
  odds_ratio:
    name: odds_ratio
    description: Genetic association odds ratio when available
    from_schema: https://cair2015.github.io/als-kg
    rank: 1000
    alias: odds_ratio
    owner: GeneDiseaseAssociation
    domain_of:
    - GeneDiseaseAssociation
    - ExposureDiseaseAssociation
    range: float
  effect_direction:
    name: effect_direction
    description: increased_risk, decreased_risk, protective, upregulated, downregulated,
      or unknown
    from_schema: https://cair2015.github.io/als-kg
    rank: 1000
    alias: effect_direction
    owner: GeneDiseaseAssociation
    domain_of:
    - GeneDiseaseAssociation
    range: string
  evidence_count:
    name: evidence_count
    description: Number of supporting studies or records
    from_schema: https://cair2015.github.io/als-kg
    rank: 1000
    alias: evidence_count
    owner: GeneDiseaseAssociation
    domain_of:
    - GeneDiseaseAssociation
    range: integer
  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: GeneDiseaseAssociation
    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: GeneDiseaseAssociation
    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: GeneDiseaseAssociation
    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: GeneDiseaseAssociation
    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: GeneDiseaseAssociation
    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: GeneDiseaseAssociation
    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: GeneDiseaseAssociation
    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: GeneDiseaseAssociation
    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: GeneDiseaseAssociation
    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: GeneDiseaseAssociation
    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: GeneDiseaseAssociation
    domain_of:
    - NamedEntity
    - Association
    range: string