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

Death

Reading from Synthea table encounters.csv

• Filter the encounter table where code=308646001 (Death certification)

| Destination Field | Source field | Logic | Comment field | | --- | --- | --- | --- | | person_id | patient | Map by mapping person.person_source_value to patient. Find person.person_id by mapping encounters.patient to person.person_source_value. | | | | | death_date| start| | | | death_datetime | start | | | | death_type_concept_id | | Set to 32817 (EHR) for all records | | | cause_concept_id | reasoncode | Use the following SQL code to lookup target_concept_id in CTE_SOURCE_VOCAB_MAP: select csvm.target_concept_id from encounters e join cte_source_vocab_map csvm on csvm.source_code = e.reasoncode and csvm.target_domain_id = 'Condition' and csvm.source_domain_id = 'Condition' and csvm.target_vocabulary_id = 'SNOMED' and csvm.source_vocabulary_id = 'SNOMED' and csvm.target_invalid_reason is NULL and csvm.target_standard_concept = 'S' | | | cause_source_value | reasoncode | | | | cause_source_concept_id | reasoncode | Use the following SQL code to lookup source_concept_id in CTE_SOURCE_VOCAB_MAP: select csvm.source_concept_id from encounters e join cte_source_vocab_map csvm on csvm.source_code = e.reasoncode and csvm.target_domain_id = 'Condition' and csvm.source_domain_id = 'Condition' and csvm.target_vocabulary_id = 'SNOMED' and csvm.source_vocabulary_id = 'SNOMED' and csvm.target_invalid_reason is NULL and csvm.target_standard_concept = 'S' | |

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