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Class: GeneExpressionMeasurement

Measurement of gene expression

URI: outcomes_model:GeneExpressionMeasurement

classDiagram class GeneExpressionMeasurement click GeneExpressionMeasurement href "../GeneExpressionMeasurement/" Measurement <|-- GeneExpressionMeasurement click Measurement href "../Measurement/" GeneExpressionMeasurement : description GeneExpressionMeasurement : gene_expression_analysis GeneExpressionMeasurement --> "0..1" GeneExpressionAnalysis : gene_expression_analysis click GeneExpressionAnalysis href "../GeneExpressionAnalysis/" GeneExpressionMeasurement : id GeneExpressionMeasurement : input_sample GeneExpressionMeasurement --> "0..1" InputSample : input_sample click InputSample href "../InputSample/" GeneExpressionMeasurement : method_assay GeneExpressionMeasurement --> "0..1" Assay : method_assay click Assay href "../Assay/" GeneExpressionMeasurement : mrna_level GeneExpressionMeasurement --> "0..1" QuantityValue : mrna_level click QuantityValue href "../QuantityValue/" GeneExpressionMeasurement : percentage_positive_cells GeneExpressionMeasurement --> "0..1" QuantityValue : percentage_positive_cells click QuantityValue href "../QuantityValue/" GeneExpressionMeasurement : protein_level GeneExpressionMeasurement --> "0..1" QuantityValue : protein_level click QuantityValue href "../QuantityValue/" GeneExpressionMeasurement : protocol_notes GeneExpressionMeasurement : staining_protocol GeneExpressionMeasurement --> "0..1" StainingProtocol : staining_protocol click StainingProtocol href "../StainingProtocol/"

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 direct
staining_protocol 0..1
StainingProtocol		 Staining protocol details direct
gene_expression_analysis 0..1
GeneExpressionAnalysis		 Gene expression analysis methodology direct
input_sample 0..1
InputSample		 Description of input samples and manipulations Measurement
method_assay 0..1
Assay		 The method or assay used Measurement
protocol_notes 0..1
String		 Protocol or SOP notes Measurement
id 1
Uriorcurie		 A unique identifier NamedEntity
description 0..1
String		 A detailed description NamedEntity

Identifier and Mapping Information

Schema Source

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

Mappings

Mapping Type Mapped Value
self outcomes_model:GeneExpressionMeasurement
native outcomes_model:GeneExpressionMeasurement

LinkML Source

Direct

name: GeneExpressionMeasurement
description: Measurement of gene expression
from_schema: https://w3id.org/EHS-Data-Standards/outcomes-model
is_a: Measurement
slots:
- mrna_level
- protein_level
- percentage_positive_cells
- staining_protocol
- gene_expression_analysis

Induced

name: GeneExpressionMeasurement
description: Measurement of gene expression
from_schema: https://w3id.org/EHS-Data-Standards/outcomes-model
is_a: Measurement
attributes:
  mrna_level:
    name: mrna_level
    description: mRNA expression level
    from_schema: https://w3id.org/EHS-Data-Standards/outcomes-model
    broad_mappings:
    - PATO:0000070
    rank: 1000
    alias: mrna_level
    owner: GeneExpressionMeasurement
    domain_of:
    - GeneExpressionMeasurement
    range: QuantityValue
    inlined: true
  protein_level:
    name: protein_level
    description: Protein expression level
    from_schema: https://w3id.org/EHS-Data-Standards/outcomes-model
    broad_mappings:
    - PATO:0000070
    rank: 1000
    alias: protein_level
    owner: GeneExpressionMeasurement
    domain_of:
    - GeneExpressionMeasurement
    range: QuantityValue
    inlined: true
  percentage_positive_cells:
    name: percentage_positive_cells
    description: Percentage of positive cells
    from_schema: https://w3id.org/EHS-Data-Standards/outcomes-model
    rank: 1000
    alias: percentage_positive_cells
    owner: GeneExpressionMeasurement
    domain_of:
    - GeneExpressionMeasurement
    range: QuantityValue
    inlined: true
  staining_protocol:
    name: staining_protocol
    description: Staining protocol details
    from_schema: https://w3id.org/EHS-Data-Standards/outcomes-model
    exact_mappings:
    - OBI:0000272
    rank: 1000
    alias: staining_protocol
    owner: GeneExpressionMeasurement
    domain_of:
    - GeneExpressionMeasurement
    - GobletCellMeasurement
    - MucinProductionMeasurement
    range: StainingProtocol
    inlined: true
  gene_expression_analysis:
    name: gene_expression_analysis
    description: Gene expression analysis methodology
    from_schema: https://w3id.org/EHS-Data-Standards/outcomes-model
    related_mappings:
    - OBI:0000424
    broad_mappings:
    - OBI:0000070
    rank: 1000
    alias: gene_expression_analysis
    owner: GeneExpressionMeasurement
    domain_of:
    - GeneExpressionMeasurement
    - GobletCellMeasurement
    range: GeneExpressionAnalysis
    inlined: true
  input_sample:
    name: input_sample
    description: Description of input samples and manipulations
    from_schema: https://w3id.org/EHS-Data-Standards/outcomes-model
    exact_mappings:
    - OBI:0100051
    related_mappings:
    - OBI:0000747
    rank: 1000
    alias: input_sample
    owner: GeneExpressionMeasurement
    domain_of:
    - Measurement
    range: InputSample
  method_assay:
    name: method_assay
    description: The method or assay used
    from_schema: https://w3id.org/EHS-Data-Standards/outcomes-model
    exact_mappings:
    - OBI:0000070
    rank: 1000
    alias: method_assay
    owner: GeneExpressionMeasurement
    domain_of:
    - Measurement
    range: Assay
  protocol_notes:
    name: protocol_notes
    description: Protocol or SOP notes
    comments:
    - For EGFR signaling include cell type, receptor location in ALI culture, probe
      method, timing
    - For goblet cells include media type, species, disease state, donor age, exposure
      conditions
    - For mucin production include focus on secreted mucins not tethered to goblet
      cells
    from_schema: https://w3id.org/EHS-Data-Standards/outcomes-model
    related_mappings:
    - IAO:0000310
    broad_mappings:
    - OBI:0000272
    rank: 1000
    alias: protocol_notes
    owner: GeneExpressionMeasurement
    domain_of:
    - Measurement
    range: string
  id:
    name: id
    description: A unique identifier
    from_schema: https://w3id.org/EHS-Data-Standards/outcomes-model
    rank: 1000
    identifier: true
    alias: id
    owner: GeneExpressionMeasurement
    domain_of:
    - NamedEntity
    range: uriorcurie
    required: true
  description:
    name: description
    description: A detailed description
    from_schema: https://w3id.org/EHS-Data-Standards/outcomes-model
    rank: 1000
    alias: description
    owner: GeneExpressionMeasurement
    domain_of:
    - NamedEntity
    range: string