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

Observation

Reading from Synthea tables allergies.csv

| Destination Field | Source field | Logic | Comment field | | --- | --- | --- | --- | | observation_id | | Autogenerated | | | person_id | patient | Map by mapping person.person_source_value to patient. Find person.person_id by mapping allergies.patient to person.person_source_value. | | | observation_concept_id | code | Use code to lookup target_concept_id in CTE_TARGET_VOCAB_MAP: select ctvm.target_concept_id from allergies a join cte_target_vocab_map ctvm on ctvm.source_code = a.code and ctvm.target_domain_id = 'Observation' and ctvm.target_vocabulary_id = 'SNOMED' and ctvm.target_standard_concept = 'S' and ctvm.target_invalid_reason is NULL | | | observation_date | start | | | | observation_datetime | start | Use 00:00:00 as time. | | | observation_type_concept_id | | Set as 38000280 (Observation recorded from EHR) for all records. | | | value_as_number | | cast(null as float) | | | value_as_string | | cast(null as varchar) | | | value_as_concept_id | | Set as 0 for all records | | | qualifier_concept_id | | Set as 0 for all records | | | unit_concept_id | | Set as 0 for all records | | | 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 add 1000000. | | | observation_source_value | code | | | | observation_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 allergies a on csvm.source_code = a.code and csvm.source_vocabulary_id = 'SNOMED' | | | unit_source_value | | cast(null as varchar) | | | qualifier_source_value | | cast(null as varchar) | | | value_source_value | | cast(null as varchar) | | | observation_event_id | |cast(null as bigint) | | | obs_event_field_concept_id | | cast(null as int) | |

Reading from Synthea table conditions.csv

| Destination Field | Source field | Logic | Comment field | | --- | --- | --- | --- | | observation_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. | | | observation_concept_id | code | Use 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 = 'Observation' and ctvm.target_vocabulary_id = 'SNOMED' | | | observation_date | start | | | | observation_datetime | start | | | | observation_type_concept_id | | Set as 38000280 (Observation recorded from EHR) for all records. | | | value_as_number | | cast(null as float) | | | value_as_string | | cast(null as varchar) | | | value_as_concept_id | | Set as 0 for all records | | | qualifier_concept_id | | Set as 0 for all records | | | unit_concept_id | | Set as 0 for all records | | | 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 add 1000000. | | | observation_source_value | code | | | | observation_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 conditions c on csvm.source_code = c.code and csvm.source_vocabulary_id = 'SNOMED' | | | unit_source_value | | cast(null as varchar) | | | qualifier_source_value | | cast(null as varchar) | | | value_source_value | | cast(null as varchar) | | | observation_event_id | |cast(null as bigint) | | | obs_event_field_concept_id | | cast(null as int) | |

Reading from Synthea table observations.csv

| Destination Field | Source field | Logic | Comment field | | --- | --- | --- | --- | | observation_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. | | | observation_concept_id | code | Use code to lookup target_concept_id in CTE_TARGET_VOCAB_MAP: select ctvm.target_concept_id from observations o join cte_target_vocab_map ctvm on ctvm.source_code = o.code and ctvm.target_domain_id = 'Observation' and ctvm.target_vocabulary_id = 'LOINC' and ctvm.standard_concept_id = 'S' and ctvm.target_invalid_reason is null | | | observation_date | date | | | | observation_datetime | date | | | | observation_type_concept_id | | Set as 32827 (EHR encounter record) for all records. | | | value_as_number | | cast(null as float) | | | value_as_string | | cast(null as varchar) | | | value_as_concept_id | | Set as 0 for all records | | | qualifier_concept_id | | Set as 0 for all records | | | unit_concept_id | | Set as 0 for all records | | | 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 add 1000000. | | | observation_source_value | code | | | | observation_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 observatitons o on csvm.source_code = o.code and csvm.source_vocabulary_id = 'LOINC' and csvm.source_domain_id = 'Observation' | | | unit_source_value | | cast(null as varchar) | | | qualifier_source_value | | cast(null as varchar) | | | value_source_value | | cast(null as varchar) | | | observation_event_id | |cast(null as bigint) | | | obs_event_field_concept_id | | cast(null as int) | |

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