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GenomicsStandardsConsortium / mixs

Minimum Information about any (X) Sequence” (MIxS) specification
https://w3id.org/mixs
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Difference in host_sex picklists #497

Closed anjijohnston closed 7 months ago

anjijohnston commented 2 years ago

We noticed differences in the picklists for host_sex in these env_packages:

[] For these packages: Host_associated package Human_associated package Human-gut package Human-oral Human-skin Human-vaginal

Host_sex [female|hermaphrodite|non-binary|male|transgender|transgender (female to male)|transgender (male to female)|undeclared]

[] For this package Symbiont_associated package

Host_sex [female|hermaphrodite|male|neuter]

We will need the picklists to be the same - can you let me know if host_sex in the symbiont package should include the longer picklist?

lschriml commented 2 years ago

Hello Anji, yes, it should include the longer pick list.

Cheers, Lynn

ramonawalls commented 7 months ago

The long list has been added as a string serialization, which resolves this issue.

Discussions from today's CIG call:

It would be better to have the list as an enum, which could then be validated.

To ensure compatibility with all formats, the parenthesis (round brackets) should be removed. Will removing them cause problems in dbs?

There is a bigger issue that this term is confounding sex and gender. We should look to use an ontology for these values, such as https://www.ebi.ac.uk/ols4/ontologies/gsso. There have been some discussions with the urobiome groups about this issue.

I will close this issue, since it is fixed, look for other issues about sex and gender, and open a new one if needed.