Stomatogastric ganglion cell types of crabs, lobsters

[stevevanhooser]

With @andreagaede, added 8 cell types from the stomatogastric ganglion of crabs and lobsters (thought to be homologous neurons).

It references a relatively new UBERON node: UBERON:8910001 ! stomatogastric ganglion

It views well in Protoge

[stevevanhooser]

Not sure which reviewer to request (apparently I cannot suggest one), but we discussed these changes with @gouttegd and @rays22 at the November meeting.

[gouttegd]

Please see the inline comments below. I only commented on the first new term, but the comments apply, mutatis mutandis, to all the proposed new terms.

It is especially important to fix the incorrect use of EquivalentClasses and of the in taxon relationship.

[stevevanhooser]

Fixes made, looks good to me in Protege, this note from @gouttegd remains relevant:

Side note (more intended for other reviewers): UBERON:8910001 has only been added to Uberon last month, and there has been no new Uberon release since then. We will need to wait for a Uberon release and then refresh the imports.

[gouttegd]

Thank you for your reactivity, much appreciated!

Out of the following comments, the critical one is the one about the duplicated definitions of CL:4070014 and CL:4070017.

With the other comments, we are entering into “nitpicking“ territory, which is good as it means that the most important issues have been addressed.

[stevevanhooser]

Thanks also for your quick responses. Updated

[gouttegd]

This looks good to me.

As previously noted though, we’ll need to wait for UBERON:8910001 to become available in the next Uberon release.

[stevevanhooser]

Thanks for your help @gouttegd!

Are these releases at regular intervals or just as the developers are ready?

Thanks again
Steve

[gouttegd]

We try to make one release every 6 to 8 weeks. The last Uberon release was in late November, so I’d expect the next one to happen before the end of the month. No promises, though.

[aleixpuigb]

This looks good to me.

As previously noted though, we’ll need to wait for UBERON:8910001 to become available in the next Uberon release.

I can run an Uberon release soon (early next week to give enough time to close PRs). I will make the announcement.

[stevevanhooser]

Did an Uberon release happen? It seems to be updated on https://www.ebi.ac.uk/ols4/ontologies/uberon

If so, then perhaps this can be merged?

[aleixpuigb]

Hi @stevevanhooser, there is a new Uberon release. Do you need help importing the term from Uberon?

[stevevanhooser]

Yes please. I don't quite follow the documentation there.

[aleixpuigb]

You need to add UBERON:8910001 in the uberon imports txt file https://github.com/obophenotype/cell-ontology/blob/master/src/ontology/imports/uberon_terms.txt . Once that is done, open the docker and in the terminal navigate to src/ontology. Then run:

sh run.sh make imports/merged_import.owl   

Once that is done you should be able to see the term in protégé inside CL. Please let me know if there are difficulties and I can assist you.

[aleixpuigb]

I have tried to push the commit with the Uberon term imported, but I don't have permission to do it.

[stevevanhooser]

Thanks @aleixpuigb. I sent an invitation to my repo if that's what you need access to. I am writing a grant this week and did not have a chance to get into learning about docker.

Thanks

[stevevanhooser]

Thanks @aleixpuigb

[aleixpuigb]

No problem!

[github-actions]

This PR has not seen any activity in the past month; if nobody comments or reviews it in the next week, the PR editor will be allowed to proceed with merging without explicit approval, should they wish to do so.

[dosumis]

Looks like this has been ready to go for over a month but there are now some conflicts? I suspect due to updates to imports in branch.

How can we get this resolved quickly to get @stevevanhooser 's rather awesome work into our next release?

[gouttegd]

I have fixed the conflicts in the https://github.com/obophenotype/cell-ontology/tree/stomatogastric_ganglion_crab_lobster_fixed branch.

Since this PR originates from another repository, I cannot push my fixes directly here. Instead, we have two solutions:

(A) I open a PR with the conflict resolution on the original repository on the Waltham Data Science account. From there, @stevevanhooser can merge it, which will automatically be reflected on this PR, which we’ll then be able to merge.

(B) We discard this PR, and I open a new one containing both the original work and the conflict resolution.

(A) is a slightly more complicated approach, but it would have the benefit that the PR that is ultimately merged would retain all the discussion that we have been having here.

(B) is more straightforward, but it would appear as a completely new PR completely unrelated to this one.

[stevevanhooser]

I can accept! A is fine. via mobileOn Mar 12, 2025, at 2:38 PM, Damien Goutte-Gattat ***@***.***> wrote: I have fixed the conflicts in the https://github.com/obophenotype/cell-ontology/tree/stomatogastric_ganglion_crab_lobster_fixed [github.com] branch. Since this PR originates from another repository, I cannot push my fixes directly here. Instead, we have two solutions: (A) I open a PR with the conflict resolution on the original repository [github.com] on the Waltham Data Science account. From there, @stevevanhooser [github.com] can merge it, which will automatically be reflected on this PR, which we’ll then be able to merge. (B) We discard this PR, and I open a new one containing both the original work and the conflict resolution. (A) is a slightly more complicated approach, but it would have the benefit that the PR that is ultimately merged would retain all the discussion that we have been having here. (B) is more straightforward, but it would appear as a completely new PR completely unrelated to this one.—Reply to this email directly, view it on GitHub [github.com], or unsubscribe [github.com].You are receiving this because you were mentioned.Message ID: ***@***.***> gouttegd left a comment (obophenotype/cell-ontology#2876) [github.com] I have fixed the conflicts in the https://github.com/obophenotype/cell-ontology/tree/stomatogastric_ganglion_crab_lobster_fixed [github.com] branch. Since this PR originates from another repository, I cannot push my fixes directly here. Instead, we have two solutions: (A) I open a PR with the conflict resolution on the original repository [github.com] on the Waltham Data Science account. From there, @stevevanhooser [github.com] can merge it, which will automatically be reflected on this PR, which we’ll then be able to merge. (B) We discard this PR, and I open a new one containing both the original work and the conflict resolution. (A) is a slightly more complicated approach, but it would have the benefit that the PR that is ultimately merged would retain all the discussion that we have been having here. (B) is more straightforward, but it would appear as a completely new PR completely unrelated to this one. —Reply to this email directly, view it on GitHub [github.com], or unsubscribe [github.com].You are receiving this because you were mentioned.Message ID: ***@***.***>

[stevevanhooser]

I’ll add you to our branch in a couple hours when I’m at a computer via mobileOn Mar 12, 2025, at 2:38 PM, Damien Goutte-Gattat ***@***.***> wrote: I have fixed the conflicts in the https://github.com/obophenotype/cell-ontology/tree/stomatogastric_ganglion_crab_lobster_fixed [github.com] branch. Since this PR originates from another repository, I cannot push my fixes directly here. Instead, we have two solutions: (A) I open a PR with the conflict resolution on the original repository [github.com] on the Waltham Data Science account. From there, @stevevanhooser [github.com] can merge it, which will automatically be reflected on this PR, which we’ll then be able to merge. (B) We discard this PR, and I open a new one containing both the original work and the conflict resolution. (A) is a slightly more complicated approach, but it would have the benefit that the PR that is ultimately merged would retain all the discussion that we have been having here. (B) is more straightforward, but it would appear as a completely new PR completely unrelated to this one.—Reply to this email directly, view it on GitHub [github.com], or unsubscribe [github.com].You are receiving this because you were mentioned.Message ID: ***@***.***> gouttegd left a comment (obophenotype/cell-ontology#2876) [github.com] I have fixed the conflicts in the https://github.com/obophenotype/cell-ontology/tree/stomatogastric_ganglion_crab_lobster_fixed [github.com] branch. Since this PR originates from another repository, I cannot push my fixes directly here. Instead, we have two solutions: (A) I open a PR with the conflict resolution on the original repository [github.com] on the Waltham Data Science account. From there, @stevevanhooser [github.com] can merge it, which will automatically be reflected on this PR, which we’ll then be able to merge. (B) We discard this PR, and I open a new one containing both the original work and the conflict resolution. (A) is a slightly more complicated approach, but it would have the benefit that the PR that is ultimately merged would retain all the discussion that we have been having here. (B) is more straightforward, but it would appear as a completely new PR completely unrelated to this one. —Reply to this email directly, view it on GitHub [github.com], or unsubscribe [github.com].You are receiving this because you were mentioned.Message ID: ***@***.***>

[gouttegd]

@stevevanhooser Great! I’ve created the PR on your repo: Waltham-Data-Science#1

You don’t even need to grant me access to your repo at all: just accept and merge the PR over there.