# Test file for ASLAssay
# Demonstrates per-condition outputs: one AssayOutputMeasurement record for
# the air control and one for the ozone-exposed cultures, each linked to its
# exposure condition via measured_under.
asl_assays:
  - id: "ASL:001"
    name: "Airway surface liquid height after ozone exposure"
    has_exposure_condition:
      - id: "EXPOSURE:asl-air-4h"
        name: "Filtered air 4 hours (control)"
        exposure_duration:
          value: "4"
          unit:
            id: "UO:0000032"
            name: "hour"
      - id: "EXPOSURE:asl-ozone-200ppb-4h"
        name: "Ozone 200 ppb for 4 hours"
        exposure_agent:
          id: "CHEBI:25812"
          name: "ozone"
        exposure_concentration:
          value: "200"
          unit:
            id: "UO:0000170"
            name: "parts per billion"
        exposure_duration:
          value: "4"
          unit:
            id: "UO:0000032"
            name: "hour"
    has_specified_output:
      - id: "ASL:001-output-control"
        name: "Air control ASL measurements"
        experimental_group: control
        measured_under: "EXPOSURE:asl-air-4h"
        asl_height_um:
          value: "7.2"
          unit:
            id: "UO:0000017"
            name: "micrometer"
          central_tendency: mean
          sample_size: 6
          variability:
            variability_type: standard_deviation
            value: "0.6"
            unit:
              id: "UO:0000017"
              name: "micrometer"
        periciliary_layer_depth:
          value: "5.1"
          unit:
            id: "UO:0000017"
            name: "micrometer"
          central_tendency: mean
          sample_size: 6
        mucus_layer_thickness:
          value: "35"
          unit:
            id: "UO:0000017"
            name: "micrometer"
          central_tendency: mean
          sample_size: 6
        ion_composition: "Cl- 125 mM, Na+ 140 mM, K+ 15 mM"
        asl_ph:
          value: "7.1"
          unit:
            id: "UO:0000196"
            name: "pH"
          central_tendency: mean
          sample_size: 6
      - id: "ASL:001-output-ozone"
        name: "Ozone-exposed ASL measurements"
        experimental_group: treated
        measured_under: "EXPOSURE:asl-ozone-200ppb-4h"
        asl_height_um:
          value: "4.8"
          unit:
            id: "UO:0000017"
            name: "micrometer"
          central_tendency: mean
          sample_size: 6
          variability:
            variability_type: standard_deviation
            value: "0.7"
            unit:
              id: "UO:0000017"
              name: "micrometer"
        periciliary_layer_depth:
          value: "3.4"
          unit:
            id: "UO:0000017"
            name: "micrometer"
          central_tendency: mean
          sample_size: 6
        mucus_layer_thickness:
          value: "48"
          unit:
            id: "UO:0000017"
            name: "micrometer"
          central_tendency: mean
          sample_size: 6
        ion_composition: "Cl- 118 mM, Na+ 145 mM, K+ 17 mM"
        asl_ph:
          value: "6.8"
          unit:
            id: "UO:0000196"
            name: "pH"
          central_tendency: mean
          sample_size: 6
    assay_date: "2024-02-10"
    informs_on_key_event:
      id: "KE:ke-decreased-asl"
      name: "Decreased ASL height"
      biological_action: decreased
      level_of_biological_organization: cellular
    study_subject:
      subject_type: CellularSystem
      id: "soma:culture-002"
      name: "Primary HBE ALI culture"
      cell_type:
        id: "CL:0002328"
        name: "bronchial epithelial cell"
      model_species:
        id: "NCBITaxon:9606"
        name: "Homo sapiens"
    follows_protocols:
      - protocol_type: ImagingProtocol
        id: "PROTOCOL:asl-001"
        name: "Confocal microscopy for ASL height"
        spatial_resolution:
          value: "1.5"
          unit:
            id: "UO:0000017"
            name: "micrometer"
        fluorescent_labeling: "Texas Red-dextran"
        temperature_control:
          value: "37"
          unit:
            id: "UO:0000027"
            name: "degree Celsius"

# Analysis layer: the change relative to control, referencing the two output
# records above rather than duplicating their values.
response_comparisons:
  - id: "COMP:ASL001-height"
    name: "Change in ASL height, ozone vs filtered air"
    derived_from_assay: "ASL:001"
    compared_measurement: "asl_height_um"
    control_output: "ASL:001-output-control"
    treated_output: "ASL:001-output-ozone"
    change_type: absolute_difference
    change_direction: decreased
    change_value:
      value: "-2.4"
      unit:
        id: "UO:0000017"
        name: "micrometer"
    p_value: 0.002
    statistical_test: "two-sample t-test"
    derivation: computed