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Class: GeneExpressionOutput

Measurement results from a gene expression assay. Contains the measured values for mRNA level, protein level, and positive cell percentage.

URI: soma:GeneExpressionOutput

 classDiagram
    class GeneExpressionOutput
    click GeneExpressionOutput href "../GeneExpressionOutput/"
      AssayOutputMeasurement <|-- GeneExpressionOutput
        click AssayOutputMeasurement href "../AssayOutputMeasurement/"

      GeneExpressionOutput : data_in_figure_only

      GeneExpressionOutput : description

      GeneExpressionOutput : evidence





        GeneExpressionOutput --> "* _recommended_" EvidenceItem : evidence
        click EvidenceItem href "../EvidenceItem/"



      GeneExpressionOutput : experimental_group





        GeneExpressionOutput --> "0..1" ExperimentalGroupEnum : experimental_group
        click ExperimentalGroupEnum href "../ExperimentalGroupEnum/"



      GeneExpressionOutput : id

      GeneExpressionOutput : measured_under





        GeneExpressionOutput --> "0..1" ExposureCondition : measured_under
        click ExposureCondition href "../ExposureCondition/"



      GeneExpressionOutput : mrna_level





        GeneExpressionOutput --> "0..1" QuantityValue : mrna_level
        click QuantityValue href "../QuantityValue/"



      GeneExpressionOutput : name

      GeneExpressionOutput : percentage_positive_cells





        GeneExpressionOutput --> "0..1" QuantityValue : percentage_positive_cells
        click QuantityValue href "../QuantityValue/"



      GeneExpressionOutput : protein_level





        GeneExpressionOutput --> "0..1" QuantityValue : protein_level
        click QuantityValue href "../QuantityValue/"

Inheritance

Slots

Name Cardinality and Range Description Inheritance
mrna_level 0..1
QuantityValue		 mRNA expression level direct
protein_level 0..1
QuantityValue		 Protein expression level direct
percentage_positive_cells 0..1
QuantityValue		 Percentage of positive cells (IHC, flow cytometry) direct
evidence * recommended
EvidenceItem		 Evidence items backing this object's claims AssayOutputMeasurement
experimental_group 0..1
ExperimentalGroupEnum		 The role of this output record's group in the experimental design: control, v... AssayOutputMeasurement
measured_under 0..1
ExposureCondition		 Reference (by id) to the specific ExposureCondition this output record was me... AssayOutputMeasurement
data_in_figure_only 0..1
Boolean		 True when the quantitative values for this output record are reported only in... AssayOutputMeasurement
id 1
Uriorcurie		 A unique identifier for the entity NamedThing
name 0..1
String		 A human-readable name for the entity NamedThing
description 0..1
String		 A detailed description of the entity NamedThing

Usages

used by used in type used
GeneExpressionAssay has_specified_output range GeneExpressionOutput

Identifier and Mapping Information

Schema Source

  • from schema: https://w3id.org/EHS-Data-Standards/soma

Mappings

Mapping Type Mapped Value
self soma:GeneExpressionOutput
native soma:GeneExpressionOutput

LinkML Source

Direct

name: GeneExpressionOutput
description: Measurement results from a gene expression assay. Contains the measured
  values for mRNA level, protein level, and positive cell percentage.
from_schema: https://w3id.org/EHS-Data-Standards/soma
is_a: AssayOutputMeasurement
slots:
- mrna_level
- protein_level
- percentage_positive_cells

Induced

name: GeneExpressionOutput
description: Measurement results from a gene expression assay. Contains the measured
  values for mRNA level, protein level, and positive cell percentage.
from_schema: https://w3id.org/EHS-Data-Standards/soma
is_a: AssayOutputMeasurement
attributes:
  mrna_level:
    name: mrna_level
    description: mRNA expression level.
    from_schema: https://w3id.org/EHS-Data-Standards/soma
    rank: 1000
    alias: mrna_level
    owner: GeneExpressionOutput
    domain_of:
    - GeneExpressionOutput
    range: QuantityValue
    inlined: true
  protein_level:
    name: protein_level
    description: Protein expression level.
    from_schema: https://w3id.org/EHS-Data-Standards/soma
    rank: 1000
    alias: protein_level
    owner: GeneExpressionOutput
    domain_of:
    - GeneExpressionOutput
    range: QuantityValue
    inlined: true
  percentage_positive_cells:
    name: percentage_positive_cells
    description: Percentage of positive cells (IHC, flow cytometry).
    from_schema: https://w3id.org/EHS-Data-Standards/soma
    rank: 1000
    alias: percentage_positive_cells
    owner: GeneExpressionOutput
    domain_of:
    - GeneExpressionOutput
    range: QuantityValue
    inlined: true
  evidence:
    name: evidence
    description: Evidence items backing this object's claims. Each one carries an
      exact quote from a cited publication.
    from_schema: https://w3id.org/EHS-Data-Standards/soma
    rank: 1000
    alias: evidence
    owner: GeneExpressionOutput
    domain_of:
    - KeyEvent
    - KeyEventRelationship
    - Assay
    - AssayOutputMeasurement
    range: EvidenceItem
    recommended: true
    multivalued: true
    inlined: true
    inlined_as_list: true
  experimental_group:
    name: experimental_group
    description: 'The role of this output record''s group in the experimental design:
      control, vehicle control, baseline, treated, recovery, or sham. Lets extraction
      distinguish the control/baseline response from the treated response so a change
      relative to control can be assembled downstream.'
    from_schema: https://w3id.org/EHS-Data-Standards/soma
    rank: 1000
    alias: experimental_group
    owner: GeneExpressionOutput
    domain_of:
    - AssayOutputMeasurement
    range: ExperimentalGroupEnum
  measured_under:
    name: measured_under
    description: Reference (by id) to the specific ExposureCondition this output record
      was measured under. Links each set of response values to the concentration/treatment
      it corresponds to, so a dose-response series keeps each response paired with
      its exposure level. The referenced condition should be listed in the assay's
      has_exposure_condition.
    from_schema: https://w3id.org/EHS-Data-Standards/soma
    rank: 1000
    alias: measured_under
    owner: GeneExpressionOutput
    domain_of:
    - AssayOutputMeasurement
    range: ExposureCondition
    inlined: false
  data_in_figure_only:
    name: data_in_figure_only
    description: True when the quantitative values for this output record are reported
      only in a figure or chart and could not be read from the text. The record then
      documents that the endpoint was measured and where its data lives (via an evidence
      item's figure_reference and article_section), without numeric values. This keeps
      figure-only results visible to reviewers in the workbook instead of silently
      dropping them.
    from_schema: https://w3id.org/EHS-Data-Standards/soma
    rank: 1000
    alias: data_in_figure_only
    owner: GeneExpressionOutput
    domain_of:
    - AssayOutputMeasurement
    range: boolean
  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: GeneExpressionOutput
    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: GeneExpressionOutput
    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: GeneExpressionOutput
    domain_of:
    - NamedThing
    range: string