1.2 Conversion of source data to the OMOP-CDM
We transformed the source data into the OMOP-CDM Version 5.3.0. The conversion process from source to CDM consisted of three key steps.
Firstly, the source data was profiled for better understanding of its structure and content. Secondly, source data elements were mapped to a specified target location on the CDM schema, through extract, transform and load (ETL) operations. This step was facilitated by the ‘Rabbit-In-a-Hat’ software, an open-source tool by OHDSI which can be used to generate flow diagrams illustrating the movement of data elements from source to target (Figure 1). Lastly, vocabulary mappings were applied to translate the codes and values used in the source data to that of the CDM (e.g. ICD 10 codes were mapped to SNOMED CT).
Only relevant tables containing information on visits, diagnoses, medication exposures and laboratory tests were converted into the OMOP-CDM.