Adding new Foundry ontology T4FS to OLS

[allysonlister]

Good morning all!

terms4FAIRskills has just been added to the OBO Foundry :-)

Please can you let me know the procedure for integrating it with OLS? I'd love to be able to point people to OLS to browse the ontology.

Thanks!

[serjoshua]

Hi Allyson,

Thank you for letting us know and upon checking it is indeed in OBO's configuration already. As of the moment, OLS is not doing regular updates. The earliest scheduled release we have is on the 18th, exactly next week. We will keep you posted regarding the deployment and we will surely include T4FS in it.

[allysonlister]

That's lovely - thank you so much, I'll take a look next week. Thanks again!

[allysonlister]

Good morning! Just checked https://www.ebi.ac.uk/ols/ontologies/t4fs and haven't seen anything. For reference when should I expect it to appear please?

Thanks again!

[serjoshua]

Good morning Allyson,

Apologies for giving you the impression it will be available today. We indeed kicked off the deployment yesterday and it is in progress. Updates will be available tomorrow at the latest. We will keep you posted, especially if we encountered any issues or the like.

[allysonlister]

No need to apologise! Just good to know, and thanks!

[serjoshua]

Hello Allyson,

This is just an FYI. So, I am testing our pre-prod environment as of the moment and I cannot seem to find your ontology at first, but then I tried searching it using the title and it worked. Apparently, the preferredPrefix is set TF4S and I was searching T4FS. Not sure if it is a discrepancy but it gave me a mini-heart attack earlier if I'm being honest :) If it really is a discrepancy, I just want to mention that any updates on your side since (start of deployment) yesterday might not be picked up until the next data release, which could be a little far off.

[allysonlister]

Oh dear - some kind of capitalisation issue - I'll check all the relevant markdown files. Thanks!

[allysonlister]

As you can see from the github notification above, I have submitted a PR. Hopefully you can still index t4fs even with preferredPrefix not being as expected.

(even if this seems to show that I cannot spell "preferred" :-) )

[serjoshua]

No worries. It's all good on our side with regards to the data release so far. The preferredPrefix has affected the UI but as you can see in the URL, it didn't affect the API cos it still uses the ontology id instead of the preferredPrefix. Hopefully, that will be the only issue.

[jamesaoverton]

I think that the problem is not capitalization, it's the order of the "4" and "F" characters ("T4FS" vs "TF4s"). Right?

[serjoshua]

It is. I checked the PR and it was corrected anyway. Once deployment is done, hopefully, it won't be too much of a bother working with the current preferredPrefix. My only worry right now are the APIs, but it seems like the APIs are using ontology id.

[allysonlister]

The PR has been updated such that preferredPrefix: T4FS - I've been told we should keep it all capitalised. Hopefully my typo will not cause any more problems!

[serjoshua]

Good day Allyson and James,

T4FS has finally been added to OLS but with the problematic prefix. Feel free to create tickets for any issues encountered in OLS or urgent updates you want to be deployed to production. Thank you so much and regards.

[allysonlister]

No worries - thank you so much!

[serjoshua]

T4FS has just been updated in OLS with the new preferred prefix. FYI. Thanks!

[allysonlister]

That's great thank you!