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Class: ASLHeightMeasurement

Measurement of airway surface liquid height

URI: outcomes_model:ASLHeightMeasurement

classDiagram class ASLHeightMeasurement click ASLHeightMeasurement href "../ASLHeightMeasurement/" Measurement <|-- ASLHeightMeasurement click Measurement href "../Measurement/" ASLHeightMeasurement : asl_height_um ASLHeightMeasurement --> "0..1" QuantityValue : asl_height_um click QuantityValue href "../QuantityValue/" ASLHeightMeasurement : culture_density ASLHeightMeasurement --> "0..1" QuantityValue : culture_density click QuantityValue href "../QuantityValue/" ASLHeightMeasurement : culture_size ASLHeightMeasurement --> "0..1" QuantityValue : culture_size click QuantityValue href "../QuantityValue/" ASLHeightMeasurement : description ASLHeightMeasurement : donor_characteristics ASLHeightMeasurement : evaporation_prevention ASLHeightMeasurement --> "0..1" EvaporationControl : evaporation_prevention click EvaporationControl href "../EvaporationControl/" ASLHeightMeasurement : id ASLHeightMeasurement : imaging_protocol ASLHeightMeasurement --> "0..1" ImagingProtocol : imaging_protocol click ImagingProtocol href "../ImagingProtocol/" ASLHeightMeasurement : input_sample ASLHeightMeasurement --> "0..1" InputSample : input_sample click InputSample href "../InputSample/" ASLHeightMeasurement : method_assay ASLHeightMeasurement --> "0..1" Assay : method_assay click Assay href "../Assay/" ASLHeightMeasurement : number_of_samples ASLHeightMeasurement : periciliary_layer_depth ASLHeightMeasurement --> "0..1" QuantityValue : periciliary_layer_depth click QuantityValue href "../QuantityValue/" ASLHeightMeasurement : protocol_notes ASLHeightMeasurement : sampling_duration ASLHeightMeasurement --> "0..1" QuantityValue : sampling_duration click QuantityValue href "../QuantityValue/" ASLHeightMeasurement : sampling_method ASLHeightMeasurement : timing_from_wash ASLHeightMeasurement --> "0..1" QuantityValue : timing_from_wash click QuantityValue href "../QuantityValue/"

Inheritance

Slots

Name Cardinality and Range Description Inheritance
asl_height_um 0..1
QuantityValue		 Airway surface liquid height in micrometers direct
periciliary_layer_depth 0..1
QuantityValue		 Depth of periciliary layer (liquid around the cilia) in micrometers - low dep... direct
imaging_protocol 0..1
ImagingProtocol		 Imaging protocol and parameters direct
evaporation_prevention 0..1
EvaporationControl		 Method used to prevent evaporation direct
sampling_method 0..1
String		 Method for sampling areas of the culture direct
culture_size 0..1
QuantityValue		 Size of the culture well or surface area direct
culture_density 0..1
QuantityValue		 Cell culture density per square centimeter direct
number_of_samples 0..1
Integer		 Number of sampling areas or technical replicates direct
donor_characteristics 0..1
String		 Characteristics of cell donors (e direct
timing_from_wash 0..1
QuantityValue		 Time elapsed since last apical wash direct
sampling_duration 0..1
QuantityValue		 Duration of the sampling period 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:ASLHeightMeasurement
native outcomes_model:ASLHeightMeasurement

LinkML Source

Direct

name: ASLHeightMeasurement
description: Measurement of airway surface liquid height
from_schema: https://w3id.org/EHS-Data-Standards/outcomes-model
is_a: Measurement
slots:
- asl_height_um
- periciliary_layer_depth
- imaging_protocol
- evaporation_prevention
- sampling_method
- culture_size
- culture_density
- number_of_samples
- donor_characteristics
- timing_from_wash
- sampling_duration

Induced

name: ASLHeightMeasurement
description: Measurement of airway surface liquid height
from_schema: https://w3id.org/EHS-Data-Standards/outcomes-model
is_a: Measurement
attributes:
  asl_height_um:
    name: asl_height_um
    description: Airway surface liquid height in micrometers
    from_schema: https://w3id.org/EHS-Data-Standards/outcomes-model
    broad_mappings:
    - PATO:0000119
    rank: 1000
    alias: asl_height_um
    owner: ASLHeightMeasurement
    domain_of:
    - ASLHeightMeasurement
    range: QuantityValue
    inlined: true
  periciliary_layer_depth:
    name: periciliary_layer_depth
    description: Depth of periciliary layer (liquid around the cilia) in micrometers
      - low depth indicates disease phenotype
    comments:
    - Important measurement for outcome as it directly indicates phenotype
    from_schema: https://w3id.org/EHS-Data-Standards/outcomes-model
    broad_mappings:
    - PATO:0001595
    rank: 1000
    alias: periciliary_layer_depth
    owner: ASLHeightMeasurement
    domain_of:
    - ASLHeightMeasurement
    range: QuantityValue
    inlined: true
  imaging_protocol:
    name: imaging_protocol
    description: Imaging protocol and parameters
    from_schema: https://w3id.org/EHS-Data-Standards/outcomes-model
    exact_mappings:
    - OBI:0000272
    rank: 1000
    alias: imaging_protocol
    owner: ASLHeightMeasurement
    domain_of:
    - CiliaBeatFrequencyMeasurement
    - ASLHeightMeasurement
    range: ImagingProtocol
    inlined: true
  evaporation_prevention:
    name: evaporation_prevention
    description: Method used to prevent evaporation
    from_schema: https://w3id.org/EHS-Data-Standards/outcomes-model
    rank: 1000
    alias: evaporation_prevention
    owner: ASLHeightMeasurement
    domain_of:
    - ASLHeightMeasurement
    range: EvaporationControl
    inlined: true
  sampling_method:
    name: sampling_method
    description: Method for sampling areas of the culture
    comments:
    - Include information about sampling strategy and distribution
    from_schema: https://w3id.org/EHS-Data-Standards/outcomes-model
    rank: 1000
    alias: sampling_method
    owner: ASLHeightMeasurement
    domain_of:
    - ASLHeightMeasurement
    range: string
  culture_size:
    name: culture_size
    description: Size of the culture well or surface area
    from_schema: https://w3id.org/EHS-Data-Standards/outcomes-model
    rank: 1000
    alias: culture_size
    owner: ASLHeightMeasurement
    domain_of:
    - ASLHeightMeasurement
    range: QuantityValue
    inlined: true
  culture_density:
    name: culture_density
    description: Cell culture density per square centimeter
    from_schema: https://w3id.org/EHS-Data-Standards/outcomes-model
    broad_mappings:
    - PATO:0001351
    rank: 1000
    alias: culture_density
    owner: ASLHeightMeasurement
    domain_of:
    - ASLHeightMeasurement
    range: QuantityValue
    inlined: true
  number_of_samples:
    name: number_of_samples
    description: Number of sampling areas or technical replicates
    comments:
    - Typically 12-20 samples per culture depending on size
    from_schema: https://w3id.org/EHS-Data-Standards/outcomes-model
    rank: 1000
    alias: number_of_samples
    owner: ASLHeightMeasurement
    domain_of:
    - ASLHeightMeasurement
    range: integer
  donor_characteristics:
    name: donor_characteristics
    description: Characteristics of cell donors (e.g., disease state, age)
    comments:
    - Critical for ASL height as disease state affects measurements
    from_schema: https://w3id.org/EHS-Data-Standards/outcomes-model
    rank: 1000
    alias: donor_characteristics
    owner: ASLHeightMeasurement
    domain_of:
    - ASLHeightMeasurement
    range: string
  timing_from_wash:
    name: timing_from_wash
    description: Time elapsed since last apical wash
    from_schema: https://w3id.org/EHS-Data-Standards/outcomes-model
    related_mappings:
    - PATO:0000165
    rank: 1000
    alias: timing_from_wash
    owner: ASLHeightMeasurement
    domain_of:
    - ASLHeightMeasurement
    range: QuantityValue
    inlined: true
  sampling_duration:
    name: sampling_duration
    description: Duration of the sampling period
    from_schema: https://w3id.org/EHS-Data-Standards/outcomes-model
    related_mappings:
    - PATO:0000165
    rank: 1000
    alias: sampling_duration
    owner: ASLHeightMeasurement
    domain_of:
    - ASLHeightMeasurement
    range: QuantityValue
    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: ASLHeightMeasurement
    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: ASLHeightMeasurement
    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: ASLHeightMeasurement
    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: ASLHeightMeasurement
    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: ASLHeightMeasurement
    domain_of:
    - NamedEntity
    range: string