In OHDSI/ETL-Synthea: A Builder for Converting the Synthea Data to the OMOP CDM

Condition_occurrence

Reading from Synthea table conditions.csv

| Destination Field | Source field | Logic | Comment field | | --- | --- | --- | --- | | condition_occurrence_id | | Autogenerated | | | person_id | patient | Map by mapping person.person_source_value to patient. Find person.person_id by mapping encouters.patient to person.person_source_value. | | | condition_concept_id | code | Use the following SQL code to lookup target_concept_id in CTE_TARGET_VOCAB_MAP: select ctvm.target_concept_id from conditions c join cte_target_vocab_map ctvm on ctvm.source_code = c.code and ctvm.target_domain_id = 'Condition' and ctvm.target_vocabulary_id = 'SNOMED' and ctvm.target_invalid_reason is NULL and ctvm.target_standard_concept = 'S' | | | condition_start_date | start | | | | condition_start_datetime | start | | | | condition_end_date | stop | | | | condition_end_datetime | stop | | | | condition_type_concept_id | | Set to 32827 (EHR Encounter Record) for all records | | | stop_reason | | cast(null as varchar) | | | provider_id | | cast(null as integer) | | | visit_occurrence_id | encounter | Lookup visit_occurrence_id using encounter, joining to temp table defined in final_visit_ids.sql. | | | visit_detail_id | encounter | Lookup visit_occurrence_id using encounter, joining to temp table defined in final_visit_ids.sql and add 1000000 | | | condition_source_value | code | | | | condition_source_concept_id | code | Use the following SQL code to lookup the source_concept_id in CTE_SOURCE_VOCAB_MAP: select csvm.source_concept_id from cte_source_vocab_map csvm join conditions c on csvm.source_code = c.code and csvm.source_vocabulary_id = 'SNOMED' | | | condition_status_source_value | | Set to null for all records | | | condition_status_concept_id | | Set to 0 for all records | |

OHDSI/ETL-Synthea documentation built on Feb. 24, 2025, 3:48 a.m.