Class: GeneExpressionAssay

name: GeneExpressionAssay
annotations:
  supported_contexts:
    tag: supported_contexts
    value: in_vitro_only
description: General assay for gene expression measurements. Renamed from TranscriptionFactorExpressionMeasurement
  per domain feedback - gene expression is more commonly the primary output.
from_schema: https://w3id.org/EHS-Data-Standards/soma
is_a: Assay
slots:
- target_gene
- gene_expression_method
- normalization_reference
slot_usage:
  has_specified_output:
    name: has_specified_output
    range: GeneExpressionOutput

name: GeneExpressionAssay
annotations:
  supported_contexts:
    tag: supported_contexts
    value: in_vitro_only
description: General assay for gene expression measurements. Renamed from TranscriptionFactorExpressionMeasurement
  per domain feedback - gene expression is more commonly the primary output.
from_schema: https://w3id.org/EHS-Data-Standards/soma
is_a: Assay
slot_usage:
  has_specified_output:
    name: has_specified_output
    range: GeneExpressionOutput
attributes:
  target_gene:
    name: target_gene
    description: Target gene being measured.
    from_schema: https://w3id.org/EHS-Data-Standards/soma
    rank: 1000
    alias: target_gene
    owner: GeneExpressionAssay
    domain_of:
    - GeneExpressionAssay
    range: uriorcurie
  gene_expression_method:
    name: gene_expression_method
    description: Method used for gene expression (qRT-PCR, RNA-seq, etc.).
    from_schema: https://w3id.org/EHS-Data-Standards/soma
    rank: 1000
    alias: gene_expression_method
    owner: GeneExpressionAssay
    domain_of:
    - GeneExpressionAssay
    range: string
  normalization_reference:
    name: normalization_reference
    description: Normalization reference (beta-actin, GAPDH, total EGFR).
    from_schema: https://w3id.org/EHS-Data-Standards/soma
    rank: 1000
    alias: normalization_reference
    owner: GeneExpressionAssay
    domain_of:
    - EGFRSignalingAssay
    - GeneExpressionAssay
    range: string
  informs_on_key_event:
    name: informs_on_key_event
    description: The Key Event that this assay provides evidence for. This establishes
      the mechanistic connection between the assay measurements and the Adverse Outcome
      Pathway framework. Multiple assays can inform on the same key event, providing
      converging evidence.
    from_schema: https://w3id.org/EHS-Data-Standards/soma
    rank: 1000
    alias: informs_on_key_event
    owner: GeneExpressionAssay
    domain_of:
    - Assay
    range: KeyEvent
    inlined: true
  study_subject:
    name: study_subject
    description: The subject of the study — what the assay is performed on. Can be
      a ModelSystem (e.g., CellularSystem), an InVivoSubject, or a PopulationSubject.
      The type of subject determines which context slots are available.
    from_schema: https://w3id.org/EHS-Data-Standards/soma
    rank: 1000
    alias: study_subject
    owner: GeneExpressionAssay
    domain_of:
    - Assay
    range: StudySubject
    inlined: true
  has_exposure_condition:
    name: has_exposure_condition
    description: The exposure condition(s) applied to the study subject. Captures
      the agent, concentration, duration, and timing of exposure/treatment. Multivalued
      to support co-exposures or dose-response series.
    from_schema: https://w3id.org/EHS-Data-Standards/soma
    rank: 1000
    alias: has_exposure_condition
    owner: GeneExpressionAssay
    domain_of:
    - Assay
    range: ExposureCondition
    multivalued: true
    inlined: true
    inlined_as_list: true
  follows_protocols:
    name: follows_protocols
    description: The Protocol(s) that this assay follows. Any Protocol or Protocol
      subclass (ImagingProtocol, StainingProtocol, SpirometryProtocol, MolecularAssayProtocol)
      is valid. Use this for general protocol references; assay subclasses also have
      typed protocol slots for domain-specific protocols.
    from_schema: https://w3id.org/EHS-Data-Standards/soma
    rank: 1000
    alias: follows_protocols
    owner: GeneExpressionAssay
    domain_of:
    - Assay
    range: Protocol
    multivalued: true
    inlined: true
    inlined_as_list: true
  has_specified_output:
    name: has_specified_output
    description: The measurement results produced by this assay — the specified output
      of a planned process (OBI). Contains the domain-specific measurement values
      (e.g., beat frequency, cilia length for CiliaryFunctionAssay).
    from_schema: https://w3id.org/EHS-Data-Standards/soma
    exact_mappings:
    - OBI:0000299
    rank: 1000
    alias: has_specified_output
    owner: GeneExpressionAssay
    domain_of:
    - Assay
    range: GeneExpressionOutput
    inlined: true
  assay_date:
    name: assay_date
    description: Date when the assay was performed.
    from_schema: https://w3id.org/EHS-Data-Standards/soma
    rank: 1000
    alias: assay_date
    owner: GeneExpressionAssay
    domain_of:
    - Assay
    range: date
  id:
    name: id
    description: A unique identifier for the entity.
    from_schema: https://w3id.org/EHS-Data-Standards/soma
    rank: 1000
    identifier: true
    alias: id
    owner: GeneExpressionAssay
    domain_of:
    - NamedThing
    - Unit
    - NamedEntity
    range: uriorcurie
    required: true
  name:
    name: name
    description: A human-readable name for the entity.
    from_schema: https://w3id.org/EHS-Data-Standards/soma
    rank: 1000
    slot_uri: schema:name
    alias: name
    owner: GeneExpressionAssay
    domain_of:
    - NamedThing
    - Unit
    - NamedEntity
    range: string
  description:
    name: description
    description: A detailed description of the entity.
    from_schema: https://w3id.org/EHS-Data-Standards/soma
    rank: 1000
    slot_uri: schema:description
    alias: description
    owner: GeneExpressionAssay
    domain_of:
    - NamedThing
    range: string