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HL/7 AdministrativeGender missing

vocabularies

(Joseph Nahmias) #1

Hello,

We are in the process of mapping our data into the omop_cdm and I noticed that the HL/7 AdministrativeGender is not present in Athena as a vocabulary for the gender domain. This is used in a number of US regulatory requirements including CCDA, FHIR, and others. Is there a reason it is not included?

Link to the valueset is: https://www.hl7.org/documentcenter/public/standards/vocabulary/vocabulary_tables/infrastructure/vocabulary/AdministrativeGender.html.

Thanks,
–Joe


(Evan Sholle) #2

My guess is that they didn’t think it was necessary to include in the vocab because there are only 3 concepts total, and most people are probably just hard-coding it as part of their ETL. We certainly are. But I can’t imagine it would be that difficult (famous last words) to add it as a non-standard vocab and put CONCEPT_RELATIONSHIP entries mapping F to 8532 and M to 8507. @Dymshyts, @aostropolets, thoughts?

W/r/t the UN code, which doesn’t map to a standard concept in the Gender domain: as per @ericaVoss’s comment, generally the idea is to put sex assigned at birth in gender_concept_id for PERSON (and, as @hripcsa pointed out there too, gender_concept_id should probably be called sex_concept_id, except for all the code we’d have to rewrite). Shouldn’t most of these people have a sex assigned at birth? From what I remember of the literature, even folks with ambiguous genitalia tend to get assigned something at birth - although I welcome being corrected if I’m wrong here. And for anyone who only has an HL7AdministrativeGender of UN, with no documentation of what they were assigned at birth, why not just put 0 as the gender_concept_id? Can’t imagine there would be that many. You could then load something into OBSERVATION along the lines of 4062097.


(Christian Reich) #3

@jnahmias:

As @esholle said.

However, the reason to make a change would come from a use case where such information is necessary and the current representation is insufficient. Both. So, just because there are data available is not a trigger to put it in. We call it “the attic” use case, discussed here.

So, in your case I can’t see you described a use case. But let’s say you have one. It would be able to use the subsequent sexes/gender information in the OBSERVATION table as determined here.

Works?


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