Closed manulera closed 2 years ago
What tool are you using to edit fypo? Protege or is anyone still using obo edit?
We are using protege @matentzn
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.
Yes, indeed only me and @ValWood are doing this now, and we both use Progete 5.5
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.
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.
Sounds good. I won't be using obo-edit
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
Oops yes. rm fypo-edit.obo
Sorry about that!
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
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
.