diff --git a/isaric/parsers/brazil-followup.toml b/isaric/parsers/brazil-followup.toml index b086b9e6..85821c3a 100644 --- a/isaric/parsers/brazil-followup.toml +++ b/isaric/parsers/brazil-followup.toml @@ -211,6 +211,16 @@ 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" }] + # context = ["Date of most recent dose"] + # VISIT # required fields - "visit_id", "subject_id", "country_iso3", "start_date", "outcome", "date_outcome" diff --git a/isaric/parsers/ccp-cameroon.toml b/isaric/parsers/ccp-cameroon.toml index aa098d0f..5c09c884 100644 --- a/isaric/parsers/ccp-cameroon.toml +++ b/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" diff --git a/isaric/parsers/ccp-uganda-v2.toml b/isaric/parsers/ccp-uganda-v2.toml index f47f0fc1..81939bc5 100644 --- a/isaric/parsers/ccp-uganda-v2.toml +++ b/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" diff --git a/isaric/parsers/datcov-southafrica.toml b/isaric/parsers/datcov-southafrica.toml index af633be8..7d03b1c7 100644 --- a/isaric/parsers/datcov-southafrica.toml +++ b/isaric/parsers/datcov-southafrica.toml @@ -291,6 +291,19 @@ { field = "flw_icu", description = "If ever admitted to hospital, were you admitted to intensive care (ICU/ITU)?", values = { 0 = false, 1 = true } }, ] + [subject.vaccinated_covid19] + field = "Vaccinated" + values = { 1 = true, 0 = false } + + [subject.vaccinated_covid19_dates] + combinedType = "set" + excludeWhen = "none" + fields = [ + { field = "First Dose Date" }, + { field = "Second Dose Date" }, + { field = "Booster Dose Date" }, + ] + [visit] country_iso3 = "ZAF" diff --git a/isaric/parsers/isaric-ccpuk.toml b/isaric/parsers/isaric-ccpuk.toml index 8de1b54c..b7dff47f 100644 --- a/isaric/parsers/isaric-ccpuk.toml +++ b/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 diff --git a/isaric/parsers/isaric-core.toml b/isaric/parsers/isaric-core.toml index c607a96b..fa00bd9f 100644 --- a/isaric/parsers/isaric-core.toml +++ b/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"] diff --git a/isaric/parsers/isaric-ecmo.toml b/isaric/parsers/isaric-ecmo.toml index 4e995179..5faa3460 100644 --- a/isaric/parsers/isaric-ecmo.toml +++ b/isaric/parsers/isaric-ecmo.toml @@ -550,6 +550,21 @@ 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" }, + ] + # context = ["Date of most recent dose"] + [visit] country_iso3 = { field = "country", ref = "countryMap" } diff --git a/isaric/parsers/isaric-rapid.toml b/isaric/parsers/isaric-rapid.toml index e1371723..75a7da32 100644 --- a/isaric/parsers/isaric-rapid.toml +++ b/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] diff --git a/isaric/parsers/isaric-tier1.toml b/isaric/parsers/isaric-tier1.toml index 38d3a698..32d9b079 100644 --- a/isaric/parsers/isaric-tier1.toml +++ b/isaric/parsers/isaric-tier1.toml @@ -198,6 +198,19 @@ ref = "Y/N" can_skip = true + [subject.vaccinated_covid19] + field = "flw_vacc_cov19_cmyn" + values = { 1 = true, 0 = false } + + [subject.vaccinated_covid19_dates] + combinedType = "set" + excludeWhen = "none" + fields = [ + { field = "flw_vacc_cov19_1_cmdat" }, + { field = "flw_vacc_cov19_2_cmdat" }, + { field = "flw_vacc_cov19_3_cmdat", source_date = "%d/%m/%Y" }, + ] + # VISIT # required fields - "visit_id", "subject_id", "country_iso3", "start_date", "outcome", "date_outcome" diff --git a/isaric/parsers/lmic.toml b/isaric/parsers/lmic.toml index 82e99757..a248b3bb 100644 --- a/isaric/parsers/lmic.toml +++ b/isaric/parsers/lmic.toml @@ -176,6 +176,17 @@ description = "Intensive Care Unit admission" ref = "Y/N/NK" +[subject.vaccinated_covid19] + field = "c19_vacc" + values = { 1 = true, 0 = false } + +[subject.vaccinated_covid19_dates] + combinedType = "list" + excludeWhen = "none" + fields = [{ field = "dose_date" }] + # context = ["Date of the most recent dose"] + + [visit] country_iso3 = "MWI" diff --git a/isaric/parsers/ncov-gambia.toml b/isaric/parsers/ncov-gambia.toml index 8d6dd46d..66138a7f 100644 --- a/isaric/parsers/ncov-gambia.toml +++ b/isaric/parsers/ncov-gambia.toml @@ -292,6 +292,16 @@ ] }, # 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" }] + # context = ["Date of last dose"] + # VISIT # required fields - "visit_id", "subject_id", "country_iso3", "start_date", "outcome", "date_outcome" diff --git a/isaric/parsers/ncov-phosp.toml b/isaric/parsers/ncov-phosp.toml index ce27e536..9f58235f 100644 --- a/isaric/parsers/ncov-phosp.toml +++ b/isaric/parsers/ncov-phosp.toml @@ -257,6 +257,18 @@ field = "crf2a_reason_not_done" values = { Language = false, Declined = false, Died = true, Other = false } +[subject.vaccinated_covid19] + field = "psq_vac_first_yn" + values = { 1 = true, 0 = false } + +[subject.vaccinated_covid19_dates] + combinedType = "set" + excludeWhen = "none" + fields = [ + { field = "psq_vac_first_date" }, + { field = "psq_vac_sec_date" }, + ] + # VISIT # required fields - "visit_id", "subject_id", "country_iso3", "start_date", "outcome", "date_outcome" diff --git a/isaric/parsers/predicovid.toml b/isaric/parsers/predicovid.toml index a63dd8f1..53f04052 100644 --- a/isaric/parsers/predicovid.toml +++ b/isaric/parsers/predicovid.toml @@ -138,6 +138,16 @@ 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 } + + [subject.vaccinated_covid19_dates] + combinedType = "list" + excludeWhen = "none" + fields = [{ field = "covax_dat" }] + # context = ["Date of last dose"] + # VISIT [visit] diff --git a/isaric/parsers/recover-eu.toml b/isaric/parsers/recover-eu.toml index 18b32d12..5726c3ec 100644 --- a/isaric/parsers/recover-eu.toml +++ b/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" diff --git a/isaric/parsers/uganda-vri-v1.toml b/isaric/parsers/uganda-vri-v1.toml index 29349916..2c1bc948 100644 --- a/isaric/parsers/uganda-vri-v1.toml +++ b/isaric/parsers/uganda-vri-v1.toml @@ -155,6 +155,7 @@ field = "outcome_date" if = { outcome = 2 } + # VISIT # required fields - "visit_id", "subject_id", "country_iso3", "start_date", "outcome", "date_outcome" diff --git a/schemas/dev/parser.schema.json b/schemas/dev/parser.schema.json index a543380c..26f2c631 100644 --- a/schemas/dev/parser.schema.json +++ b/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" } } },