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Class: GobletCellMeasurement

Measurement of goblet cell number or mucin production

URI: outcomes_model:GobletCellMeasurement

classDiagram class GobletCellMeasurement click GobletCellMeasurement href "../GobletCellMeasurement/" Measurement <|-- GobletCellMeasurement click Measurement href "../Measurement/" GobletCellMeasurement : description GobletCellMeasurement : dose_response_data GobletCellMeasurement : gene_expression_analysis GobletCellMeasurement --> "0..1" GeneExpressionAnalysis : gene_expression_analysis click GeneExpressionAnalysis href "../GeneExpressionAnalysis/" GobletCellMeasurement : goblet_cell_count GobletCellMeasurement --> "0..1" QuantityValue : goblet_cell_count click QuantityValue href "../QuantityValue/" GobletCellMeasurement : id GobletCellMeasurement : input_sample GobletCellMeasurement --> "0..1" InputSample : input_sample click InputSample href "../InputSample/" GobletCellMeasurement : method_assay GobletCellMeasurement --> "0..1" Assay : method_assay click Assay href "../Assay/" GobletCellMeasurement : mucin_expression_level GobletCellMeasurement --> "0..1" QuantityValue : mucin_expression_level click QuantityValue href "../QuantityValue/" GobletCellMeasurement : mucin_protein_concentration GobletCellMeasurement --> "0..1" QuantityValue : mucin_protein_concentration click QuantityValue href "../QuantityValue/" GobletCellMeasurement : pathway_enrichment_scores GobletCellMeasurement : protocol_notes GobletCellMeasurement : staining_protocol GobletCellMeasurement --> "0..1" StainingProtocol : staining_protocol click StainingProtocol href "../StainingProtocol/"

Inheritance

Slots

Name Cardinality and Range Description Inheritance
goblet_cell_count 0..1
QuantityValue		 Number or percentage of goblet cells (include both raw counts and relative pe... direct
mucin_expression_level 0..1
QuantityValue		 Level of mucin gene or protein expression (e direct
staining_protocol 0..1
StainingProtocol		 Staining protocol details direct
gene_expression_analysis 0..1
GeneExpressionAnalysis		 Gene expression analysis methodology direct
mucin_protein_concentration 0..1
QuantityValue		 Concentration of mucin protein (both direct quantification and comparative me... direct
pathway_enrichment_scores *
String		 Enrichment scores for biological pathways direct
dose_response_data 0..1
String		 Dose-response relationship data 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:GobletCellMeasurement
native outcomes_model:GobletCellMeasurement

LinkML Source

Direct

name: GobletCellMeasurement
description: Measurement of goblet cell number or mucin production
from_schema: https://w3id.org/EHS-Data-Standards/outcomes-model
is_a: Measurement
slots:
- goblet_cell_count
- mucin_expression_level
- staining_protocol
- gene_expression_analysis
- mucin_protein_concentration
- pathway_enrichment_scores
- dose_response_data

Induced

name: GobletCellMeasurement
description: Measurement of goblet cell number or mucin production
from_schema: https://w3id.org/EHS-Data-Standards/outcomes-model
is_a: Measurement
attributes:
  goblet_cell_count:
    name: goblet_cell_count
    description: Number or percentage of goblet cells (include both raw counts and
      relative percentages)
    from_schema: https://w3id.org/EHS-Data-Standards/outcomes-model
    related_mappings:
    - CL:0000160
    broad_mappings:
    - PATO:0000070
    rank: 1000
    alias: goblet_cell_count
    owner: GobletCellMeasurement
    domain_of:
    - GobletCellMeasurement
    range: QuantityValue
    inlined: true
  mucin_expression_level:
    name: mucin_expression_level
    description: Level of mucin gene or protein expression (e.g., MUC5AC to MUC5B
      ratio)
    from_schema: https://w3id.org/EHS-Data-Standards/outcomes-model
    related_mappings:
    - GO:0070254
    broad_mappings:
    - PATO:0000070
    rank: 1000
    alias: mucin_expression_level
    owner: GobletCellMeasurement
    domain_of:
    - GobletCellMeasurement
    - MucinProductionMeasurement
    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: GobletCellMeasurement
    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: GobletCellMeasurement
    domain_of:
    - GeneExpressionMeasurement
    - GobletCellMeasurement
    range: GeneExpressionAnalysis
    inlined: true
  mucin_protein_concentration:
    name: mucin_protein_concentration
    description: Concentration of mucin protein (both direct quantification and comparative
      measures, e.g., percent solids from apical secretion)
    from_schema: https://w3id.org/EHS-Data-Standards/outcomes-model
    broad_mappings:
    - PATO:0000033
    rank: 1000
    alias: mucin_protein_concentration
    owner: GobletCellMeasurement
    domain_of:
    - GobletCellMeasurement
    - MucinProductionMeasurement
    range: QuantityValue
    inlined: true
  pathway_enrichment_scores:
    name: pathway_enrichment_scores
    description: Enrichment scores for biological pathways
    from_schema: https://w3id.org/EHS-Data-Standards/outcomes-model
    rank: 1000
    alias: pathway_enrichment_scores
    owner: GobletCellMeasurement
    domain_of:
    - GobletCellMeasurement
    range: string
    multivalued: true
  dose_response_data:
    name: dose_response_data
    description: Dose-response relationship data
    from_schema: https://w3id.org/EHS-Data-Standards/outcomes-model
    rank: 1000
    alias: dose_response_data
    owner: GobletCellMeasurement
    domain_of:
    - GobletCellMeasurement
    range: string
  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: GobletCellMeasurement
    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: GobletCellMeasurement
    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: GobletCellMeasurement
    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: GobletCellMeasurement
    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: GobletCellMeasurement
    domain_of:
    - NamedEntity
    range: string