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: stem_table

Reading from Blood pressure

Destination Field Source field Logic Comment field
domain_id      
person_id     eid
visit_occurrence_id 93-3.1 Lookup by eid and instance_id lookup
provider_id      
id     Auto-increment
concept_id 93-3.1 Lookup  
source_value 93-3.1 variable name  
source_concept_id 93-3.1 TBD  
type_concept_id     45905771 (Observation recorded from a Survey, Observation Type, Type Concept)
start_date 93-3.1 Lookup field  
start_datetime 93-3.1 Lookup field  
end_date      
end_datetime      
verbatim_end_date      
days_supply      
dose_unit_source_value      
lot_number      
modifier_concept_id      
modifier_source_value      
operator_concept_id      
modifier_source_value      
quantity      
range_high      
range_low      
refills      
route_concept_id      
route_source_value      
sig      
stop_reason      
unique_device_id      
unit_concept_id 93-3.1 Lookup if numeric mapping approach  
unit_source_value 93-3.1 Lookup if numeric mapping approach  
value_as_concept_id 93-3.1 Lookup if discrete post-coordinated mapping approach  
value_as_number 93-3.1 If numeric mapping approach  
value_as_string      
value_source_value      
anatomic_site_concept_id      
disease_status_concept_id      
specimen_source_id      
anatomic_site_source_value      
disease_status_source_value      
condition_status_concept_id      
condition_status_source_value      
qualifier_concept_id      
qualifier_source_value