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Added gender_identity field and ontology. Fixes #1409. #1475

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merged 12 commits into from
Dec 11, 2024

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Release notes

For type/biomaterial/donor_organism.json schema:

  • Added ontologised gender_identity field

For module/gender_identity_ontology.json schema:

  • Created ontology module for terms under Gender

Reviews requested

  • This is a major update for all dependencies of the new module (donor_organism)

Rationale

This change was requested to support the metadata for the "Testis cell atlas" dataset, in which there are 2 testis samples from female-gendered individuals. It will also help wranglers in the future to be more inclusive for non-cis individuals.

@ESapenaVentura ESapenaVentura added the content Any PR that incorporates changes to the schema label Jul 6, 2022
@ESapenaVentura ESapenaVentura self-assigned this Jul 6, 2022
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Please ignore the "schema linting" failed action, it is complaining that the ontology branch has not been yet imported to the HCAO.

The HCAO works by releases and this will be imported in our next release (~18th) HumanCellAtlas/ontology#113

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@ncalvanese1 ncalvanese1 left a comment

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Looks good to me!

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@amnonkhen amnonkhen left a comment

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a few comments

docs/jsonBrowser/type.md Outdated Show resolved Hide resolved
json_schema/versions.json Outdated Show resolved Hide resolved
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@ruchim ruchim left a comment

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looks good to me!

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arschat commented Nov 27, 2024

This was previously blocked by an ontology update that is now completed.
Furthermore, Genetic Diversity network has requested the genderidentity_selfreported field, using the NCIT:C17357 ontology branch.

This PR is updated with the GD network preferred ontology and merged current staging branch into this, so we are re-requesting reviews.

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LGTM

@arschat arschat requested a review from ncalvanese1 November 27, 2024 14:17
@arschat arschat assigned arschat and unassigned ESapenaVentura Nov 27, 2024
@arschat arschat merged commit 7d8aeed into staging Dec 11, 2024
2 of 5 checks passed
@arschat arschat deleted the esv-gender-identity-Issue1409 branch December 11, 2024 09:32
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7 participants