# Test file for CFTRFunctionAssay
# Demonstrates per-condition outputs: a vehicle control record and a
# cigarette-smoke-extract record, each linked to its exposure condition.
cftr_assays:
  - id: "CFTR:001"
    name: "CFTR chloride secretion after cigarette smoke extract exposure"
    has_exposure_condition:
      - id: "EXPOSURE:cftr-vehicle-4h"
        name: "Culture medium vehicle 4 hours (control)"
        exposure_duration:
          value: "4"
          unit:
            id: "UO:0000032"
            name: "hour"
      - id: "EXPOSURE:cftr-cse-5pct-4h"
        name: "Cigarette smoke extract 5% for 4 hours"
        exposure_agent:
          id: "ENVO:01000838"
          name: "smoke"
        exposure_concentration:
          value: "5"
          unit:
            id: "UO:0000187"
            name: "percent"
        exposure_duration:
          value: "4"
          unit:
            id: "UO:0000032"
            name: "hour"
    has_specified_output:
      - id: "CFTR:001-output-control"
        name: "Vehicle control CFTR measurements"
        experimental_group: vehicle_control
        measured_under: "EXPOSURE:cftr-vehicle-4h"
        cftr_chloride_secretion:
          value: "15.2"
          unit:
            id: "UCUM:uA/cm2"
            name: "microampere per square centimeter"
          central_tendency: mean
          sample_size: 6
          variability:
            variability_type: standard_error
            value: "1.1"
            unit:
              id: "UCUM:uA/cm2"
              name: "microampere per square centimeter"
        cftr_forskolin_response:
          value: "12.8"
          unit:
            id: "UCUM:uA/cm2"
            name: "microampere per square centimeter"
          central_tendency: mean
          sample_size: 6
        inhibitor_sensitive_current:
          value: "14.5"
          unit:
            id: "UCUM:uA/cm2"
            name: "microampere per square centimeter"
          central_tendency: mean
          sample_size: 6
        cftr_specific_current:
          value: "13.9"
          unit:
            id: "UCUM:uA/cm2"
            name: "microampere per square centimeter"
          central_tendency: mean
          sample_size: 6
        sweat_chloride_concentration:
          value: "25"
          unit:
            id: "UCUM:meq/L"
            name: "milliequivalent per liter"
          central_tendency: mean
          sample_size: 6
        nasal_potential_difference:
          value: "-18.5"
          unit:
            id: "UO:0000247"
            name: "millivolt"
          central_tendency: mean
          sample_size: 6
      - id: "CFTR:001-output-cse"
        name: "Cigarette smoke extract CFTR measurements"
        experimental_group: treated
        measured_under: "EXPOSURE:cftr-cse-5pct-4h"
        cftr_chloride_secretion:
          value: "8.4"
          unit:
            id: "UCUM:uA/cm2"
            name: "microampere per square centimeter"
          central_tendency: mean
          sample_size: 6
          variability:
            variability_type: standard_error
            value: "1.3"
            unit:
              id: "UCUM:uA/cm2"
              name: "microampere per square centimeter"
        cftr_forskolin_response:
          value: "6.1"
          unit:
            id: "UCUM:uA/cm2"
            name: "microampere per square centimeter"
          central_tendency: mean
          sample_size: 6
        inhibitor_sensitive_current:
          value: "7.9"
          unit:
            id: "UCUM:uA/cm2"
            name: "microampere per square centimeter"
          central_tendency: mean
          sample_size: 6
        cftr_specific_current:
          value: "7.2"
          unit:
            id: "UCUM:uA/cm2"
            name: "microampere per square centimeter"
          central_tendency: mean
          sample_size: 6
        sweat_chloride_concentration:
          value: "38"
          unit:
            id: "UCUM:meq/L"
            name: "milliequivalent per liter"
          central_tendency: mean
          sample_size: 6
        nasal_potential_difference:
          value: "-9.2"
          unit:
            id: "UO:0000247"
            name: "millivolt"
          central_tendency: mean
          sample_size: 6
    stimulation_agent: "forskolin 10 uM"
    inhibitor_used: "CFTRinh-172"
    assay_date: "2024-04-12"
    informs_on_key_event:
      id: "KE:ke-decreased-cftr"
      name: "Decreased CFTR function"
      biological_action: decreased
      level_of_biological_organization: molecular
    study_subject:
      subject_type: CellularSystem
      id: "soma:culture-006"
      name: "Primary HBE ALI culture"
      cell_type:
        id: "CL:0002328"
        name: "bronchial epithelial cell"
      model_species:
        id: "NCBITaxon:9606"
        name: "Homo sapiens"
    follows_protocols:
      - id: "PROTOCOL:cftr-001"
        name: "Ussing chamber short-circuit current protocol"
      - id: "PROTOCOL:cftr-prep-001"
        name: "Tissue mounting and equilibration protocol"
        description: "Pre-assay protocol for mounting tissue in Ussing chamber and equilibrating"

# Analysis layer: the drop in CFTR-mediated chloride secretion, expressed as
# a fold change so it can be compared with fold-change reports elsewhere.
response_comparisons:
  - id: "COMP:CFTR001-chloride-secretion"
    name: "Change in CFTR chloride secretion, CSE vs vehicle"
    derived_from_assay: "CFTR:001"
    compared_measurement: "cftr_chloride_secretion"
    control_output: "CFTR:001-output-control"
    treated_output: "CFTR:001-output-cse"
    change_type: fold_change
    change_direction: decreased
    change_value:
      value: "0.55"
      unit:
        id: "STATO:0000169"
        name: "fold change"
    p_value: 0.004
    statistical_test: "two-sample t-test"
    derivation: computed