Schema update priority ticket - gender/Visium 2022-07-05

[Wkt8]

What are the next schema updates?
Schema Update 1: Gender field
PR here
Schema Update 2: Visium permeabilisation time field
PR here

What schemas will they affect?
These changes will affect the following schemas:

• type/biomaterial/donor_organism.json
• module/ontology/gender_identity.json
• type/protocol/imaging/imaging_preparation_protocol.json

Why are these changes needed?
We currently lack the metadata field to store gender. There are datasets with trans donors (TestisCellAtlas) where gathering and storing this metadata is vital. The dataset is blocked by this. This schema change adds an optional ontologised gender field to donor_organism.

Data contributors want to be able to store the permeabilisation time field in our metadata schema as it is a key field that they want to search and filter through.

Type of change and time frame
Update number 1 constitutes a minor change.
Update number 2 constitutes a minor change.

We are expecting to push both updates before 20/07/2022 (Wednesday, 20th July)

[ESapenaVentura]

Enrique to check the PRs for the comments

[Wkt8]

Gender field PR is waiting on the ontology release
Visium permeabilisation time PR is waiting on Hannes to reply to Ida's comments

[MightyAx]

@ESapenaVentura to check if review has gone through today.

[ESapenaVentura]

Gender_identity is ready, waiting on ontology ticket
Visium permeabilisation field will be merged by EOD wednesday

[ESapenaVentura]

EOD friday as hannes is on holidays

[gabsie]

The Visium update will be merged, as approved by Hannes.

[ESapenaVentura]

This will be included in the next ontology release

[ESapenaVentura]

Ontology release to staging has been done - I am pushing the PR to staging

[idazucchi]

enrique is investigating the linter faliure in the schema repo

[ESapenaVentura]

@ESapenaVentura chatted with Zoe about the issue - Created ticket in HCAO repo

[Wkt8]

Stalled until we hear back about gender_identity ontology term.

[ESapenaVentura]

Still not solved with this month's release...

[ESapenaVentura]

Had a discussion with Zoe, they couldn't get to fix the issue and will work on it for the next release!

[gabsie]

The gender_identity ontology term needs a meeting setup with OLS. @ESapenaVentura to action this.

[ESapenaVentura]

I have sent an email to Henriette, copying in CC Zoe and the wrangler team