What value should be used to populate gender_concept_id?

[clairblacketer]

What value should be used to populate gender_concept_id?

CDM or THEMIS convention?

THEMIS

Is this a general convention?

No

Summary of issues

• The term "gender_concept_id" is outdated and really should be "sex_concept_id". Since changing gender_concept_id is a huge lift for developers and package maintainers, this change will be implemented at the next major release. In the meantime, what value should be used to populate gender_concept_id?

Summary of answer

• Gender_concept_id should hold the standard concept representing the patient's assigned sex at birth

Related links

• https://forums.ohdsi.org/t/can-we-migrate-from-gender-to-sex-please/18875/22
• https://forums.ohdsi.org/t/can-we-migrate-from-gender-to-sex-please/18875

Other comments/notes

• This is challenging because of different cultural understanding of sex at birth, legal sex, genetic sex, and gender identity. Most sources will just have one value for a patient's sex so that can be used as the gender_concept_id with the understanding that it may not be assigned sex at birth.

[askanter]

So the title is even misleading since this really is about how to store the biological sex :)

[clairblacketer]

So the title is even misleading since this really is about how to store the biological sex :)

Yeah that is a good point, I will update the title. I am going back and forth on the gender fields because they are meant to capture sex but really most of the time we get a sex value for a person and we don't know if it is biological sex or gender identity

[clairblacketer]

@askanter I am going to open a second one specifically about gender identity

[MelaniePhilofsky]

Issue # and location

Forum

Format as follows:

• Forum
• Forum

Issue summary

he term "gender_concept_id" is outdated and really should be "sex_concept_id". Since changing gender_concept_id is a huge lift for developers and package maintainers, this change will be implemented at the next major release. In the meantime, what value should be used to populate gender_concept_id?

Convention type

Table

CDM table

Person

CDM field

gender_concept_id

Links to issue discussion

Links to location of discussion on forums, CDM GitHub, Themis GitHub, etc.

Format as follows:

• OHDSI Forums discussion
• OHDSI Forums discussion

Provenance of data

All data

The ratified convention

PERSON.Gender_concept_id should hold the standard concept representing the patient's assigned sex at birth

Date of ratification/published

NA

Downstream implications

No

Link to DQD check

isRequired cdmDatatype isForeignKey fkDomain isStandardValidConcept standardRecordConceptCompleteness

Related conventions/further information

If the source data captures gender identity it should be stored in the OBSERVATION table.

#Tags Sex, gender, gender identity

[clairblacketer]

opened PR #114