Class: GeneExpressionAssociation

Optional association for Gene -> Anatomy when expression level, specificity, tissue, cell type, disease stage, or differential-expression qualifiers are needed. Materializes to gene_expressed_in_anatomy.

URI: alskb:GeneExpressionAssociation

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

      GeneExpressionAssociation : adjusted_p_value

      GeneExpressionAssociation : association_id

      GeneExpressionAssociation : association_label

      GeneExpressionAssociation : confidence

      GeneExpressionAssociation : disease_stage

      GeneExpressionAssociation : evidence_source

      GeneExpressionAssociation : evidence_type

      GeneExpressionAssociation : expression_level

      GeneExpressionAssociation : has_anatomy





        GeneExpressionAssociation --> "1" Anatomy : has_anatomy
        click Anatomy href "../Anatomy/"



      GeneExpressionAssociation : has_gene





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



      GeneExpressionAssociation : ingest_date

      GeneExpressionAssociation : last_updated

      GeneExpressionAssociation : log2_fold_change

      GeneExpressionAssociation : object

      GeneExpressionAssociation : predicate

      GeneExpressionAssociation : source

      GeneExpressionAssociation : source_version

      GeneExpressionAssociation : specificity_index

      GeneExpressionAssociation : subject

      GeneExpressionAssociation : tissue_or_cell_type

Inheritance

Relationship
- Association
  - GeneExpressionAssociation

Slots

Name	Cardinality and Range	Description	Inheritance
has_gene	1 Gene		direct
has_anatomy	1 Anatomy		direct
predicate	0..1 String		direct
expression_level	0..1 String	high, medium, low, absent, upregulated, downregulated, or not_detected	direct
specificity_index	0..1 Float	Tissue-specificity score from 0 to 1	direct
log2_fold_change	0..1 Float	Differential expression log2 fold change when available	direct
adjusted_p_value	0..1 Float	Multiple-testing-adjusted p-value when available	direct
tissue_or_cell_type	0..1 String	Tissue or cell-type context	direct
disease_stage	0..1 String	Disease stage or clinical context	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:GeneExpressionAssociation
native	alskb:GeneExpressionAssociation

LinkML Source

Direct

name: GeneExpressionAssociation
description: Optional association for Gene -> Anatomy when expression level, specificity,
  tissue, cell type, disease stage, or differential-expression qualifiers are needed.
  Materializes to gene_expressed_in_anatomy.
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_anatomy:
    name: has_anatomy
    from_schema: https://cair2015.github.io/als-kg
    domain_of:
    - GeneExpressionAssociation
    range: Anatomy
    required: true
  predicate:
    name: predicate
    from_schema: https://cair2015.github.io/als-kg
    slot_uri: rdf:predicate
    ifabsent: alskb:gene_expressed_in_anatomy
    domain_of:
    - Relationship
    - Association
    - DiseasePhenotypeAssociation
    - GeneDiseaseAssociation
    - VariantDiseaseAssociation
    - VariantProteinEffectAssociation
    - ProteinProteinInteractionAssociation
    - ProteinPathwayAssociation
    - DrugTargetAssociation
    - DrugDiseaseTherapeuticAssociation
    - ExposureDiseaseAssociation
    - TranscriptionFactorRegulationAssociation
    - GeneExpressionAssociation
    - DiseaseDiseaseAssociation
  expression_level:
    name: expression_level
    description: high, medium, low, absent, upregulated, downregulated, or not_detected
    from_schema: https://cair2015.github.io/als-kg
    rank: 1000
    domain_of:
    - GeneExpressionAssociation
  specificity_index:
    name: specificity_index
    description: Tissue-specificity score from 0 to 1
    from_schema: https://cair2015.github.io/als-kg
    rank: 1000
    domain_of:
    - GeneExpressionAssociation
    range: float
  log2_fold_change:
    name: log2_fold_change
    description: Differential expression log2 fold change when available
    from_schema: https://cair2015.github.io/als-kg
    rank: 1000
    domain_of:
    - GeneExpressionAssociation
    range: float
  adjusted_p_value:
    name: adjusted_p_value
    description: Multiple-testing-adjusted p-value when available
    from_schema: https://cair2015.github.io/als-kg
    rank: 1000
    domain_of:
    - GeneExpressionAssociation
    range: float
  tissue_or_cell_type:
    name: tissue_or_cell_type
    description: Tissue or cell-type context
    from_schema: https://cair2015.github.io/als-kg
    domain_of:
    - TranscriptionFactorRegulationAssociation
    - GeneExpressionAssociation
  disease_stage:
    name: disease_stage
    description: Disease stage or clinical context
    from_schema: https://cair2015.github.io/als-kg
    rank: 1000
    domain_of:
    - GeneExpressionAssociation

Induced

name: GeneExpressionAssociation
description: Optional association for Gene -> Anatomy when expression level, specificity,
  tissue, cell type, disease stage, or differential-expression qualifiers are needed.
  Materializes to gene_expressed_in_anatomy.
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: GeneExpressionAssociation
    domain_of:
    - GeneDiseaseAssociation
    - GeneExpressionAssociation
    range: Gene
    required: true
  has_anatomy:
    name: has_anatomy
    from_schema: https://cair2015.github.io/als-kg
    alias: has_anatomy
    owner: GeneExpressionAssociation
    domain_of:
    - GeneExpressionAssociation
    range: Anatomy
    required: true
  predicate:
    name: predicate
    from_schema: https://cair2015.github.io/als-kg
    slot_uri: rdf:predicate
    ifabsent: alskb:gene_expressed_in_anatomy
    alias: predicate
    owner: GeneExpressionAssociation
    domain_of:
    - Relationship
    - Association
    - DiseasePhenotypeAssociation
    - GeneDiseaseAssociation
    - VariantDiseaseAssociation
    - VariantProteinEffectAssociation
    - ProteinProteinInteractionAssociation
    - ProteinPathwayAssociation
    - DrugTargetAssociation
    - DrugDiseaseTherapeuticAssociation
    - ExposureDiseaseAssociation
    - TranscriptionFactorRegulationAssociation
    - GeneExpressionAssociation
    - DiseaseDiseaseAssociation
    range: string
  expression_level:
    name: expression_level
    description: high, medium, low, absent, upregulated, downregulated, or not_detected
    from_schema: https://cair2015.github.io/als-kg
    rank: 1000
    alias: expression_level
    owner: GeneExpressionAssociation
    domain_of:
    - GeneExpressionAssociation
    range: string
  specificity_index:
    name: specificity_index
    description: Tissue-specificity score from 0 to 1
    from_schema: https://cair2015.github.io/als-kg
    rank: 1000
    alias: specificity_index
    owner: GeneExpressionAssociation
    domain_of:
    - GeneExpressionAssociation
    range: float
  log2_fold_change:
    name: log2_fold_change
    description: Differential expression log2 fold change when available
    from_schema: https://cair2015.github.io/als-kg
    rank: 1000
    alias: log2_fold_change
    owner: GeneExpressionAssociation
    domain_of:
    - GeneExpressionAssociation
    range: float
  adjusted_p_value:
    name: adjusted_p_value
    description: Multiple-testing-adjusted p-value when available
    from_schema: https://cair2015.github.io/als-kg
    rank: 1000
    alias: adjusted_p_value
    owner: GeneExpressionAssociation
    domain_of:
    - GeneExpressionAssociation
    range: float
  tissue_or_cell_type:
    name: tissue_or_cell_type
    description: Tissue or cell-type context
    from_schema: https://cair2015.github.io/als-kg
    alias: tissue_or_cell_type
    owner: GeneExpressionAssociation
    domain_of:
    - TranscriptionFactorRegulationAssociation
    - GeneExpressionAssociation
    range: string
  disease_stage:
    name: disease_stage
    description: Disease stage or clinical context
    from_schema: https://cair2015.github.io/als-kg
    rank: 1000
    alias: disease_stage
    owner: GeneExpressionAssociation
    domain_of:
    - GeneExpressionAssociation
    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: GeneExpressionAssociation
    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: GeneExpressionAssociation
    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: GeneExpressionAssociation
    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: GeneExpressionAssociation
    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: GeneExpressionAssociation
    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: GeneExpressionAssociation
    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: GeneExpressionAssociation
    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: GeneExpressionAssociation
    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: GeneExpressionAssociation
    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: GeneExpressionAssociation
    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: GeneExpressionAssociation
    domain_of:
    - NamedEntity
    - Association
    range: string