# Test file for LungFunctionAssay (in vivo only)
# This assay is IN VIVO ONLY (supported_contexts: in_vivo_only)
# Requires a whole lung to assess function.
#
# Demonstrates per-condition outputs for a pre/post design: the same subject
# is measured before bronchodilator (experimental_group: baseline) and again
# after albuterol (experimental_group: treated), each record linked to the
# condition it was measured under.
lung_function_assays:
  - id: "LF:001"
    name: "Pre- and post-bronchodilator spirometry"
    has_exposure_condition:
      - id: "COND:lf-pre-bronchodilator"
        name: "Pre-bronchodilator (baseline spirometry)"
      - id: "COND:lf-post-albuterol"
        name: "15 minutes after albuterol 400 ug"
        exposure_concentration:
          value: "400"
          unit:
            id: "UO:0000023"
            name: "microgram"
        timing_post_exposure:
          value: "15"
          unit:
            id: "UO:0000031"
            name: "minute"
    has_specified_output:
      - id: "LF:001-output-pre"
        name: "Pre-bronchodilator spirometry results"
        description: "FEV1, FVC, DLCO and peak expiratory flow are expressed as percent of predicted (GLI-2012 reference); FEV1/FVC ratio is a plain percentage."
        experimental_group: baseline
        measured_under: "COND:lf-pre-bronchodilator"
        fev1:
          value: "82.5"
          unit:
            id: "UO:0000187"
            name: "percent"
          central_tendency: single_value
          sample_size: 1
        fvc:
          value: "95.0"
          unit:
            id: "UO:0000187"
            name: "percent"
          central_tendency: single_value
          sample_size: 1
        fev1_fvc_ratio:
          value: "86.8"
          unit:
            id: "UO:0000187"
            name: "percent"
          central_tendency: single_value
          sample_size: 1
        feno:
          value: "22"
          unit:
            id: "UO:0000170"
            name: "parts per billion"
          central_tendency: single_value
          sample_size: 1
        dlco:
          value: "88"
          unit:
            id: "UO:0000187"
            name: "percent"
          central_tendency: single_value
          sample_size: 1
        peak_expiratory_flow:
          value: "92"
          unit:
            id: "UO:0000187"
            name: "percent"
          central_tendency: single_value
          sample_size: 1
      - id: "LF:001-output-post"
        name: "Post-bronchodilator spirometry results"
        description: "FEV1, FVC and peak expiratory flow are expressed as percent of predicted (GLI-2012 reference); FEV1/FVC ratio and bronchodilator response are plain percentages."
        experimental_group: treated
        measured_under: "COND:lf-post-albuterol"
        fev1:
          value: "89.5"
          unit:
            id: "UO:0000187"
            name: "percent"
          central_tendency: single_value
          sample_size: 1
        fvc:
          value: "97.8"
          unit:
            id: "UO:0000187"
            name: "percent"
          central_tendency: single_value
          sample_size: 1
        fev1_fvc_ratio:
          value: "91.5"
          unit:
            id: "UO:0000187"
            name: "percent"
          central_tendency: single_value
          sample_size: 1
        bronchodilator_response:
          value: "8.5"
          unit:
            id: "UO:0000187"
            name: "percent"
          central_tendency: single_value
          sample_size: 1
        peak_expiratory_flow:
          value: "98"
          unit:
            id: "UO:0000187"
            name: "percent"
          central_tendency: single_value
          sample_size: 1
    reference_dataset: "GLI-2012"
    assay_date: "2024-08-10"
    informs_on_key_event:
      id: "KE:ao-decreased-lung-function"
      name: "Decreased lung function"
      biological_action: decreased
      level_of_biological_organization: organ
    study_subject:
      subject_type: InVivoSubject
      id: "SUBJECT:002"
      name: "Subject B"
      model_species:
        id: "NCBITaxon:9606"
        name: "Homo sapiens"
      age:
        value: "52"
        unit:
          id: "UO:0000036"
          name: "year"
      sex: "male"
      subject_characteristics: "Non-smoker, no respiratory disease"
      clinical_context: "Pre- and post-bronchodilator spirometry at a single visit"
    follows_protocols:
      - protocol_type: SpirometryProtocol
        id: "PROTOCOL:spiro-001"
        name: "Pre- and post-bronchodilator spirometry"
        spirometry_standard: "ATS/ERS 2019"
        bronchodilator_agent: "albuterol"
        bronchodilator_dose:
          value: "400"
          unit:
            id: "UO:0000023"
            name: "microgram"

# Analysis layer: the bronchodilator response, which the assay also records
# directly as a measurement, expressed here as a change relative to the
# pre-bronchodilator baseline.
response_comparisons:
  - id: "COMP:LF001-fev1"
    name: "Change in FEV1, post-bronchodilator vs pre-bronchodilator"
    derived_from_assay: "LF:001"
    compared_measurement: "fev1"
    control_output: "LF:001-output-pre"
    treated_output: "LF:001-output-post"
    change_type: percent_change
    change_direction: increased
    change_value:
      value: "8.5"
      unit:
        id: "UO:0000187"
        name: "percent"
    derivation: computed