# Test file for MucociliaryClearanceAssay
# Demonstrates per-condition outputs: an air control record and an
# ozone-exposed record, each linked to its exposure condition.
mcc_assays:
  - id: "MCC:001"
    name: "Mucociliary transport rate after ozone exposure"
    has_exposure_condition:
      - id: "EXPOSURE:mcc-air-4h"
        name: "Filtered air 4 hours (control)"
        exposure_duration:
          value: "4"
          unit:
            id: "UO:0000032"
            name: "hour"
      - id: "EXPOSURE:mcc-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: "MCC:001-output-control"
        name: "Air control transport measurements"
        experimental_group: control
        measured_under: "EXPOSURE:mcc-air-4h"
        transport_rate:
          value: "45.3"
          unit:
            id: "UCUM:um/s"
            name: "micrometer per second"
          central_tendency: mean
          sample_size: 5
          variability:
            variability_type: standard_deviation
            value: "5.1"
            unit:
              id: "UCUM:um/s"
              name: "micrometer per second"
        transport_directionality: normal
        mucus_layer_thickness:
          value: "28"
          unit:
            id: "UO:0000017"
            name: "micrometer"
          central_tendency: mean
          sample_size: 5
        percentage_active_transport:
          value: "82"
          unit:
            id: "UO:0000187"
            name: "percent"
          central_tendency: mean
          sample_size: 5
        particle_clearance_time:
          value: "120"
          unit:
            id: "UO:0000010"
            name: "second"
          central_tendency: mean
          sample_size: 5
      - id: "MCC:001-output-ozone"
        name: "Ozone-exposed transport measurements"
        experimental_group: treated
        measured_under: "EXPOSURE:mcc-ozone-200ppb-4h"
        transport_rate:
          value: "22.1"
          unit:
            id: "UCUM:um/s"
            name: "micrometer per second"
          central_tendency: mean
          sample_size: 5
          variability:
            variability_type: standard_deviation
            value: "6.4"
            unit:
              id: "UCUM:um/s"
              name: "micrometer per second"
        transport_directionality: variable
        mucus_layer_thickness:
          value: "41"
          unit:
            id: "UO:0000017"
            name: "micrometer"
          central_tendency: mean
          sample_size: 5
        percentage_active_transport:
          value: "54"
          unit:
            id: "UO:0000187"
            name: "percent"
          central_tendency: mean
          sample_size: 5
        particle_clearance_time:
          value: "245"
          unit:
            id: "UO:0000010"
            name: "second"
          central_tendency: mean
          sample_size: 5
    assay_date: "2024-03-05"
    informs_on_key_event:
      id: "KE:ke3-impaired-mcc"
      name: "Impaired mucociliary clearance"
      biological_action: impaired
      level_of_biological_organization: tissue
    study_subject:
      subject_type: CellularSystem
      id: "soma:culture-007"
      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:mcc-001"
        name: "Fluorescent microsphere tracking for MCC"
        fluorescent_tracer: "1-um fluorescent microspheres"
        particle_tracking_method: "automated particle tracking"
        particle_size:
          value: "1"
          unit:
            id: "UO:0000017"
            name: "micrometer"
        imaging_frame_rate:
          value: "30"
          unit:
            id: "UO:0000105"
            name: "hertz"

# Analysis layer: percent change in transport rate relative to air control.
response_comparisons:
  - id: "COMP:MCC001-transport-rate"
    name: "Change in mucociliary transport rate, ozone vs filtered air"
    derived_from_assay: "MCC:001"
    compared_measurement: "transport_rate"
    control_output: "MCC:001-output-control"
    treated_output: "MCC:001-output-ozone"
    change_type: percent_change
    change_direction: decreased
    change_value:
      value: "-51.2"
      unit:
        id: "UO:0000187"
        name: "percent"
    p_value: 0.001
    statistical_test: "two-sample t-test"
    derivation: computed