OHDSI Home | Forums | Wiki | Github

Standard values for gender

Vocabulary Users
#21

And I see that since the above concept in our source system is legal sex, this is the entirely wrong set of concepts to use. We need to map these natively to HL7 v3 AdministrativeGender values or HL7 FHIR v4.0.1 administrative-gender values.

So now back to the original (common sense) mapping. So much for trying to get fancy! :slight_smile: :crazy_face:

#22

Colorado has Epic Caboodle data. It’s more or less the same as Clarity’s patient sex data.

Yes, do this. And map Male/M to gender_concept_id 8507 and Female/F to gender_concept_id = 8532.

For the above fields, you could map Gender Identity to the Observation table IF you have a use case for these data. I would be very conscious about trying to map ALL Epic data to the CDM, you’ll still be mapping years from now. Take the Pragmatic CDM approach and map the most commonly used data for Observational research and then map as use cases arise.

#23

Thanks @MPhilofsky,

Regarding concept mapping for OMOP, we’re hoping that as long as we have our content mapped to industry standard codes, we will be able to run a standard query using a view of industry standard code to omop standard concept_id (created from omop vocabulary tables).

For example, if we have a data structure containing local codes and industry standard codes as follows

Fig 1:

image
image787×268 7.41 KB

We would like to just run a query to automatically retreive the OMOP standard concept using a query like this (using the appropriate value for LOCAL_CODESET in the where clause) :

Fig 2a.

image
image970×365 152 KB

In the above query

  • LOCAL_CODE_MAP contains local code to industry standard code mappings (Fig 1 above)
  • SRC_TO_CONCEPT_MAP is a view of omop mappings from any industry standard code to the standard industry standard code (or OMOP generated code) and OMOP concept_id
  • SRC_CONCEPT_ID is the concept_id for the industry standard code in the local system
  • DEST_CONCEPT_ID is the concept_id for the OMOP standard concept associated with the industry standard code

For most of our data, this works perfectly.

However, since no industry standard code for (birth) sex in any industry standard terminology is defined as belonging to the ‘Gender’ domain (or mapped in the CONCEPT_RELATIONSHIP table to the omop standard concepts for gender) we are forced to manually map this concept.

Bottom line, it would be nice to leverage industry standard vocabulaires and concepts to automate the mapping from local codes to omop codes (via mapping of local codes to industry standard codes in our system).

Is this possible?
Piper

t