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

Procedure_occurrence

Reading from Synthea table procedures.csv

| Destination Field | Source field | Logic | Comment field | | --- | --- | --- | --- | | procedure_occurrence_id | | | | | 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. | | | procedure_concept_id | code | Use code to lookup target_concept_id in CTE_TARGET_VOCAB_MAP: select ctvm.target_concept_id from procedures pr join cte_target_vocab_map ctvm on ctvm.source_code = pr.code and ctvm.target_domain_id = 'Procedure' and ctvm.target_vocabulary_id = 'SNOMED' and ctvm.target_invalid_reason is NULL and ctvm.target_standard_concept = 'S' | | | procedure_date | date, start(v3.0.0) | | | | procedure_datetime | date, start(v3.0.0) | Use 00:00:00 as the time. | | | procedure_end_date | stop(v3.0.0) | | | | procedure_end_datetime | stop(v3.0.0) | Use 00:00:00 as the time. | | | procedure_type_concept_id | | | Use concept_id 32827 (EHR encounter record) for all records. | | modifier_concept_id | | Set to 0 for all records | | | quantity | |cast(null as integer) | | | provider_id | encounters.provider | | | | 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 all 1000000. | | | procedure_source_value | code | | | | procedure_source_concept_id | code | Use code to lookup source_concept_id in CTE_SOURCE_VOCAB_MAP: select csvm.source_concept_id from cte_source_vocab_map csvm join procedures pr on csvm.source_code = pr.code and csvm.source_vocabulary_id = 'SNOMED' | | | modifier_source_value | | Set to null for all records | |

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