I am new to OMOP and have been working to map the source data to OMOP data model.
I have few questions on source data mapping.
- If the source data can be mapped to standard concepts look for mapping in concept relationship table if not then the steps that need to be followed is make an entry in concept table( >2000000000) and an entry as “maps to” standard concept in concept relationship table. the conceptid_1 field from concept relationship table goes to source concept id field and conceptid_2 into concept if field of clinical table. Is this understanding correct?
- If the source data cannot be mapped to standard vocabulary then do we make a new entry in the concept table or what goes in concept id field and source concept id field of the clinical table is my question.very confused on this
- Source data has multiple ethnicity values whereas OMOP has only hispanic and non-hispanic as standard concepts. for the other ethnicity values in source data like costa rican is there any mapping that is already done for such ethnicity to the hispanic and non hispanic. what is the general approach taken for such data?