ukbiobank-omop-etl

Resources and documentation for UK Biobank to OMOP CDM v5.3.1 conversion

View the Project on GitHub thehyve/ukbiobank-omop-etl

Table name: observation

Reading from stem_table

Destination Field Source field Logic Comment field
observation_id id    
person_id person_id   Use eid (not included)
observation_concept_id concept_id    
observation_date start_date    
observation_datetime start_datetime    
observation_type_concept_id type_concept_id   In between patient reported and clinical study? = population study Best fit would be from visit types = Health Examination Current options: 45905771 - Observation Recorded from a Survey or 581413 - Observation from Measurement
value_as_number value_as_number    
value_as_string value_as_string    
value_as_concept_id value_as_concept_id    
qualifier_concept_id qualifier_concept_id    
unit_concept_id unit_concept_id    
provider_id provider_id    
visit_occurrence_id visit_occurrence_id   Lookup visit occurrence belonging to this person (eid) and this instance_id.
visit_detail_id      
observation_source_value source_value    
observation_source_concept_id source_concept_id    
unit_source_value unit_source_value    
qualifier_source_value qualifier_source_value