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phenopackets / phenopacket-schema

Repository for the GA4GH phenopacket schema
https://phenopacket-schema.readthedocs.io/
BSD 3-Clause "New" or "Revised" License
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sex and gender #232

Closed heikkil closed 3 years ago

heikkil commented 4 years ago

This is another (#231) complex issue that still needs to be tackled.

The discussion last night emphasized that the phenopackets sex is the biological feature that can be determined by text. It was suggested that it should be stated more strongly, perhaps in the name. Gender is a more fluid entity that has to be asked from the person. Sounds like a great target for an ontology. Does such an ontology exist?

julesjacobsen commented 4 years ago

We've mapped to the Ontology terms in NCIT for this - see https://phenopackets-schema.readthedocs.io/en/latest/sex.html

Gender is another matter and there are a great deal of people cogitating on this within the FHIR gender harmony group

mbaudis commented 4 years ago

I am not getting why the mapping is needed & not an ontologyTerm with recommended values (as are shown in the documentation) is being used?

cmungall commented 3 years ago

Hi @heikkil long time no see!

Just as hANCESTRO can be used in #231 can we use GSSPO as the vocabulary here? This is just about to be added to OBO

heikkil commented 3 years ago

Hi Chris! Yep, I am back in the infrastructure stuff.

You must mean Gender, Sex, and Sexual Orientation (GSSO) ontology?

Clair A. Kronk and Judith W. Dexheime: Development of the Gender, Sex, and Sexual Orientation ontology: Evaluation and workflow. Journal of the American Medical Informatics Association, 27(7), 2020, 1110–1115 doi: 10.1093/jamia/ocaa061

It has everything needed.

 -Heikki

Heikki Lehväslaiho - skype:heikki_lehvaslaiho cell: +358 40 850 6640 http://about.me/heikki

On Wed, 4 Nov 2020 at 00:19, Chris Mungall notifications@github.com wrote:

Hi @heikkil https://github.com/heikkil long time no see!

Just as hANCESTRO can be used in #231 https://github.com/phenopackets/phenopacket-schema/issues/231 can we use GSSPO as the vocabulary here? This is just about to be added to OBO

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/phenopackets/phenopacket-schema/issues/232#issuecomment-721403611, or unsubscribe https://github.com/notifications/unsubscribe-auth/AAASPGWTMDUNPH3V74AZXTDSOB6VJANCNFSM4O5Q6TOQ .

heikkil commented 3 years ago

I've been thinking about this recently.

There are three ways of looking into sex in an informative way. Phenopackets has two. It is either one too many or one missing:

  1. chromosomes (and genes) : Phenopacket:KaryotypicSex
  2. secondary, external sexual marks : Phenopacket:Sex

  3. hormonal effects, self-identification : Phenopacket:Gender (?)

    -Heikki

Heikki Lehväslaiho - skype:heikki_lehvaslaiho cell: +358 40 850 6640 http://about.me/heikki

On Wed, 4 Nov 2020 at 07:42, Heikki Lehvaslaiho < heikki.lehvaslaiho@gmail.com> wrote:

Hi Chris! Yep, I am back in the infrastructure stuff.

You must mean Gender, Sex, and Sexual Orientation (GSSO) ontology?

Clair A. Kronk and Judith W. Dexheime: Development of the Gender, Sex, and Sexual Orientation ontology: Evaluation and workflow. Journal of the American Medical Informatics Association, 27(7), 2020, 1110–1115 doi: 10.1093/jamia/ocaa061

It has everything needed.

 -Heikki

Heikki Lehväslaiho - skype:heikki_lehvaslaiho cell: +358 40 850 6640 http://about.me/heikki

On Wed, 4 Nov 2020 at 00:19, Chris Mungall notifications@github.com wrote:

Hi @heikkil https://github.com/heikkil long time no see!

Just as hANCESTRO can be used in #231 https://github.com/phenopackets/phenopacket-schema/issues/231 can we use GSSPO as the vocabulary here? This is just about to be added to OBO

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/phenopackets/phenopacket-schema/issues/232#issuecomment-721403611, or unsubscribe https://github.com/notifications/unsubscribe-auth/AAASPGWTMDUNPH3V74AZXTDSOB6VJANCNFSM4O5Q6TOQ .

pnrobinson commented 3 years ago

Thanks! I think that we do need to add an element for gender that would be an ontology term. The GSSA could be one option for this. It would also be good to examine how FHIR and other clinical terminologies deal with this.

cmungall commented 3 years ago

You must mean Gender, Sex, and Sexual Orientation (GSSO) ontology?

Yes, that's the one!

http://obofoundry.org/ontology/gsso

pnrobinson commented 3 years ago

It seems NCIT has a collection of terms for gender (https://www.ebi.ac.uk/ols/ontologies/ncit/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FNCIT_C17357)

Would

OntologyTerm gender

be approppriate?

mbaudis commented 3 years ago

@pnrobinson For gender it is o.k. IMO.

heikkil commented 3 years ago

Looks great.

 -Heikki

Heikki Lehväslaiho - skype:heikki_lehvaslaiho cell: +358 40 850 6640 http://about.me/heikki

On Wed, 16 Dec 2020 at 18:11, Michael Baudis notifications@github.com wrote:

@pnrobinson https://github.com/pnrobinson For gender it is o.k. IMO.

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