I'm just starting to implementing OMOP and am starting with the person table. I'd like to verify that I am doing things correctly before I get too far.
First of all, am I correct that USAGI is the correct tool for mapping custom codes like race, gender, and ethnicity? Is this what people are doing generally, or do most just map these in their ETL?
Secondly, if for say "Asian or Pacific Islander" (in race) can I map to two different concepts in the Target Concepts, or should I map to only one? (see below)
At present, I limiting it to one. (In this case Other Pacific Islander).
Third, I am assuming that things like "Other" and "Multiracial", which don't have a matching concept should be left unmapped.
Fourth, I assume that because they are unmapped, I also should leave them unapproved, so they won't be included in the Export source_to_concept_map output.
Fifth, I discovered that before I could append the data to "source_to concept_map", I had to create a related field in "vocabulary", which I did, but I could not figure out what, if any, value should go into vocabulary_concept_id. Is this needed? I just entered 0 (zero).
Sixth, I was then able to append the exported files from USAGI into the vocabulary_concept_id. However, to use that table, I had to JOIN it in the SQL statement as follows:
PATIENT_RACE AS z_race
z_race.PATIENT_RACE_C = p_race.PATIENT_RACE_C
LEFT OUTER JOIN
OMOP.source_to_concept_map AS source_to_concept_map_race
source_to_concept_map_race.source_code = z_race.PATIENT_RACE_C
AND source_to_concept_map_race.source_vocabulary_id = 'SH_race'
The final "AND" above being necessary to match correctly to race.
Am I doing this correctly? Or am I missing something obvious?