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pombase / fypo

Fission Yeast Phenotype Ontology
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Using Protege 5.6 for editing #4366

Closed manulera closed 11 months ago

manulera commented 1 year ago

Hello @matentzn

@ValWood has to upgrade to Protege v5.6 for her GO work and we were wondering what we have to do in the repository to be able to start using it for FYPO as well. Is there some documentation somewhere from the OBO foundry?

matentzn commented 1 year ago

Here is a course taught by @gouttegd of the new 5.6 features. You need to do two things:

docker pull obolibrary/odkfull

If you have not done so, to get the latest ODK and

Do a normalisation PR:

Open fypo-edit, make NO change, save it with the new protege, make PR, let QC pass, merge. Thats all!

manulera commented 1 year ago

Hi @matentzn thanks for your quick reply, but it took me a while to get to it. I have done as you said, and it seems to have gone OK. The pull request is below

https://github.com/pombase/fypo/pull/4385

Just one question. We no longer need to run the normalise_xsd_string, right? I have seen a lot of changes in those lines after saving the file, but I guess from now on the new protege handles this properly, right?

BTW, it's great to see that the id ranges are working with the local file. Surely editors of multiple ontologies will greatly appreciate!

matentzn commented 1 year ago

Yep, you wont need normalise_xsd_string anymore!

manulera commented 1 year ago

Thanks @matentzn!

This is done @ValWood. I will make a release tomorrow, since today I had already done one release for some terms I needed for Canto (I did not want to do a release with both new terms and repository-wide changes).

ValWood commented 11 months ago

closing, thanks both!