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pombase / fypo

Fission Yeast Phenotype Ontology
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We can't edit the ontology in parallel #4180

Closed manulera closed 2 years ago

manulera commented 2 years ago

cc: @nicolevasilevsky @matentzn I post this question in the Slack channel, but I also tag you here.

We have a question in PomBase regarding collaborative editing of our phenotype ontology.

We use the file src/ontology/fypo-edit.obo in FYPO repository to make our edits, and we have a release pipeline after that.

We would like to be able to work on branches on fypo-edit in parallel, and merge changes for a certain release. The problem is the line that starts with -owl-axioms: (with a lot of \n characters). Any time the file is saved (even without changes, e.g. add a subclass, undo, save), this line changes. Since all the information is in a single line, there is no way to merge different contributions prior to the release. Is there a way to tell protege to store this information in a different way so that we can edit the ontology in parallel?

This would also be important for revising changes prior to making a release, since right now we cannot see changes to logical definitions using git diff.

matentzn commented 2 years ago

What tool are you using to edit fypo? Protege or is anyone still using obo edit?

manulera commented 2 years ago

We are using protege @matentzn

matentzn commented 2 years ago

Excellent. Can I confirm that all of you are using Protege, and no one will use OBO Edit again? If so, the problem is easily solved.

manulera commented 2 years ago

Yes, indeed only me and @ValWood are doing this now, and we both use Progete 5.5

matentzn commented 2 years ago

Excellent. Solution:

IN the terminal run the following command:

cd src/ontology
sh run.sh robot convert -i fypo-edit.obo -o fypo-edit.ofn
mv fypo-edit.ofn fypo-edit.owl
rm fypo-edit.owl

From now on, you will use OWL functional syntax as the editing language like all other phenotype ontologies and you wont run into merge conflicts.

manulera commented 2 years ago

Thanks for the quick reply @matentzn.

I will wait for an OK on this from @ValWood and @kimrutherford before doing it, and then I will close the issue.

ValWood commented 2 years ago

Sounds good. I won't be using obo-edit

manulera commented 2 years ago

Hi @matentzn, I was about to do what you said here:

IN the terminal run the following command:

I wonder if in the last command, you mean rm fypo-edit.obo

And from then on, work with the owl file

matentzn commented 2 years ago

Oops yes. rm fypo-edit.obo Sorry about that!

manulera commented 2 years ago

Solved in #4192 documentation in the wiki changed (fypo-edit.owl instead of fypo-edit.obo), and this extra step added:

https://github.com/pombase/fypo/wiki/FYPO-release-procedure

See % sh run.sh make normalise_xsd_string