diff --git a/carrot/data/config/omop.json b/carrot/data/config/omop.json index 6ae8aa4..b9f17d7 100644 --- a/carrot/data/config/omop.json +++ b/carrot/data/config/omop.json @@ -1,6 +1,7 @@ { + "omop_version": "5.3.1", "all_columns": { - "condition_occurrence": ["condition_occurrence_id", "person_id", + "condition_occurrence": ["condition_occurrence_id", "person_id", "condition_concept_id", "condition_start_date", "condition_start_datetime", "condition_end_date", "condition_end_datetime", "condition_type_concept_id", @@ -18,31 +19,31 @@ "drug_source_value", "drug_source_concept_id", "route_source_value", "dose_unit_source_value"], "measurement": ["measurement_id", "person_id", "measurement_concept_id", - "measurement_date", "measurement_datetime", "measurement_type_concept_id", + "measurement_date", "measurement_datetime", "measurement_type_concept_id", "operator_concept_id", "value_as_number", "value_as_concept_id", - "unit_concept_id", "range_low", "range_high", "provider_id", + "unit_concept_id", "range_low", "range_high", "provider_id", "visit_occurrence_id", "measurement_source_value", "measurement_source_concept_id", - "unit_source_value", "value_source_value"], + "unit_source_value", "value_source_value"], "observation": ["observation_id", "person_id", "observation_concept_id", "observation_date", "observation_datetime", "observation_type_concept_id", "value_as_number", "value_as_string", "value_as_concept_id", "qualifier_concept_id", - "unit_concept_id provider_id", "visit_occurrence_id", "observation_source_value", - "observation_source_concept_id", "unit_source_value", "qualifier_source_value"], + "unit_concept_id provider_id", "visit_occurrence_id", "observation_source_value", + "observation_source_concept_id", "unit_source_value", "qualifier_source_value"], "person": ["person_id", "gender_concept_id", "year_of_birth", "month_of_birth", - "day_of_birth", "birth_datetime", "race_concept_id", "ethnicity_concept_id", - "location_id", "provider_id", "care_site_id", "person_source_value", - "gender_source_value", "gender_source_concept_id", - "race_source_value", "race_source_concept_id", - "ethnicity_source_value", "ethnicity_source_concept_id"], + "day_of_birth", "birth_datetime", "race_concept_id", "ethnicity_concept_id", + "location_id", "provider_id", "care_site_id", "person_source_value", + "gender_source_value", "gender_source_concept_id", + "race_source_value", "race_source_concept_id", + "ethnicity_source_value", "ethnicity_source_concept_id"], "procedure_occurrence": ["procedure_occurrence_id", "person_id", "procedure_concept_id", - "procedure_date", "procedure_datetime", - "procedure_type_concept_id", "modifier_concept_id", - "quantity", "provider_id", "visit_occurrence_id", - "procedure_source_value", "procedure_source_concept_id", "qualifier_source_value"], + "procedure_date", "procedure_datetime", + "procedure_type_concept_id", "modifier_concept_id", + "quantity", "provider_id", "visit_occurrence_id", + "procedure_source_value", "procedure_source_concept_id", "qualifier_source_value"], "specimen": ["specimen_id", "person_id", "specimen_concept_id", "specimen_type_concept_id", - "specimen_date", "specimen_datetime", "quantity", "unit_concept_id", - "anatomic_site_concept_id", "disease_status_concept_id", "specimen_source_id", "specimen_source_value", - "unit_source_value", "anatomic_site_source_value", "disease_status_source_value"], + "specimen_date", "specimen_datetime", "quantity", "unit_concept_id", + "anatomic_site_concept_id", "disease_status_concept_id", "specimen_source_id", "specimen_source_value", + "unit_source_value", "anatomic_site_source_value", "disease_status_source_value"], "visit_occurrence": ["visit_occurrence_id", "person_id", "visit_concept_id", "visit_start_date", "visit_start_datetime", "visit_end_date", "visit_end_datetime", "visit_type_concept_id", "provider_id", "care_site_id", "visit_source_value", "visit_source_concept_id", "admitting_source_concept_id", "admitting_source_value", @@ -61,7 +62,7 @@ "date_field_components": { "person": {"birth_datetime": {"year":"year_of_birth", "month":"month_of_birth", "day":"day_of_birth"}} }, - "datetime_fields": { + "datetime_fields": { "condition_occurrence": ["condition_start_datetime", "condition_end_datetime"], "death": ["death_datetime"], "drug_exposure": ["drug_exposure_start_datetime", "drug_exposure_end_datetime"], @@ -71,8 +72,8 @@ "procedure_occurrence": ["procedure_datetime"], "specimen": ["specimen_datetime"], "visit_occurrence": ["visit_start_datetime", "visit_end_datetime"] - }, - "person_id_field": { + }, + "person_id_field": { "condition_occurrence": "person_id", "death": "person_id", "drug_exposure": "person_id", @@ -82,8 +83,8 @@ "procedure_occurrence": "person_id", "specimen": "person_id", "visit_occurrence": "person_id" - }, - "auto_number_field": { + }, + "auto_number_field": { "condition_occurrence": "condition_occurrence_id", "death": "death_id", "drug_exposure": "drug_exposure_id", @@ -92,5 +93,18 @@ "procedure_occurrence": "procedure_occurrence_id", "specimen": "specimen_id", "visit_occurrence": "visit_occurrence_id" - } -} + }, + "required_integer_columns": { + "description": "Required integer columns (NOT NULL)", + "condition_occurrence": ["condition_occurrence_id", "person_id", + "condition_concept_id", "condition_type_concept_id"], + "death": ["person_id"], + "drug_exposure": ["drug_exposure_id", "person_id", "drug_concept_id", "drug_type_concept_id"], + "measurement": ["measurement_id", "person_id", "measurement_concept_id", "measurement_type_concept_id"], + "observation": ["observation_id", "person_id", "observation_concept_id", "observation_type_concept_id"], + "person": ["person_id", "gender_concept_id", "race_concept_id", "ethnicity_concept_id"], + "procedure_occurrence": ["procedure_occurrence_id", "person_id", "procedure_concept_id", "procedure_type_concept_id"], + "specimen": ["specimen_id", "person_id", "specimen_concept_id", "specimen_type_concept_id"], + "visit_occurrence": ["visit_occurrence_id", "person_id", "visit_concept_id", "visit_type_concept_id"] + } + }