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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 : description

      GeneExpressionOutput : id

      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
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
  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