# Test file for GobletCellAssay
# Demonstrates per-condition outputs: a vehicle control record and an
# IL-13-treated record, each linked to its exposure condition.
goblet_cell_assays:
  - id: "GCM:001"
    name: "MUC5AC expression and goblet cell quantification after IL-13 treatment"
    has_exposure_condition:
      - id: "EXPOSURE:gcm-vehicle-14d"
        name: "Vehicle (0.1% BSA in PBS) for 14 days (control)"
        exposure_duration:
          value: "14"
          unit:
            id: "UO:0000033"
            name: "day"
      - id: "EXPOSURE:gcm-il13-14d"
        name: "IL-13 10 ng/mL for 14 days"
        exposure_concentration:
          value: "10"
          unit:
            id: "UO:0000275"
            name: "nanogram per milliliter"
        exposure_duration:
          value: "14"
          unit:
            id: "UO:0000033"
            name: "day"
    has_specified_output:
      - id: "GCM:001-output-control"
        name: "Vehicle control goblet cell and mucin measurements"
        experimental_group: vehicle_control
        measured_under: "EXPOSURE:gcm-vehicle-14d"
        muc5ac_mrna_expression:
          value: "1.0"
          unit:
            id: "STATO:0000169"
            name: "fold change"
          central_tendency: mean
          sample_size: 4
        goblet_cell_percentage:
          value: "9"
          unit:
            id: "UO:0000187"
            name: "percent"
          central_tendency: mean
          sample_size: 4
          variability:
            variability_type: standard_deviation
            value: "1.8"
            unit:
              id: "UO:0000187"
              name: "percent"
        goblet_cell_count:
          value: "27"
          unit:
            id: "UO:0000189"
            name: "count unit"
          central_tendency: mean
          sample_size: 4
        muc5ac_protein_expression:
          value: "1.0"
          unit:
            id: "STATO:0000169"
            name: "fold change"
          central_tendency: mean
          sample_size: 4
        muc5b_mrna_expression:
          value: "1.0"
          unit:
            id: "STATO:0000169"
            name: "fold change"
          central_tendency: mean
          sample_size: 4
        muc5b_protein_expression:
          value: "1.0"
          unit:
            id: "STATO:0000169"
            name: "fold change"
          central_tendency: mean
          sample_size: 4
        muc5ac_muc5b_ratio:
          value: "0.9"
          unit:
            id: "UO:0000190"
            name: "ratio unit"
          central_tendency: mean
          sample_size: 4
        mucin_secretion_rate:
          value: "4.1"
          unit:
            id: "UCUM:ug/h"
            name: "microgram per hour"
          central_tendency: mean
          sample_size: 4
        percent_solids:
          value: "2.3"
          unit:
            id: "UO:0000187"
            name: "percent"
          central_tendency: mean
          sample_size: 4
        goblet_to_ciliated_ratio:
          value: "0.13"
          unit:
            id: "UO:0000190"
            name: "ratio unit"
          central_tendency: mean
          sample_size: 4
      - id: "GCM:001-output-il13"
        name: "IL-13-treated goblet cell and mucin measurements"
        experimental_group: treated
        measured_under: "EXPOSURE:gcm-il13-14d"
        muc5ac_mrna_expression:
          value: "4.8"
          unit:
            id: "STATO:0000169"
            name: "fold change"
          central_tendency: mean
          sample_size: 4
          variability:
            variability_type: standard_deviation
            value: "0.7"
            unit:
              id: "STATO:0000169"
              name: "fold change"
        goblet_cell_percentage:
          value: "28"
          unit:
            id: "UO:0000187"
            name: "percent"
          central_tendency: mean
          sample_size: 4
          variability:
            variability_type: standard_deviation
            value: "3.4"
            unit:
              id: "UO:0000187"
              name: "percent"
        goblet_cell_count:
          value: "85"
          unit:
            id: "UO:0000189"
            name: "count unit"
          central_tendency: mean
          sample_size: 4
        muc5ac_protein_expression:
          value: "3.2"
          unit:
            id: "STATO:0000169"
            name: "fold change"
          central_tendency: mean
          sample_size: 4
        muc5b_mrna_expression:
          value: "1.8"
          unit:
            id: "STATO:0000169"
            name: "fold change"
          central_tendency: mean
          sample_size: 4
        muc5b_protein_expression:
          value: "1.5"
          unit:
            id: "STATO:0000169"
            name: "fold change"
          central_tendency: mean
          sample_size: 4
        muc5ac_muc5b_ratio:
          value: "2.7"
          unit:
            id: "UO:0000190"
            name: "ratio unit"
          central_tendency: mean
          sample_size: 4
        mucin_secretion_rate:
          value: "12.5"
          unit:
            id: "UCUM:ug/h"
            name: "microgram per hour"
          central_tendency: mean
          sample_size: 4
        percent_solids:
          value: "4.2"
          unit:
            id: "UO:0000187"
            name: "percent"
          central_tendency: mean
          sample_size: 4
        goblet_to_ciliated_ratio:
          value: "0.45"
          unit:
            id: "UO:0000190"
            name: "ratio unit"
          central_tendency: mean
          sample_size: 4
    assay_date: "2024-06-15"
    informs_on_key_event:
      id: "KE:ke2-goblet-hyperplasia"
      name: "Goblet cell hyperplasia"
      biological_action: increased
      level_of_biological_organization: cellular
    study_subject:
      subject_type: CellularSystem
      id: "soma:culture-004"
      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: StainingProtocol
        id: "PROTOCOL:stain-001"
        name: "AB-PAS staining for goblet cells"
        staining_type: "AB-PAS"
        fixation_method: "4% paraformaldehyde"
        counterstain: "hematoxylin"

# Analysis layer: goblet cell percentage is a percentage measurement, so its
# change is an absolute difference in percentage points; MUC5AC mRNA is
# already a fold change.
response_comparisons:
  - id: "COMP:GCM001-goblet-percentage"
    name: "Change in goblet cell percentage, IL-13 vs vehicle"
    derived_from_assay: "GCM:001"
    compared_measurement: "goblet_cell_percentage"
    control_output: "GCM:001-output-control"
    treated_output: "GCM:001-output-il13"
    change_type: absolute_difference
    change_direction: increased
    change_value:
      value: "19"
      unit:
        id: "UO:0000187"
        name: "percent"
    p_value: 0.001
    statistical_test: "two-sample t-test"
    derivation: computed
  - id: "COMP:GCM001-muc5ac-mrna"
    name: "Change in MUC5AC mRNA expression, IL-13 vs vehicle"
    derived_from_assay: "GCM:001"
    compared_measurement: "muc5ac_mrna_expression"
    control_output: "GCM:001-output-control"
    treated_output: "GCM:001-output-il13"
    change_type: fold_change
    change_direction: increased
    change_value:
      value: "4.8"
      unit:
        id: "STATO:0000169"
        name: "fold change"
    p_value: 0.0004
    statistical_test: "two-sample t-test"
    derivation: reported_in_paper