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Merge pull request #170 from HDRUK/default_concept_ids
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DDL load / omop config chages
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@PhilAppleby
PhilAppleby authored Mar 25, 2024
2 parents 763ad85 + 016c28f commit ae9c036
Showing 1 changed file with 39 additions and 25 deletions.
64 changes: 39 additions & 25 deletions carrot/data/config/omop.json
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Original file line number Diff line number Diff line change
@@ -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",
Expand All @@ -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",
Expand All @@ -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"],
Expand All @@ -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",
Expand All @@ -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",
Expand All @@ -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"]
}
}

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