# Test file for OxidativeStressAssay
oxidative_stress_assays:
  - id: "OX:001"
    name: "ROS level after PM2.5 exposure"
    has_specified_output:
      id: "OX:001-output"
      name: "OX:001 measurement results"
      reactive_oxygen_species:
        value: "2.5"
        unit:
          id: "UO:0000193"
          name: "fold change"
      lipid_peroxidation:
        value: "1.8"
        unit:
          id: "UO:0000193"
          name: "fold change"
      malondialdehyde_level:
        value: "3.2"
        unit:
          id: "UO:0000063"
          name: "nanomole per milligram protein"
      protein_carbonyl_content:
        value: "2.1"
        unit:
          id: "UO:0000063"
          name: "nanomole per milligram protein"
      glutathione_ratio:
        value: "0.65"
        unit:
          id: "UO:0000190"
          name: "ratio"
      eight_ohdg_level:
        value: "12.5"
        unit:
          id: "UO:0000275"
          name: "nanogram per milligram creatinine"
      superoxide_dismutase_activity:
        value: "0.75"
        unit:
          id: "UO:0000193"
          name: "fold change"
      catalase_activity:
        value: "0.82"
        unit:
          id: "UO:0000193"
          name: "fold change"
      nrf2_activation:
        value: "2.8"
        unit:
          id: "UO:0000193"
          name: "fold change"
      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
    has_exposure_condition:
      - id: "EXPOSURE:pm25-24h"
        name: "PM2.5 10 ug/cm2 for 24 hours"
        exposure_agent:
          id: "CHEBI:74481"
          name: "PM2.5"
        exposure_concentration:
          value: "10"
          unit:
            id: "UO:0000274"
            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"
    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"