add covid19 vaccination info

isaric/parsers/brazil-followup.toml

@@ -211,6 +211,15 @@
   description = "Admission to an Intensive Care Unit (ICU / CTI)"
   ref = "Y/N"
 
+[subject.vaccinated_covid19]
+  field = "flw_cov_vacc"
+  values = { 1 = true, 0 = false }
+
+[subject.vaccinated_covid19_dates]
+  combinedType = "list"
+  excludeWhen = "none"
+  fields = [{ field = "flw_vacc_last_dose" }]
+
   # VISIT
   # required fields - "visit_id", "subject_id", "country_iso3", "start_date", "outcome", "date_outcome"
 

isaric/parsers/ccp-cameroon.toml

@@ -272,6 +272,19 @@
     { field = "q14_treatment_outcome", if = { q1_treatment_outcome = 5 } },
   ]
 
+[subject.vaccinated_covid19]
+  field = "q1_vaccination"
+  values = { 1 = true, 0 = false }
+
+[subject.vaccinated_covid19_dates]
+  combinedType = "list"
+  excludeWhen = "none"
+  fields = [
+    { field = "q5_vaccination" },
+    { field = "q6_vaccination" },
+    { field = "q7_vaccination" },
+  ]
+
 [visit]
   country_iso3 = "CMR"
 

isaric/parsers/ccp-uganda-v2.toml

@@ -243,6 +243,15 @@
       { field = "icu_date", apply = { function = "isNotNull" } },
     ]
 
+  [subject.vaccinated_covid19]
+    field = "vaccin_covid"
+    values = { 1 = true, 0 = false }
+
+  [subject.vaccinated_covid19_dates]
+    combinedType = "list"
+    excludeWhen = "none"
+    fields = [{ field = "vaccin_date" }]
+
     # VISIT
     # required fields - "visit_id", "subject_id", "country_iso3", "start_date", "outcome", "date_outcome"
 

isaric/parsers/isaric-ccpuk.toml

@@ -343,6 +343,14 @@
   description = "Admitted to ICU?"
   apply = { function = "isNotNull" }
 
+[subject.vaccinated_covid19]
+  field = "covid19_vaccine"
+  values = { 1 = true, 0 = false }
+
+[subject.vaccinated_covid19_dates]
+  combinedType = "list"
+  excludeWhen = "none"
+  fields = [{ field = "covid19_vaccined" }, { field = "covid19_vaccine2d" }]
 
   ## VISITS
 

isaric/parsers/isaric-core.toml

@@ -430,7 +430,7 @@
   description = "Smoking at least one cigarette, cigar, pipe or equivalent per day before the onset of the current illness."
 
   [subject.has_smoking.values]
-    1 = "yes"
+    1 = "current"
     2 = "never"
     3 = "former"
 
@@ -550,6 +550,21 @@
     { field = "flw2_date_death", description = "If known, date of death" },
   ]
 
+[subject.vaccinated_covid19]
+  field = "vacc_cov19_cmyn"
+  can_skip = true
+  values = { 1 = true, 0 = false }
+
+[subject.vaccinated_covid19_dates]
+  combinedType = "set"
+  excludeWhen = "none"
+  fields = [
+    { field = "vacc_cov19_1_cmdat", can_skip = true },
+    { field = "vacc_cov19_2_cmdat", can_skip = true },
+    { field = "vacc_cov19_3_cmdat", can_skip = true },
+    { field = "vacc_cov19_4_cmdat", can_skip = true },
+  ]
+
 [visit]
   country_iso3 = { field = "country", ref = "countryMap" }
 
@@ -736,6 +751,7 @@
 
   [[visit.treatment_corticosteroid_type.fields]]
     field = "corticost_cmtrt"
+    can_skip = true
     apply.function = "wordSubstituteSet"
     apply.params = [
       ["D[e,é][x,s]a?m[e,é]th?a[s,z]one?", "Dexamethasone"],
@@ -1436,14 +1452,14 @@
 [[observation]]
   name = "inability_to_walk_scale"
   phase = "admission"
-  date = { field = "admissionDateHierarchy" }
+  date = { ref = "admissionDateHierarchy" }
   value = { field = "flw_walking_pre_c19", values = { 1 = 1, 2 = 2, 3 = 3, 4 = 4 } }
   context = ["Ability to walk or climb steps prior to COVID-19 illness"]
 
 [[observation]]
   name = "inability_to_walk_scale"
   phase = "admission"
-  date = { field = "admissionDateHierarchy" }
+  date = { ref = "admissionDateHierarchy" }
   value = { field = "flw_eq5d_mb_5l_uk_eng", values = { 1 = 1, 2 = 2, 3 = 2, 4 = 3, 5 = 4 } }
   context = ["Ability to walk prior to COVID-19 illness"]
 

isaric/parsers/isaric-ecmo.toml

@@ -550,6 +550,20 @@
   description = "Admitted to ICU?"
   apply = { function = "isNotNull" }
 
+[subject.vaccinated_covid19]
+  field = "vacc_cov19_cmyn"
+  values = { 1 = true, 0 = false }
+
+[subject.vaccinated_covid19_dates]
+  combinedType = "list"
+  excludeWhen = "none"
+  fields = [
+    { field = "vacc_cov19_1_cmdat" },
+    { field = "vacc_cov19_2_cmdat" },
+    { field = "vacc_cov19_3_cmdat" },
+    { field = "vacc_cov19_cmdat" },
+  ]
+
 [visit]
   country_iso3 = { field = "country", ref = "countryMap" }
 

isaric/parsers/isaric-followup-fr.toml

@@ -60,7 +60,6 @@
   [subject.date_death]
     field = "ca_death_date"
 
-
     # No visit table as data is followup only
 
 [visit]

isaric/parsers/isaric-rapid.toml

@@ -482,6 +482,20 @@
     { field = "icu_hoterm", description = "first day of admission", values = { 1 = true, 2 = false } },
   ]
 
+[subject.vaccinated_covid19]
+  field = "vacc_cov19_cmyn"
+  values = { 1 = true, 0 = false }
+
+[subject.vaccinated_covid19_dates]
+  combinedType = "list"
+  excludeWhen = "none"
+  fields = [
+    { field = "vacc_cov19_1_cmdat" },
+    { field = "vacc_cov19_2_cmdat" },
+    { field = "vacc_cov19_3_cmdat" },
+    { field = "vacc_cov19_4_cmdat" },
+  ]
+
   ## VISIT
 
 [visit]

isaric/parsers/isaric-tier1.toml

@@ -198,6 +198,22 @@
     ref = "Y/N"
     can_skip = true
 
+  [subject.vaccinated_covid19]
+    combinedType = "firstNonNull"
+    fields = [
+      { fieldPattern = 'flw\d*_vacc_cov19_cmyn', values = { 1 = true, 0 = false } },
+    ]
+
+
+  [subject.vaccinated_covid19_dates]
+    combinedType = "set"
+    excludeWhen = "none"
+    fields = [
+      { fieldPattern = 'flw\d*_vacc_cov19_1_cmdat' },
+      { fieldPattern = 'flw\d*_vacc_cov19_2_cmdat' },
+      { fieldPattern = 'flw\d*_vacc_cov19_3_cmdat', source_date = "%d/%m/%Y" },
+    ]
+
     # VISIT
     # required fields - "visit_id", "subject_id", "country_iso3", "start_date", "outcome", "date_outcome"
 

isaric/parsers/ncov-gambia.toml

@@ -292,6 +292,15 @@
     ] }, # followup field at day 90
   ]
 
+[subject.vaccinated_covid19]
+  field = "q_68"
+  ref = "Y/N"
+
+[subject.vaccinated_covid19_dates]
+  combinedType = "list"
+  excludeWhen = "none"
+  fields = [{ field = "q_68a_i", source_date = "%Y-%m-%d" }]
+
   # VISIT
   # required fields - "visit_id", "subject_id", "country_iso3", "start_date", "outcome", "date_outcome"
 

isaric/parsers/predicovid.toml

@@ -138,6 +138,10 @@
     field = "questionaire"        # added into merged data to distinguish between questionaires
     values = { month_12 = false }
 
+  [subject.vaccinated_covid19]
+    field = "covid_vaccine"
+    values = { 1 = true, 0 = false }
+
     # VISIT
 
 [visit]

isaric/parsers/recover-eu.toml

@@ -210,6 +210,15 @@
   description = "Did episode included ICU/High Care Unit admission?"
   ref = "Y/N"
 
+[subject.vaccinated_covid19]
+  field = "VACC_REC"
+  ref = "Y/N"
+
+[subject.vaccinated_covid19_dates]
+  combinedType = "list"
+  excludeWhen = "none"
+  fields = [{ field = "DOSE1_DT" }, { field = "DOSE2_DT" }]
+
   # VISIT
   # required fields - "visit_id", "subject_id", "country_iso3", "start_date", "outcome", "date_outcome"
 

isaric/parsers/uganda-vri-v1.toml

@@ -155,6 +155,11 @@
   field = "outcome_date"
   if = { outcome = 2 }
 
+[subject.vaccinated_covid19]
+  field = "vcard"
+  values = { 1 = true, 0 = false }
+
+
   # VISIT
   # required fields - "visit_id", "subject_id", "country_iso3", "start_date", "outcome", "date_outcome"
 

schemas/dev/parser.schema.json

@@ -525,6 +525,14 @@
         "icu_admitted": {
           "description": "Admitted to ICU",
           "$ref": "#/definitions/mapping"
+        },
+        "vaccinated_covid19": {
+          "description": "Received a COVID19 vaccination",
+          "$ref": "#/definitions/mapping"
+        },
+        "vaccinated_covid19_dates": {
+          "description": "Date(s) of covid vaccination",
+          "$ref": "#/definitions/mapping"
         }
       }
     },