# Test file for OxidativeStressAssay
# Demonstrates per-condition outputs: a vehicle control record that anchors
# the fold-change scale at 1.0 and a PM2.5-exposed record, each linked to its
# exposure condition via measured_under.
oxidative_stress_assays:
  - id: "OX:001"
    name: "ROS level after PM2.5 exposure"
    has_exposure_condition:
      - id: "EXPOSURE:ox-vehicle-24h"
        name: "Culture medium vehicle 24 hours (control)"
        exposure_duration:
          value: "24"
          unit:
            id: "UO:0000032"
            name: "hour"
        timing_post_exposure:
          value: "0"
          unit:
            id: "UO:0000032"
            name: "hour"
      - id: "EXPOSURE:pm25-24h"
        name: "PM2.5 10 ug/cm2 for 24 hours"
        exposure_agent:
          id: "ENVO:01000415"
          name: "fine respirable suspended particulate matter"
        exposure_concentration:
          value: "10"
          unit:
            id: "UO:0010071"
            name: "microgram per square centimeter"
        exposure_duration:
          value: "24"
          unit:
            id: "UO:0000032"
            name: "hour"
        timing_post_exposure:
          value: "0"
          unit:
            id: "UO:0000032"
            name: "hour"
    has_specified_output:
      - id: "OX:001-output-control"
        name: "Vehicle control oxidative stress measurements"
        experimental_group: vehicle_control
        measured_under: "EXPOSURE:ox-vehicle-24h"
        reactive_oxygen_species:
          value: "1.0"
          unit:
            id: "STATO:0000169"
            name: "fold change"
          central_tendency: mean
          sample_size: 6
        lipid_peroxidation:
          value: "1.0"
          unit:
            id: "STATO:0000169"
            name: "fold change"
          central_tendency: mean
          sample_size: 6
        malondialdehyde_level:
          value: "1.4"
          unit:
            id: "UCUM:nmol/mg"
            name: "nanomole per milligram protein"
          central_tendency: mean
          sample_size: 6
          variability:
            variability_type: standard_deviation
            value: "0.3"
            unit:
              id: "UCUM:nmol/mg"
              name: "nanomole per milligram protein"
        protein_carbonyl_content:
          value: "0.9"
          unit:
            id: "UCUM:nmol/mg"
            name: "nanomole per milligram protein"
          central_tendency: mean
          sample_size: 6
        glutathione_ratio:
          value: "0.95"
          unit:
            id: "UO:0000190"
            name: "ratio unit"
          central_tendency: mean
          sample_size: 6
        eight_ohdg_level:
          value: "4.1"
          unit:
            id: "UCUM:ng/mg"
            name: "nanogram per milligram creatinine"
          central_tendency: mean
          sample_size: 6
        superoxide_dismutase_activity:
          value: "1.0"
          unit:
            id: "STATO:0000169"
            name: "fold change"
          central_tendency: mean
          sample_size: 6
        catalase_activity:
          value: "1.0"
          unit:
            id: "STATO:0000169"
            name: "fold change"
          central_tendency: mean
          sample_size: 6
        nrf2_activation:
          value: "1.0"
          unit:
            id: "STATO:0000169"
            name: "fold change"
          central_tendency: mean
          sample_size: 6
        protein_oxidation_markers:
          - "carbonyl"
          - "nitrotyrosine"
        antioxidant_enzyme_activities: "SOD, catalase, GPx measured"
      - id: "OX:001-output-pm25"
        name: "PM2.5-exposed oxidative stress measurements"
        experimental_group: treated
        measured_under: "EXPOSURE:pm25-24h"
        reactive_oxygen_species:
          value: "2.5"
          unit:
            id: "STATO:0000169"
            name: "fold change"
          central_tendency: mean
          sample_size: 6
          variability:
            variability_type: standard_deviation
            value: "0.35"
            unit:
              id: "STATO:0000169"
              name: "fold change"
        lipid_peroxidation:
          value: "1.8"
          unit:
            id: "STATO:0000169"
            name: "fold change"
          central_tendency: mean
          sample_size: 6
        malondialdehyde_level:
          value: "3.2"
          unit:
            id: "UCUM:nmol/mg"
            name: "nanomole per milligram protein"
          central_tendency: mean
          sample_size: 6
          variability:
            variability_type: standard_deviation
            value: "0.5"
            unit:
              id: "UCUM:nmol/mg"
              name: "nanomole per milligram protein"
        protein_carbonyl_content:
          value: "2.1"
          unit:
            id: "UCUM:nmol/mg"
            name: "nanomole per milligram protein"
          central_tendency: mean
          sample_size: 6
        glutathione_ratio:
          value: "0.65"
          unit:
            id: "UO:0000190"
            name: "ratio unit"
          central_tendency: mean
          sample_size: 6
        eight_ohdg_level:
          value: "12.5"
          unit:
            id: "UCUM:ng/mg"
            name: "nanogram per milligram creatinine"
          central_tendency: mean
          sample_size: 6
        superoxide_dismutase_activity:
          value: "0.75"
          unit:
            id: "STATO:0000169"
            name: "fold change"
          central_tendency: mean
          sample_size: 6
        catalase_activity:
          value: "0.82"
          unit:
            id: "STATO:0000169"
            name: "fold change"
          central_tendency: mean
          sample_size: 6
        nrf2_activation:
          value: "2.8"
          unit:
            id: "STATO:0000169"
            name: "fold change"
          central_tendency: mean
          sample_size: 6
        protein_oxidation_markers:
          - "carbonyl"
          - "nitrotyrosine"
        antioxidant_enzyme_activities: "SOD, catalase, GPx measured"
    ros_probe_type: "DCFDA"
    assay_date: "2024-01-20"
    informs_on_key_event:
      id: "KE:mie-oxidative-stress"
      name: "Increased oxidative stress"
      biological_action: increased
      level_of_biological_organization: molecular
    study_subject:
      subject_type: CellularSystem
      id: "soma:culture-003"
      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: MolecularAssayProtocol
        id: "PROTOCOL:ros-001"
        name: "DCFDA ROS detection in ALI cultures"
        detection_method: "fluorescence plate reader"
        normalization_method: "cell count normalization"

# Analysis layer: MDA is measured in its own unit, so its change relative to
# control is an absolute difference; ROS is already reported as fold change.
response_comparisons:
  - id: "COMP:OX001-ros"
    name: "Change in reactive oxygen species, PM2.5 vs vehicle"
    derived_from_assay: "OX:001"
    compared_measurement: "reactive_oxygen_species"
    control_output: "OX:001-output-control"
    treated_output: "OX:001-output-pm25"
    change_type: fold_change
    change_direction: increased
    change_value:
      value: "2.5"
      unit:
        id: "STATO:0000169"
        name: "fold change"
    p_value: 0.001
    statistical_test: "two-sample t-test"
    derivation: reported_in_paper
  - id: "COMP:OX001-mda"
    name: "Change in malondialdehyde level, PM2.5 vs vehicle"
    derived_from_assay: "OX:001"
    compared_measurement: "malondialdehyde_level"
    control_output: "OX:001-output-control"
    treated_output: "OX:001-output-pm25"
    change_type: absolute_difference
    change_direction: increased
    change_value:
      value: "1.8"
      unit:
        id: "UCUM:nmol/mg"
        name: "nanomole per milligram protein"
    p_value: 0.003
    statistical_test: "two-sample t-test"
    derivation: computed