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Class: DiseasePhenotypeAssociation

Optional association for Disease -> Phenotype when the clinical feature requires edge metadata such as frequency, onset, severity, source cohort, or evidence. Materializes to disease_manifests_as_phenotype.

URI: alskb:DiseasePhenotypeAssociation

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

      DiseasePhenotypeAssociation : association_id

      DiseasePhenotypeAssociation : association_label

      DiseasePhenotypeAssociation : cohort

      DiseasePhenotypeAssociation : confidence

      DiseasePhenotypeAssociation : evidence_source

      DiseasePhenotypeAssociation : evidence_type

      DiseasePhenotypeAssociation : frequency

      DiseasePhenotypeAssociation : has_disease





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



      DiseasePhenotypeAssociation : has_phenotype





        DiseasePhenotypeAssociation --> "1" Phenotype : has_phenotype
        click Phenotype href "../Phenotype/"



      DiseasePhenotypeAssociation : ingest_date

      DiseasePhenotypeAssociation : last_updated

      DiseasePhenotypeAssociation : object

      DiseasePhenotypeAssociation : onset_type





        DiseasePhenotypeAssociation --> "0..1" OnsetTypeEnum : onset_type
        click OnsetTypeEnum href "../OnsetTypeEnum/"



      DiseasePhenotypeAssociation : predicate

      DiseasePhenotypeAssociation : severity

      DiseasePhenotypeAssociation : source

      DiseasePhenotypeAssociation : source_version

      DiseasePhenotypeAssociation : subject

Inheritance

Slots

Name Cardinality and Range Description Inheritance
has_disease 1
Disease		 direct
has_phenotype 1
Phenotype		 direct
predicate 0..1
String		 direct
frequency 0..1
String		 Frequency in affected population or cohort direct
severity 0..1
String		 Typical severity or severity distribution direct
onset_type 0..1
OnsetTypeEnum		 Onset pattern when phenotype is onset-specific direct
cohort 0..1
String		 Cohort or study population supporting this phenotype 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:DiseasePhenotypeAssociation
native alskb:DiseasePhenotypeAssociation

LinkML Source

Direct

name: DiseasePhenotypeAssociation
description: Optional association for Disease -> Phenotype when the clinical feature
  requires edge metadata such as frequency, onset, severity, source cohort, or evidence.
  Materializes to disease_manifests_as_phenotype.
from_schema: https://cair2015.github.io/als-kg
is_a: Association
attributes:
  has_disease:
    name: has_disease
    from_schema: https://cair2015.github.io/als-kg
    domain_of:
    - DiseasePhenotypeAssociation
    - GeneDiseaseAssociation
    - VariantDiseaseAssociation
    - DrugDiseaseTherapeuticAssociation
    - ExposureDiseaseAssociation
    range: Disease
    required: true
  has_phenotype:
    name: has_phenotype
    from_schema: https://cair2015.github.io/als-kg
    domain_of:
    - DiseasePhenotypeAssociation
    range: Phenotype
    required: true
  predicate:
    name: predicate
    from_schema: https://cair2015.github.io/als-kg
    slot_uri: rdf:predicate
    ifabsent: alskb:disease_manifests_as_phenotype
    domain_of:
    - Relationship
    - Association
    - DiseasePhenotypeAssociation
    - GeneDiseaseAssociation
    - VariantDiseaseAssociation
    - VariantProteinEffectAssociation
    - ProteinProteinInteractionAssociation
    - ProteinPathwayAssociation
    - DrugTargetAssociation
    - DrugDiseaseTherapeuticAssociation
    - ExposureDiseaseAssociation
    - TranscriptionFactorRegulationAssociation
    - GeneExpressionAssociation
    - DiseaseDiseaseAssociation
  frequency:
    name: frequency
    description: Frequency in affected population or cohort
    from_schema: https://cair2015.github.io/als-kg
    domain_of:
    - Phenotype
    - DiseasePhenotypeAssociation
  severity:
    name: severity
    description: Typical severity or severity distribution
    from_schema: https://cair2015.github.io/als-kg
    domain_of:
    - Phenotype
    - DiseasePhenotypeAssociation
  onset_type:
    name: onset_type
    description: Onset pattern when phenotype is onset-specific
    from_schema: https://cair2015.github.io/als-kg
    domain_of:
    - Disease
    - DiseasePhenotypeAssociation
    range: OnsetTypeEnum
  cohort:
    name: cohort
    description: Cohort or study population supporting this phenotype annotation
    from_schema: https://cair2015.github.io/als-kg
    domain_of:
    - DiseaseSubtype
    - DiseasePhenotypeAssociation

Induced

name: DiseasePhenotypeAssociation
description: Optional association for Disease -> Phenotype when the clinical feature
  requires edge metadata such as frequency, onset, severity, source cohort, or evidence.
  Materializes to disease_manifests_as_phenotype.
from_schema: https://cair2015.github.io/als-kg
is_a: Association
attributes:
  has_disease:
    name: has_disease
    from_schema: https://cair2015.github.io/als-kg
    alias: has_disease
    owner: DiseasePhenotypeAssociation
    domain_of:
    - DiseasePhenotypeAssociation
    - GeneDiseaseAssociation
    - VariantDiseaseAssociation
    - DrugDiseaseTherapeuticAssociation
    - ExposureDiseaseAssociation
    range: Disease
    required: true
  has_phenotype:
    name: has_phenotype
    from_schema: https://cair2015.github.io/als-kg
    alias: has_phenotype
    owner: DiseasePhenotypeAssociation
    domain_of:
    - DiseasePhenotypeAssociation
    range: Phenotype
    required: true
  predicate:
    name: predicate
    from_schema: https://cair2015.github.io/als-kg
    slot_uri: rdf:predicate
    ifabsent: alskb:disease_manifests_as_phenotype
    alias: predicate
    owner: DiseasePhenotypeAssociation
    domain_of:
    - Relationship
    - Association
    - DiseasePhenotypeAssociation
    - GeneDiseaseAssociation
    - VariantDiseaseAssociation
    - VariantProteinEffectAssociation
    - ProteinProteinInteractionAssociation
    - ProteinPathwayAssociation
    - DrugTargetAssociation
    - DrugDiseaseTherapeuticAssociation
    - ExposureDiseaseAssociation
    - TranscriptionFactorRegulationAssociation
    - GeneExpressionAssociation
    - DiseaseDiseaseAssociation
    range: string
  frequency:
    name: frequency
    description: Frequency in affected population or cohort
    from_schema: https://cair2015.github.io/als-kg
    alias: frequency
    owner: DiseasePhenotypeAssociation
    domain_of:
    - Phenotype
    - DiseasePhenotypeAssociation
    range: string
  severity:
    name: severity
    description: Typical severity or severity distribution
    from_schema: https://cair2015.github.io/als-kg
    alias: severity
    owner: DiseasePhenotypeAssociation
    domain_of:
    - Phenotype
    - DiseasePhenotypeAssociation
    range: string
  onset_type:
    name: onset_type
    description: Onset pattern when phenotype is onset-specific
    from_schema: https://cair2015.github.io/als-kg
    alias: onset_type
    owner: DiseasePhenotypeAssociation
    domain_of:
    - Disease
    - DiseasePhenotypeAssociation
    range: OnsetTypeEnum
  cohort:
    name: cohort
    description: Cohort or study population supporting this phenotype annotation
    from_schema: https://cair2015.github.io/als-kg
    alias: cohort
    owner: DiseasePhenotypeAssociation
    domain_of:
    - DiseaseSubtype
    - DiseasePhenotypeAssociation
    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: DiseasePhenotypeAssociation
    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: DiseasePhenotypeAssociation
    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: DiseasePhenotypeAssociation
    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: DiseasePhenotypeAssociation
    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: DiseasePhenotypeAssociation
    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: DiseasePhenotypeAssociation
    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: DiseasePhenotypeAssociation
    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: DiseasePhenotypeAssociation
    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: DiseasePhenotypeAssociation
    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: DiseasePhenotypeAssociation
    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: DiseasePhenotypeAssociation
    domain_of:
    - NamedEntity
    - Association
    range: string