Gender/Sex NAACCR

Vocabulary Users
1

We are using the SEER/NAACCR codes for Sex/Gender.
http://datadictionary.naaccr.org/default.aspx?c=10#sources

So my initial thought was to map Gender in SNOMED (ID 4135376) then have this point to a custom table with our own codes since none of the standard vocabularies have the terms NAACCR uses for sex such as “Transsexual, natal male”

Does this make sense or is my logic all wrong?

2

OPOP provides a table for you to use: SOURCE_TO_CONCEPT_MAP

You can use USAGI http://www.ohdsi.org/web/wiki/doku.php?id=documentation:software:usagi to map the NAACCR codes to the SNOMED standard codes and put this information in the SOURCE_TO_CONCEPT_MAP table.

Added:
You don’t actually have to use USAGI. You could enter the data directly in Source_to_concept_map. But it would be good practice for mapping other codes which do not exist in the vocabularies.

3

So map Transsexual, natal male (NAACCR) to Male-to-female transsexual (SNOMED) for example?

I’ve already used USAGI to do a lot of my mapping

4

Currently, we only capture 2 genders in the PERSON table, by convention. Multiple genders or sexes, or atypical ones are all in the OBSERVATION table.

5

Got it. I still have a lot to learn here for sure. So does OMOP in general not use the term “sex”? Gender and Sex are different terms in today’s world I believe. I see not mention of Sex int he Observation description.