ccp-drc.toml

#:schema ../../schemas/dev/parser.schema.json

[adtl]
  name = "ccp-drc.toml"
  description = "ccp-drc.toml"

  [adtl.defs."Y/N/NK"]
    values = { 0 = false, 1 = true }

  [adtl.defs.admissionDateHierarchy]
    combinedType = "firstNonNull"
    fields = [
      { field = "add_date", description = "Admission date at this facility" },
      { field = "fever_date" },
      { field = "fatigue_date" },
      { field = "dyspnea_date" },
      { field = "anosmia_date" },
      { field = "sore_throat_date" },
      { field = "headache_date" },
      { field = "signs_symps_date", description = "Date of signs&symptoms during study form" },
    ]

  [adtl.defs."ss_datetime"]
    field = "signs_symps_date"
    apply = { function = "makeDateTime", params = [
      "$signs_symps_time",
      "%Y-%m-%d",
      "Africa/Lubumbashi",
    ] }

  [adtl.defs."vitals_datetime"]
    field = "vitals_date"
    apply = { function = "makeDateTime", params = [
      "$vitals_time",
      "%Y-%m-%d",
      "Africa/Lubumbashi",
    ] }

  [adtl.tables.subject]
    kind = "groupBy"
    groupBy = "subject_id"
    aggregation = "lastNotNull"
    schema = "../../schemas/dev/subject.schema.json"

  [adtl.tables.visit]
    kind = "groupBy"
    groupBy = "subject_id"
    aggregation = "lastNotNull"
    schema = "../../schemas/dev/visit.schema.json"

  [adtl.tables.observation]
    kind = "oneToMany"
    schema = "../../schemas/dev/observation.schema.json"
    common = { visit_id = { field = "record_id", sensitive = true } }

[subject]
  pathogen = "COVID-19"

  [subject.subject_id]
    field = "record_id"
    sensitive = true

  [subject.earliest_admission_date]
    combinedType = "min"
    fields = [{ ref = "admissionDateHierarchy" }]

  [subject.age]
    field = "age"
    description = "Age"
    source_unit = { field = "age_unit", unit = "years", values = { 1 = "years", 2 = "months", 3 = "days" } }

  [subject.date_of_birth]
    field = "dob"

  [subject.dob_year]
    combinedType = "firstNonNull"
    fields = [
      { field = "dob", apply = { function = "splitDate", params = [
        "year",
        2022,
      ] } },
      { field = "age", if.any = [
        { age_unit = 1 },
        { age_unit = "" },
      ], apply = { function = "startYear", params = [
        [
          "$add_date",
          "$fever_date",
          "$fatigue_date",
          "$dyspnea_date",
          "$anosmia_date",
          "$sore_throat_date",
          # "$headache_date",
          # "$signs_symps_date",
        ],
        2022,
      ] } },
      { field = "age", if = { age_unit = 2 }, apply = { function = "startYear", params = [
        [
          "$add_date",
          "$fever_date",
          "$fatigue_date",
          "$dyspnea_date",
          "$anosmia_date",
          "$sore_throat_date",
          # "$headache_date",
          # "$signs_symps_date",
        ],
        2022,
        "%Y-%m-%d",
        "months",
      ] } },
    ]

  [subject.dob_month]
    combinedType = "firstNonNull"
    fields = [
      { field = "dob", apply = { function = "splitDate", params = [
        "month",
        2022,
      ] } },
      { field = "age", if = { age_unit = 2 }, apply = { function = "startMonth", params = [
        [
          "$add_date",
          "$fever_date",
          "$fatigue_date",
          "$dyspnea_date",
          "$anosmia_date",
          "$sore_throat_date",
          # "$headache_date",
          # "$signs_symps_date",
        ],
        2022,
        "%Y-%m-%d",
      ] } },
    ]

  [subject.dob_day]
    field = "dob"
    apply = { function = "splitDate", params = ["day", 2022] }

  [subject.ethnicity]
    description = "race/ethnicity"
    combinedType = "set"
    excludeWhen = "none"
    fields = [
      { field = "race", values = { 1 = "Arab", 2 = "Black", 3 = "South Asian", 4 = "East Asian", 5 = "West Asian", 6 = "Latin American", 7 = "White", 8 = "Aboriginal/First Nations", 9 = "Other", 10 = "Unknown" } },
      { field = "race_oth" },
    ]

  [subject.has_asthma]
    field = "asthma"
    ref = "Y/N/NK"

  [subject.has_asplenia]
    field = "asplenia"
    description = "Splenectomized"
    ref = "Y/N/NK"

  [subject.has_chronic_cardiac_disease]
    field = "cardiac"
    ref = "Y/N/NK"

  [subject.has_chronic_hematologic_disease]
    field = "hem_dse"
    description = "Chronic hematological disease"
    ref = "Y/N/NK"

  [subject.has_chronic_kidney_disease]
    field = "ckd"
    description = "Chronic kidney disease"
    ref = "Y/N/NK"

  [subject.has_dementia]
    field = "dement"
    description = "Dementia"
    ref = "Y/N/NK"

  [subject.has_diabetes]
    field = "diab_yn"
    description = "Diabetes"
    ref = "Y/N/NK"

  [subject.has_hiv]
    field = "aids"
    description = "HIV/AIDS"
    ref = "Y/N/NK"

  [subject.has_hypertension]
    field = "hypertension"
    description = "Hypertension"
    ref = "Y/N/NK"

  [subject.has_immunosuppression]
    field = "other_imm_su"
    description = "Other immunosuppression agents"
    ref = "Y/N/NK"

  [subject.has_liver_disease]
    combinedType = "any"
    fields = [
      { field = "hep_dse_mild", description = "Light liver disease", ref = "Y/N/NK" },
      { field = "hep_dse_mod_sev", description = "Moderate or severe liver disease", ref = "Y/N/NK" },
    ]

  [subject.has_malignant_neoplasm]
    field = "neopla"
    description = "Malignant tumor"
    ref = "Y/N/NK"

  [subject.has_malnutrition]
    field = "malnu"
    description = "Malnutrition"
    ref = "Y/N/NK"

  [subject.has_obesity]
    field = "obesity"
    description = "Obesity (as defined by nursing staff)"
    ref = "Y/N/NK"

  [subject.has_rheumatologic_disorder]
    field = "rheuma"
    description = "Rheumatological disorders/diseases"
    ref = "Y/N/NK"

  [subject.has_smoking]
    field = "smoke"
    description = "Smoking"
    values = { 0 = "never", 1 = "current", 2 = "former" }

  [subject.has_solid_organ_transplant]
    field = "organ_rec"
    description = "Transplanted (organ or bone marrow)"
    ref = "Y/N/NK"

  [subject.has_tuberculosis]
    field = "tuberculosis"
    description = "Tuberculosis"
    ref = "Y/N/NK"

  [subject.has_comorbidity_other]
    combinedType = "set"
    excludeWhen = "none"
    fields = [
      { field = "risks_fac1" },
      { field = "risks_fac2" },
      { field = "risks_fac3" },
      { field = "risks_fac4" },
    ]

  [subject.icu_admitted]
    combinedType = "any"

    [[subject.icu_admitted.fields]]
      field = "on_admn"
      description = "Currently hospitalised in ICU?"
      values = { 1 = true, 0 = false }

    [[subject.icu_admitted.fields]]
      field = "icu_or_high"
      description = "Admission to the intensive care unit?"
      values = { 1 = true, 0 = false }

[subject.pregnancy]
  field = "preg"
  description = "Is the patient pregnant?"
  ref = "Y/N/NK"

[subject.pregnancy_post_partum]
  field = "post_partum"
  values = { 1 = true, 0 = false }

[subject.pregnancy_birth_weight_kg]
  field = "birthweigh"
  description = "Birth weight (kg)"

[subject.pregnancy_date_of_delivery]
  field = "del_date"
  description = "Date of delivery"

[subject.pregnancy_gestational_outcome]
  field = "gest_out"
  description = "Birth"
  values = { 0 = "term_birth", 1 = "preterm_birth" }

[subject.pregnancy_outcome]
  field = "del_outcome"
  description = "From pregnancy"
  values = { 0 = "still birth", 1 = "live birth" }

[subject.sex]
  field = "sex"
  description = "Sex"
  values = { 0 = "female", 1 = "male" }

[subject.works_healthcare]
  field = "hth_wrk"
  description = "Health worker?"
  ref = "Y/N/NK"

[subject.works_lab]
  field = "microb"
  description = "Employee of a microbiology laboratory"
  values = { 1 = true }

[subject.works_microbiology_lab]
  field = "microb"
  description = "Employee of a microbiology laboratory"
  ref = "Y/N/NK"

[subject.has_died]
  field = "outcome"
  values = { 4 = true }

[subject.date_death]
  field = "outcome_date"
  if = { outcome = 4 }

[visit]
  country_iso3 = "DRC"

  [visit.subject_id]
    field = "record_id"
    sensitive = true

  [visit.visit_id]
    field = "record_id"
    sensitive = true

  [visit.start_date]
    ref = "admissionDateHierarchy"

  [visit.icu_admission]
    combinedType = "any"

    [[visit.icu_admission.fields]]
      field = "on_admn"
      description = "Currently hospitalized in intensive care?"
      values = { 1 = true, 0 = false }

    [[visit.icu_admission.fields]]
      field = "icu_or_high"
      description = "Admission to the intensive care unit?"
      values = { 1 = true, 0 = false }

[visit.icu_admission_dates]
  combinedType = "set"
  excludeWhen = "none"
  fields = [{ field = "date_icu_adm", description = "Date of ICU Admission:" }]

[visit.pathogen_test_date]
  field = "sample_taken_date"

[visit.outcome]
  field = "outcome"
  description = "Date of the outcome"
  values = { 1 = "discharged", 2 = "discharged", 3 = "transferred", 4 = "death", 5 = "discharged", 6 = "palliative discharge" }

[visit.date_outcome]
  field = "outcome_date"

[visit.treatment_antibiotics]
  combinedType = "any"

  [[visit.treatment_antibiotics.fields]]
    field = "outcome_azith"
    description = "Azithromycine"
    values = { 1 = true }

  [[visit.treatment_antibiotics.fields]]
    field = "outcome_antibiotic1"
    description = "Other antibiotics?"
    ref = "Y/N/NK"

[visit.treatment_antibiotics_type]
  combinedType = "set"
  excludeWhen = "none"
  fields = [
    { field = "outcome_azith", values = { 1 = "Azithromycine" } },
    { field = "outcome_antibiotic_agent1" },
    { field = "outcome_antibiotic_agent2" },
    { field = "outcome_antibiotic_agent3" },
    { field = "outcome_antibiotic_agent4" },
    { field = "outcome_antibiotic_agent5" },
  ]

[visit.treatment_anticoagulation]
  field = "outcome_heparin"
  ref = "Y/N/NK"

[visit.treatment_antimalarial]
  combinedType = "any"
  fields = [
    { field = "outcome_hydro", values = { 1 = true } },
    { field = "outcome_chlo", values = { 1 = true } },
  ]

[visit.treatment_antimalarial_type]
  combinedType = "set"
  excludeWhen = "none"
  fields = [
    { field = "outcome_chlo", values = { 1 = "Chloroquine" } },
    { field = "outcome_hydro", values = { 1 = "Hydroxychloroquine" } },
  ]

[visit.treatment_antivirals]
  field = "outcome_antiviral_cmyn"
  description = "Antivirals?"
  ref = "Y/N/NK"

[visit.treatment_antiviral_type]
  combinedType = "set"
  excludeWhen = "none"
  fields = [
    { field = "outcome_antiviral_cmtrt___1", values = { 1 = "Ribavirin" } },
    { field = "outcome_antiviral_cmtrt___2", values = { 1 = "Lopinavir/Ritonavir" } },
    { field = "outcome_antiviral_cmtrt___3", values = { 1 = "Interferon alpha" } },
    { field = "outcome_antiviral_cmtrt___4", values = { 1 = "Interferon beta" } },
    { field = "outcome_antiviral_cmtrt___5", values = { 1 = "Neuraminidase inhibitor" } },
  ]

[visit.treatment_corticosteroid]
  combinedType = "any"

  [[visit.treatment_corticosteroid.fields]]
    field = "outcome_corticost"
    description = "Corticosteroids"
    ref = "Y/N/NK"

  [[visit.treatment_corticosteroid.fields]]
    field = "inhala_neb"
    description = "Inhaled/nebulised corticosteroids"
    ref = "Y/N/NK"

  [[visit.treatment_corticosteroid.fields]]
    field = "sys_ster"
    description = "systemic steroids (oral/IV/IM)"
    ref = "Y/N/NK"

[visit.treatment_corticosteroid_type]
  combinedType = "set"
  excludeWhen = "none"
  fields = [
    { field = "dexamet", values = { 1 = "Dexamethasone" } },
    { field = "hydr", values = { 1 = "Hydrocortisone" } },
    { field = "pred", values = { 1 = "Prednisolone" } },
    { field = "meth", values = { 1 = "Methylprednisolone" } },
  ]

[visit.treatment_cardiovascular_support]
  combinedType = "any"
  fields = [
    { field = "vaso_or_inot", description = "Vasopressor/inotropic administrations", values = { 1 = true, 0 = false } },
    { field = "any_vas_ino_out_yn", description = "Vasopressor/inotropic administrations", values = { 1 = true, 0 = false } },
    { field = "ecls_out_yn", description = "Circulation extracorporelle (CEC)", values = { 1 = true, 0 = false } },
    { field = "ecls", description = "Circulation extracorporelle (CEC)", values = { 1 = true, 0 = false } },
  ]

[visit.treatment_dialysis]
  combinedType = "any"

  [[visit.treatment_dialysis.fields]]
    field = "dialysis_hemof"
    description = "Dialysis/hemofiltration"
    ref = "Y/N/NK"

  [[visit.treatment_dialysis.fields]]
    field = "dialysis_hemofil_out_yn"
    description = "Dialysis/hemofiltration"
    ref = "Y/N/NK"

[visit.treatment_immunosuppressant]
  field = "imm_ag"
  description = "Other immunosuppressant (non -steroidal)"
  ref = "Y/N/NK"

[visit.treatment_inhaled_nitric_oxide]
  combinedType = "any"
  fields = [
    { field = "nitric_oxide", description = "Nitric oxide inhalation", ref = "Y/N/NK" },
    { field = "nitric_oxide_out_yn", description = "Nitric oxide inhalation", ref = "Y/N/NK" },
  ]

[visit.treatment_inotropes_vasopressors]
  combinedType = "any"
  fields = [
    { field = "vaso_or_inot", description = "Vasopressor/inotropic administrations", values = { 1 = true, 0 = false } },
    { field = "any_vas_ino_out_yn", description = "Vasopressor/inotropic administrations", values = { 1 = true, 0 = false } },
  ]

[visit.treatment_neuromuscular_blocking_agents]
  combinedType = "any"
  fields = [
    { field = "neuro_block_out_yn", description = "Blocking neuromuscular agent", ref = "Y/N/NK" },
    { field = "neuro_block", description = "Blocking neuromuscular agent", ref = "Y/N/NK" },
  ]

[visit.treatment_other]
  combinedType = "set"
  excludeWhen = "none"
  fields = [
    { field = "outcome_oth_med_agent1", description = "Other treatments?" },
    { field = "outcome_oth_med_agent2", description = "Other treatments?" },
    { field = "outcome_oth_med_agent3", description = "Other treatments?" },
    { field = "outcome_oth_med_agent4", description = "Other treatments?" },
    { field = "outcome_oth_med_agent5", description = "Other treatments?" },
    { field = "other_intervs1", description = "ICU: Other interventions?" },
    { field = "other_intervs2", description = "ICU: Other interventions?" },
    { field = "other_intervs3", description = "ICU: Other interventions?" },
  ]

[visit.treatment_oxygen_therapy]
  combinedType = "any"
  fields = [
    # on admission
    { field = "oxy_vsorresu", description = "on oxygen therapy?", values = { 1 = true, 2 = false } },
    # during study
    { field = "ox_type", description = "with oxygen", values = { 1 = true } },
    { field = "can_oxy_ther", description = "Oxygen therapy with high speed by nasal glass", ref = "Y/N/NK" },
    { field = "non_inv_vent", description = "Non-invasive ventilation", ref = "Y/N/NK" },
    { field = "inv_vent", description = "Invasive ventilation", ref = "Y/N/NK" },
    { field = "ecls", description = "Circulation extracorporelle (CEC)", ref = "Y/N/NK" },
    { field = "can_oxy_ther_out_yn", description = "Oxygen therapy with high speed by nasal glass", ref = "Y/N/NK" },
    { field = "non_inv_vent_out_yn", description = "Non-invasive ventilation", ref = "Y/N/NK" },
    { field = "inv_vent_out_yn", description = "Invasive ventilation", ref = "Y/N/NK" },
    { field = "ecls_out_yn", description = "Circulation extracorporelle (CEC)", ref = "Y/N/NK" },
  ]

[visit.treatment_high_flow_nasal_cannula]
  combinedType = "any"
  fields = [
    { field = "can_oxy_ther", ref = "Y/N/NK" },
    { field = "can_oxy_ther_out_yn", ref = "Y/N/NK" },
  ]

[visit.treatment_noninvasive_ventilation]
  combinedType = "any"
  fields = [
    { field = "non_inv_vent", description = "Non-invasive ventilation", ref = "Y/N/NK" },
    { field = "non_inv_vent_out_yn", description = "Non-invasive ventilation", ref = "Y/N/NK" },
  ]

[visit.treatment_invasive_ventilation]
  combinedType = "any"
  fields = [
    { field = "inv_vent", description = "Invasive ventilation", ref = "Y/N/NK" },
    { field = "inv_vent_out_yn", description = "Invasive ventilation", ref = "Y/N/NK" },
  ]

[visit.treatment_ecmo]
  combinedType = "any"
  fields = [
    { field = "ecls", description = "Circulation extracorporelle (CEC)", ref = "Y/N/NK" },
    { field = "ecls_out_yn", description = "Circulation extracorporelle (CEC)", ref = "Y/N/NK" },
  ]

[visit.treatment_prone_position]
  combinedType = "any"
  fields = [
    { field = "prone", description = "Prone position", values = { 1 = true, 0 = false } },
    { field = "decu_vent_out_yn", description = "Décubitus ventral (prone position)", values = { 1 = true, 0 = false } },
  ]

[visit.transfer_from_other_facility]
  field = "was_trans"
  description = "Referred from another structure"
  values = { 1 = true, 0 = false }

[[observation]]
  name = "abdominal_pain"
  phase = "admission"
  date = { ref = "admissionDateHierarchy" }
  start_date = { field = "abd_pain_date" }
  duration_type = "event"
  is_present = { field = "abd_pain", description = "Abdominal pain", ref = "Y/N/NK" }

[[observation]]
  name = "abdominal_pain"
  phase = "study"
  date = { ref = "ss_datetime" }
  is_present = { field = "abd_pain_v2", description = "Abdominal pain", ref = "Y/N/NK" }

[[observation]]
  name = "altered_consciousness_confusion"
  phase = "admission"
  start_date = { field = "consciousness_date" }
  duration_type = "event"
  date = { ref = "admissionDateHierarchy" }
  is_present = { field = "consciousness", description = "Alterations of consciousness/confusion", ref = "Y/N/NK" }

[[observation]]
  name = "altered_consciousness_confusion"
  phase = "study"
  date = { ref = "ss_datetime" }

  [observation.is_present]
    field = "consciousness_coma_v2"
    description = "Alteration of consciousness/confusion/coma"
    ref = "Y/N/NK"

[[observation]]
  name = "altered_consciousness_confusion"
  phase = "study"
  date = { ref = "ss_datetime" }
  is_present = { field = "consciousness_v2", description = "Alteration of consciousness", ref = "Y/N/NK" }

[[observation]]
  name = "bleeding_haemorrhage"
  phase = "admission"
  start_date = { field = "bleeding_date" }
  date = { ref = "admissionDateHierarchy" }
  duration_type = "event"
  is_present = { field = "bleeding", description = "Bleeding (hemorrhage)", ref = "Y/N/NK" }

[[observation]]
  name = "bleeding_haemorrhage"
  phase = "study"
  date = { ref = "ss_datetime" }
  is_present = { field = "bleeding_v2", description = "Bleeding (hemorrhage)", ref = "Y/N/NK" }

[[observation]]
  name = "sternal_capillary_refill_time_greater_2s"
  phase = "admission"
  date = { ref = "admissionDateHierarchy" }
  is_present = { field = "caps_iso", values = { 1 = true, 0 = false } }

[[observation]]
  name = "sternal_capillary_refill_time_greater_2s"
  phase = "study"
  date = { ref = "vitals_datetime" }
  is_present = { field = "caps", values = { 1 = true, 0 = false } }

[[observation]]
  name = "chest_pain"
  phase = "admission"
  start_date = { field = "chest_pain_date" }
  date = { ref = "admissionDateHierarchy" }
  duration_type = "event"
  is_present = { field = "chest_pain", description = "Chest pain", ref = "Y/N/NK" }

[[observation]]
  name = "chest_pain"
  phase = "study"
  date = { ref = "ss_datetime" }
  is_present = { field = "chest_pain_v2", description = "Chest pain", ref = "Y/N/NK" }

[[observation]]
  name = "pneumonia"
  phase = "study"
  date = { ref = "ss_datetime" }                                                                    # vitals_date (only because the data indicates this is the date recorded
  is_present = { field = "clipneu", description = "Clinical pneumonia diagnosed?", ref = "Y/N/NK" }

[[observation]]
  name = "pneumonia"
  phase = "admission"
  start_date = { field = "pneumo_cli_date" }
  date = { ref = "admissionDateHierarchy" }
  duration_type = "event"
  is_present = { field = "pneumo_cli", description = "Clinical pneumonia diagnosed?", ref = "Y/N/NK" }

[[observation]]
  name = "pneumonia"
  phase = "study"
  start_date = { field = "date_comp_viral_pneu2" }
  date = { field = "comp_date" }
  duration_type = "block"
  is_present = { field = "viral_pneumo2", ref = "Y/N/NK" }
  context = ['viral']

[[observation]]
  name = "pneumonia"
  phase = "study"
  start_date = { field = "date_comp_bact_pneu2" }
  date = { field = "comp_date" }
  duration_type = "block"
  is_present = { field = "bact_pneumo2", ref = "Y/N/NK" }
  context = ['bacterial']

[[observation]]
  name = "pneumonia"
  phase = "study"
  start_date = { field = "date_comp_cryp_org2" }
  date = { field = "comp_date" }
  duration_type = "block"
  is_present = { field = "cop2", ref = "Y/N/NK" }
  context = ['cryptogenic organising pneumonia']

[[observation]]
  name = "conjunctivitis"
  phase = "admission"
  start_date = { field = "conjunc_date" }
  date = { ref = "admissionDateHierarchy" }
  duration_type = "event"
  is_present = { field = "conjunc", description = "Conjunctivitis", ref = "Y/N/NK" }

[[observation]]
  name = "conjunctivitis"
  phase = "study"
  date = { ref = "ss_datetime" }
  is_present = { field = "conjunc_v2", description = "Conjunctivitis", ref = "Y/N/NK" }

[[observation]]
  name = "cough"
  phase = "admission"
  date = { ref = "admissionDateHierarchy" }
  duration_type = "event"

  [observation.start_date]
    combinedType = "min"
    fields = [
      { field = "dry_cough_date" },
      { field = "wet_cough_date" },
      { field = "blood_cough_date" },
    ]

  [observation.is_present]
    combinedType = "any"
    fields = [
      { field = "cough", description = "Cough", ref = "Y/N/NK" },
      { field = "dry_cough", description = "Dry cough", ref = "Y/N/NK" },
      { field = "wet_cough", description = "Wet cough", ref = "Y/N/NK" },
      { field = "blood_cough", description = "Blood cough", ref = "Y/N/NK" },
    ]

[[observation]]
  name = "cough_dry"
  phase = "admission"
  start_date = { field = "dry_cough_date" }
  date = { ref = "admissionDateHierarchy" }
  duration_type = "block"
  is_present = { field = "dry_cough", description = "Cough", ref = "Y/N/NK" }

[[observation]]
  name = "cough_with_sputum_production"
  phase = "admission"
  start_date = { field = "wet_cough_date" }
  date = { ref = "admissionDateHierarchy" }
  duration_type = "block"
  is_present = { field = "wet_cough", description = "Cough", ref = "Y/N/NK" }

[[observation]]
  name = "cough_with_haemoptysis"
  phase = "admission"
  start_date = { field = "blood_cough_date" }
  date = { ref = "admissionDateHierarchy" }
  duration_type = "block"
  is_present = { field = "blood_cough", description = "Cough", ref = "Y/N/NK" }

[[observation]]
  name = "cough"
  phase = "study"
  date = { ref = "ss_datetime" }
  [observation.is_present]
    combinedType = "any"
    fields = [
      { field = "cough_v2", description = "Cough", ref = "Y/N/NK" },
      { field = "dry_cough_v2", description = "Dry cough", ref = "Y/N/NK" },
      { field = "wet_cough_v2", description = "Cough with sput", ref = "Y/N/NK" },
      { field = "blood_cough_v2", description = "Cough with blood", ref = "Y/N/NK" },
    ]

[[observation]]
  name = "cough_dry"
  phase = "study"
  date = { ref = "ss_datetime" }
  is_present = { field = "dry_cough_v2", description = "Cough", ref = "Y/N/NK" }

[[observation]]
  name = "cough_with_sputum_production"
  phase = "study"
  date = { ref = "ss_datetime" }
  is_present = { field = "wet_cough_v2", description = "Cough with sput", ref = "Y/N/NK" }

[[observation]]
  name = "cough_with_haemoptysis"
  phase = "study"
  date = { ref = "ss_datetime" }
  is_present = { field = "blood_cough_v2", description = "Cough with blood", ref = "Y/N/NK" }

[[observation]]
  name = "diarrhoea"
  phase = "admission"
  start_date = { field = "diarrhea_date" }
  date = { ref = "admissionDateHierarchy" }
  duration_type = "event"
  is_present = { field = "diarrhea", ref = "Y/N/NK" }

[[observation]]
  name = "diarrhoea"
  phase = "study"
  date = { ref = "ss_datetime" }
  is_present = { field = "diarrhea_v2", ref = "Y/N/NK" }

[[observation]]
  name = "diastolic_blood_pressure_mmHg"
  phase = "admission"
  date = { ref = "admissionDateHierarchy" }
  value = { field = "diastol_iso", description = "Blood pressure -diastolic" }

[[observation]]
  name = "diastolic_blood_pressure_mmHg"
  phase = "study"
  date = { ref = "vitals_datetime" }
  value = { field = "diastol", description = "Diastolic" }

[[observation]]
  name = "ear_pain"
  phase = "admission"
  start_date = { field = "ear_pain_date" }
  date = { ref = "admissionDateHierarchy" }
  duration_type = "event"
  is_present = { field = "ear_pain", ref = "Y/N/NK" }

[[observation]]
  name = "ear_pain"
  phase = "study"
  date = { ref = "ss_datetime" }
  is_present = { field = "ear_pain_v2", ref = "Y/N/NK" }

[[observation]]
  name = "fatigue_malaise"
  phase = "study"
  date = { ref = "ss_datetime" }
  is_present = { field = "fatigue_v2", description = "Fatigue", ref = "Y/N/NK" }

[[observation]]
  name = "fatigue_malaise"
  phase = "admission"
  start_date = { field = "fatigue_date" }
  date = { ref = "admissionDateHierarchy" }
  duration_type = "event"
  is_present = { field = "fatigue", description = "Fatigue", ref = "Y/N/NK" }

[[observation]]
  name = "glasgow_coma_score"
  phase = "admission"
  value = { field = "score_glasgow", description = "Glasgow score" }
  [observation.date]
    combinedType = "min"
    fields = [
      { field = "o2_date", source_date = "Y-%m-%d %H:%M" },
      { ref = "admissionDateHierarchy" },
    ]

[[observation]]
  name = "glasgow_coma_score"
  phase = "study"
  date = { ref = "vitals_datetime" }
  value = { field = "gcs2", description = "Glasgow score" }

[[observation]]
  name = "headache"
  phase = "admission"
  start_date = { field = "headache_date" }
  date = { ref = "admissionDateHierarchy" }
  duration_type = "event"
  is_present = { field = "headache", description = "Headache", ref = "Y/N/NK" }

[[observation]]
  name = "headache"
  phase = "study"
  date = { ref = "ss_datetime" }
  is_present = { field = "headache_v2", description = "Headache", ref = "Y/N/NK" }

[[observation]]
  name = "heart_rate_bpm"
  phase = "admission"
  date = { ref = "admissionDateHierarchy" }
  value = { field = "pulse_iso" }

[[observation]]
  name = "heart_rate_bpm"
  phase = "study"
  date = { ref = "vitals_datetime" }
  value = { field = "hr" }

[[observation]]
  name = "history_of_fever"
  phase = "study"
  date = { ref = "ss_datetime" }
  is_present = { field = "fever_v2", description = "Fever", ref = "Y/N/NK" }

[[observation]]
  name = "history_of_fever"
  phase = "admission"
  start_date = { field = "fever_date" }
  date = { ref = "admissionDateHierarchy" }
  duration_type = "event"
  is_present = { field = "fever", description = "Fever", ref = "Y/N/NK" }

[[observation]]
  name = "joint_pain"
  phase = "admission"
  start_date = { field = "jt_pain_date" }
  date = { ref = "admissionDateHierarchy" }
  duration_type = "event"
  is_present = { field = "jt_pain", description = "Joint pain (arthralgia)", ref = "Y/N/NK" }

[[observation]]
  name = "joint_pain"
  phase = "study"
  date = { ref = "ss_datetime" }
  is_present = { field = "jt_pain_v2", description = "Joint pain (arthralgia)", ref = "Y/N/NK" }

[[observation]]
  name = "loss_of_smell_or_taste"
  phase = "admission"
  date = { ref = "admissionDateHierarchy" }
  duration_type = "event"

  [observation.start_date]
    combinedType = "min"
    fields = [{ field = "anosmia_date" }, { field = "ageusia_date" }]

  [observation.is_present]
    combinedType = "any"
    fields = [
      { field = "anosmia", description = "Anosmia (loss of smell)", ref = "Y/N/NK" },
      { field = "ageusia", description = "AGUEUSIE (loss of taste)", ref = "Y/N/NK" },
    ]

[[observation]]
  name = "loss_of_smell_or_taste"
  phase = "study"
  date = { ref = "ss_datetime" }

  [observation.is_present]
    combinedType = "any"
    fields = [
      { field = "anosmia_v2", description = "Anosmia (loss of smell)", ref = "Y/N/NK" },
      { field = "ageusia_v2", description = "AGUEUSIE (loss of taste)", ref = "Y/N/NK" },
    ]

[[observation]]
  name = "loss_of_smell"
  phase = "admission"
  start_date = { field = "anosmia_date" }
  date = { ref = "admissionDateHierarchy" }
  duration_type = "event"
  is_present = { field = "anosmia", description = "Anosmia (loss of smell)", ref = "Y/N/NK" }

[[observation]]
  name = "loss_of_smell"
  phase = "study"
  date = { ref = "ss_datetime" }
  is_present = { field = "anosmia_v2", description = "Anosmia (loss of smell)", ref = "Y/N/NK" }

[[observation]]
  name = "loss_of_taste"
  phase = "study"
  date = { ref = "ss_datetime" }
  is_present = { field = "ageusia_v2", description = "AGUEUSIE (loss of taste)", ref = "Y/N/NK" }

[[observation]]
  name = "loss_of_taste"
  phase = "admission"
  start_date = { field = "ageusia_date" }
  date = { ref = "admissionDateHierarchy" }
  duration_type = "event"
  is_present = { field = "ageusia", description = "AGUEUSIE (loss of taste)", ref = "Y/N/NK" }

[[observation]]
  name = "lower_chest_wall_indrawing"
  phase = "study"
  date = { ref = "ss_datetime" }
  is_present = { field = "lowerchesdrawing", ref = "Y/N/NK" }

[[observation]]
  name = "lymphadenopathy"
  phase = "admission"
  start_date = { field = "adenop_sign_spe" }
  date = { ref = "admissionDateHierarchy" }
  duration_type = "block"
  is_present = { field = "adenop_sign", description = "Adénopathies", values = { 1 = true, 0 = false } }

[[observation]]
  name = "lymphadenopathy"
  phase = "study"
  date = { ref = "ss_datetime" }
  is_present = { field = "lymph_ulcers_v2", description = "Adénopathies", values = { 1 = true, 0 = false } }

[[observation]]
  name = "muscle_aches"
  phase = "admission"
  start_date = { field = "myalagia_date" }
  date = { ref = "admissionDateHierarchy" }
  duration_type = "event"
  is_present = { field = "myalagia", description = "Muscle pain (Myalgia)", ref = "Y/N/NK" }

[[observation]]
  name = "muscle_aches"
  phase = "study"
  date = { ref = "ss_datetime" }
  is_present = { field = "myalagia_v2", description = "Muscle pain (Myalgia)", ref = "Y/N/NK" }

[[observation]]
  name = "musculoskeletal_pain"
  phase = "admission"
  date = { ref = "admissionDateHierarchy" }
  duration_type = "event"

  [observation.start_date]
    combinedType = "min"
    fields = [{ field = "myalagia_date" }, { field = "jt_pain_date" }]

  [observation.is_present]
    combinedType = "any"
    excludeWhen = "none"
    fields = [
      { field = "myalagia", values = { 1 = true } },
      { field = "jt_pain", values = { 1 = true } },
    ]

[[observation]]
  name = "musculoskeletal_pain"
  phase = "study"
  date = { ref = "ss_datetime" }

  [observation.is_present]
    combinedType = "any"
    excludeWhen = "none"
    fields = [
      { field = "myalagia_v2", values = { 1 = true } },
      { field = "jt_pain_v2", values = { 1 = true } },
    ]

[[observation]]
  name = "other_symptom"
  phase = "admission"
  start_date = { field = "other_1_date" }
  date = { ref = "admissionDateHierarchy" }
  duration_type = "event"
  text = { field = "other_0" }

[[observation]]
  name = "other_symptom"
  phase = "admission"
  start_date = { field = "other_date" }
  date = { ref = "admissionDateHierarchy" }
  duration_type = "event"
  text = { field = "other_1" }

[[observation]]
  name = "other_symptom"
  phase = "admission"
  start_date = { field = "other_2_date" }
  date = { ref = "admissionDateHierarchy" }
  duration_type = "event"
  text = { field = "other_2" }

[[observation]]
  name = "other_symptom"
  phase = "study"
  date = { ref = "ss_datetime" }
  text = { field = "other_0_v2", description = "Other symptom 1" }

[[observation]]
  name = "other_symptom"
  phase = "study"
  date = { ref = "ss_datetime" }
  text = { field = "other_1_v2", description = "Other symptom 2" }

[[observation]]
  name = "other_symptom"
  phase = "study"
  date = { ref = "ss_datetime" }
  text = { field = "other_2_v2", description = "Other symptom 3" }

[[observation]]
  name = "oxygen_o2hb"
  phase = "study"
  date = { field = "hema_date" }
  value = { field = "hemo", unit = "g/dL", source_unit = { field = "hemo_type", values = { 1 = "g/L", 2 = "g/dL" } } }

[[observation]]
  name = "oxygen_saturation_percent"
  phase = "study"
  date = { ref = "vitals_datetime" }
  value = { field = "o2_sate", description = "Oxygen saturation" }
  [observation.context]
    combinedType = "set"
    excludeWhen = "none"
    fields = [
      { field = "ox_type", values = { 1 = "on oxygen", 2 = "on room air" } },
    ]

[[observation]]
  name = "oxygen_saturation_percent"
  phase = "admission"
  value = { field = "oxy_vsorres", description = "Oxygen saturation" }
  [observation.date]
    combinedType = "min"
    fields = [
      { field = "o2_date", source_date = "Y-%m-%d %H:%M" },
      { ref = "admissionDateHierarchy" },
    ]
  [observation.context]
    combinedType = "set"
    excludeWhen = "none"
    fields = [
      { field = "oxy_vsorresu", values = { 1 = "on oxygen", 2 = "on room air" } },
    ]

[[observation]]
  name = "pH"
  phase = "study"
  date = { field = "icu_date" }
  value = { field = "ph", description = "PH" }

  # [[observation]]
  #   name = "pao2_mmHg"
  #   phase = "study"
  #   date = { ref = "ss_datetime" }
  #   value = { field = "pa02", unit = "mmHg", description = "PAO2 at the time of the superior FIO2", source_unit = { field = "pa02_type", values = { 1 = "kPa", 2 = "mmHg" } } }
  #   [observation.context]
  #     combinedType = "set"
  #     fields = [
  #       { field = "pa02_samp_type", values = { 1 = "Arterial", 2 = "Venous", 3 = "Capillary" } },
  #     ]

  # [[observation]]
  #   name = "pco2_mmHg"
  #   phase = "study"
  #   date = { ref = "ss_datetime" }
  #   value = { field = "pcc02", description = "PCO2 Value", unit = "mmHg", source_unit = { field = "pc02_type", values = { 1 = "kPa", 2 = "mmHg" } } }
  #   [observation.context]
  #     combinedType = "set"
  #     fields = [
  #       { field = "pcc02_source", values = { 1 = "From the same blood gas recording as the PaO2" } },
  #     ]

[[observation]]
  name = "respiratory_rate"
  phase = "admission"
  date = { ref = "admissionDateHierarchy" }
  value = { field = "rr_iso", description = "Respiratory rate" }

[[observation]]
  name = "respiratory_rate"
  phase = "study"
  date = { ref = "vitals_datetime" }
  value = { field = "rr", description = "Respiratory rate" }

[[observation]]
  name = "runny_nose"
  phase = "admission"
  start_date = { field = "rhinorrhea_date" }
  date = { ref = "admissionDateHierarchy" }
  duration_type = "event"
  is_present = { field = "rhinorrhea", ref = "Y/N/NK" }

[[observation]]
  name = "runny_nose"
  phase = "study"
  date = { ref = "ss_datetime" }
  is_present = { field = "rhinorrhea_v2", ref = "Y/N/NK" }

[[observation]]
  name = "seizures"
  phase = "admission"
  start_date = { field = "seizures_date_s_and_s" }
  date = { ref = "admissionDateHierarchy" }
  duration_type = "event"
  is_present = { field = "seizures", ref = "Y/N/NK" }

[[observation]]
  name = "seizures"
  phase = "study"
  date = { ref = "ss_datetime" }
  is_present = { field = "seizures_v2", ref = "Y/N/NK" }

  # [[observation]]
  #   name = "seizures"
  #   phase = "study"
  #   is_present = { field = "comps_seizures2", ref = "Y/N/NK" }
  #   date = { field = "comp_date2" } # no dates

[[observation]]
  name = "shortness_of_breath"
  phase = "study"
  date = { ref = "ss_datetime" }
  is_present = { field = "dyspnea_v2", description = "Shortness of breath (dyspnea)", ref = "Y/N/NK" }

[[observation]]
  name = "shortness_of_breath"
  phase = "admission"
  start_date = { field = "dyspnea_date" }
  date = { ref = "admissionDateHierarchy" }
  duration_type = "event"
  is_present = { field = "dyspnea", description = "Shortness of breath (dyspnea)", ref = "Y/N/NK" }

[[observation]]
  name = "skin_rash"
  phase = "study"
  date = { ref = "ss_datetime" }
  is_present = { field = "skin_rash_v2", description = "Skin rash /discoloration", ref = "Y/N/NK" }

[[observation]]
  name = "skin_rash"
  phase = "admission"
  start_date = { field = "skin_rash_date" }
  date = { ref = "admissionDateHierarchy" }
  duration_type = "event"
  is_present = { field = "skin_rash", description = "Skin/discoloration of the skin", ref = "Y/N/NK" }

[[observation]]
  name = "skin_ulcers"
  phase = "study"
  date = { ref = "ss_datetime" }
  is_present = { field = "skin_ulcers_v2", description = "Skin ulcer", ref = "Y/N/NK" }

[[observation]]
  name = "skin_ulcers"
  phase = "admission"
  start_date = { field = "skin_ulcers_date" }
  date = { ref = "admissionDateHierarchy" }
  duration_type = "event"
  is_present = { field = "skin_ulcers", description = "Skin ulcer", ref = "Y/N/NK" }

[[observation]]
  name = "sore_throat"
  phase = "admission"
  start_date = { field = "sore_throat_date" }
  date = { ref = "admissionDateHierarchy" }
  duration_type = "event"
  is_present = { field = "sore_throat", description = "Sore throat", ref = "Y/N/NK" }

[[observation]]
  name = "sore_throat"
  phase = "study"
  date = { ref = "ss_datetime" }
  is_present = { field = "sore_throat_v2", description = "Sore throat", ref = "Y/N/NK" }

[[observation]]
  name = "systolic_blood_pressure_mmHg"
  phase = "admission"
  date = { ref = "admissionDateHierarchy" }
  value = { field = "systol_iso", description = "Blood pressure - Systolic" }

[[observation]]
  name = "systolic_blood_pressure_mmHg"
  phase = "study"
  date = { ref = "vitals_datetime" }
  value = { field = "systol", description = "Systolic" }

[[observation]]
  name = "temperature_celsius"
  phase = "study"
  date = { ref = "vitals_datetime" }
  value = { field = "temperature", description = "Temperature" }

[[observation]]
  name = "temperature_celsius"
  phase = "admission"
  date = { ref = "admissionDateHierarchy" }
  value = { field = "temperature_iso", description = "Temperature" }

[[observation]]
  name = "vomiting_nausea"
  phase = "admission"
  start_date = { field = "nausea_date" }
  date = { ref = "admissionDateHierarchy" }
  duration_type = "event"
  is_present = { field = "nausea", description = "Vomiting / nausea", ref = "Y/N/NK" }

[[observation]]
  name = "vomiting_nausea"
  phase = "study"
  date = { ref = "ss_datetime" }
  is_present = { field = "nausea_v2", description = "Vomiting / nausea", ref = "Y/N/NK" }

[[observation]]
  name = "wheezing"
  phase = "admission"
  start_date = { field = "wheezing_date" }
  date = { ref = "admissionDateHierarchy" }
  duration_type = "event"
  is_present = { field = "wheezing", ref = "Y/N/NK" }

[[observation]]
  name = "wheezing"
  phase = "study"
  date = { ref = "ss_datetime" }
  is_present = { field = "wheezing_v2", ref = "Y/N/NK" }