kanta to visit_occurrence
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flowchart LR
subgraph Source
finngenid
approx_event_datetime
coding_system_oid
end
subgraph CDM-OMOP-v5.4
person_id
visit_start_datetime
provider_id
end
finngenid-->person_id
approx_event_datetime-->visit_start_datetime
coding_system_oid-->provider_id
Destination Field | Source field | Logic | Comment field |
---|---|---|---|
visit_occurrence_id | Incremental integer. Unique value per finngenid + 117000000000 (offset). | Generated | |
person_id | finngenid | person_id from person table where person_source_value equals finngenid | Calculated |
visit_concept_id | concept_id_2 from concept_relationship table where concept_id_1 equals visit_source_concept_id and relationship_id equals “Maps to”. | Calculated NOTE: 0 when visit_source_concept_id is NULL | |
visit_start_date | approx_visit_date is calculated by extracting the date from visit_start_datetime . | Calculated | |
visit_start_datetime | approx_event_datetime | Copied from approx_event_datetime | Copied |
visit_end_date | copied from visit_start_date | Copied | |
visit_end_datetime | copied from visit_start_datetime | Copied | |
visit_type_concept_id | Set 32879 - ‘Registry’ for all | Calculated | |
provider_id | coding_system_oid | provider_id from provider table where coding_system_oid equals speciality_source_value . | |
care_site_id | Set 0 for all | Info not available | |
visit_source_value | String build as “SOURCE=KANTA;INDEX=” | Calculated | |
visit_source_concept_id | omop_concept_id from fg_codes_info where source equals “KANTA” | Calculated using the fg_codes_info table. | |
admitted_from_concept_id | Set 0 for all | Info not available | |
admitted_from_source_value | Set NULL for all | Info not available | |
discharged_to_concept_id | Set 0 for all | Info not available | |
discharged_to_source_value | Set NULL for all | Info not available | |
preceding_visit_occurrence_id | Set 0 for all | Info not available |