Hi all, I apologize in advance if this is redundant, but I can’t find the answers to my questions.
I am in the process of implementing OMOP from a CERNER database and have lots of doubts about the concepts. I will greatly appreciate if someone can answer the following questions with “Correct” or “Incorrect, do this instead”. My confusion is that seems like I need to convert everything to SNOMED.
Starting with PERSON, the Gender, Race and Ethnicity concepts should be from the domain/vocabulary Gender, Race and Ethnicity respectively, if unknown concept is 0, correct?
For the DEATH table, “death type concept” should be from the domain/vocabulary Type Concept/Death Type and “cause concept” should be a a domain/vocabulary condition/SNOMED, correct?
Similarly for table CARE_SITE “place of service”, OBSERVATION_PERIOD “period type” and VISIT_OCCURRENCE “visit” and “visit type” should be from the domain/vocabulary Place of service/Place of Service, Type Concept/Obs Period Type, Visit/Visit and Type Concept/Visit Type, correct?
For CONDITION_OCCURRENCE and PROCEDURE_OCURRENCE the “concept_id” should be SNOMED from the Condition/SNOMED, the “type concept” should be from the Type Concept/Condition (or Procedure) Type and the source concepts are the ones in which my original data is, which in this case will me mostly ICD9 and 10 and CPT, correct?
Finally… if my data is in ICD or CPT, I need to map it to SNOMED first, should I use the CONCEPT_RELATIONSHIP table to do this with a relationship field to “Maps to” and the concept be Condition/SNOMED ?
Thanks in advance.