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obophenotype / uberon

An ontology of gross anatomy covering metazoa. Works in concert with https://github.com/obophenotype/cell-ontology
http://obophenotype.github.io/uberon/
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SPARC terms #2781

Open shawntanzk opened 1 year ago

shawntanzk commented 1 year ago

This unfortunately slipped my radar, but we really need to follow up with @tgbugs and the SPARC team to add these terms: https://docs.google.com/spreadsheets/d/11wkPENtwcOkolALFi3mVWhuJ38Z4hrmXCGwEbhaSFeA/edit#gid=0 @dosumis I will assign you this for now, it will need to be assigned to someone to properly take a look at it. @tgbugs - could you add Sue to this ticket please? Thanks

shawntanzk commented 1 year ago

Email from Sue:

Hi Shawn,

For this year’s SPARC research goals, we are expecting to comprehensively map the vagus nerve and it’s branches, which will be added to and retrievable within our connectivity knowledge base that we are building, SCKAN. As you know, I’m preparing a number of terms to be considered for addition to UBERON, based on our work with ApiNATOMY models. And, we have decided to unify on using UBERON curie representation as much as possible. Thus, we’d like to expand UBERON’s representation to include all the sub-branches and terminal branches of the vagus. FMA has more terminal and subbranches available, and also includes “branch_of” or “branching_part_of” relationship.

The team and I wanted to raise a couple questions with you to get your feedback on the best way we might plan to approach the following:

  1. Would you be able to recommend how we might take steps to provide the information to include “branch_of” relationships for nerves (especially cranial nerves, like the vagus) in our planned upstream effort, and
  2. Any thoughts on how we might be able to establish the order of the vagus nerve from primary to terminal branch? (both sensory and motor) Is this possible with UBERON?

While we’re starting with the vagus, it’s certainly possible that we may need to do this with other peripheral nerves.

Thanks very much for thinking about this with us, Sue

tgbugs commented 1 year ago

@stappan

tgbugs commented 1 year ago

There is also https://github.com/obophenotype/uberon/pull/1606 that has languished, but I do have https://github.com/SciCrunch/sparc-curation/blob/master/sparcur_internal/sparc-to-uberon.py that might help a bit with this.

dosumis commented 1 year ago

I'd like to add this to the Uberon call on Monday 30th at 6pm GMT @tgbugs @stappan - can you join?

tgbugs commented 1 year ago

I have another meeting in that slot but can probably skip it to come. Will confirm.

stappan commented 1 year ago

I can attend. Pls send meeting details. Thanks!

From: Tom @.> Sent: Tuesday, January 24, 2023 6:35 PM To: @.> Cc: Sue @.>; @.> Subject: Re: [obophenotype/uberon] SPARC terms (Issue #2781)

I have another meeting in that slot but can probably skip it to come. Will confirm.

— Reply to this email directly, view it on GitHubhttps://github.com/obophenotype/uberon/issues/2781#issuecomment-1402830331, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AZKA6QXN6VUOBPOQE7U6J4TWUBRM3ANCNFSM6AAAAAAUFMHSCM. You are receiving this because you were mentioned.Message ID: @.***>

tgbugs commented 1 year ago

Confirming that yes I will be there.

github-actions[bot] commented 1 year ago

This issue has not seen any activity in the past 6 months; it will be closed automatically one year from now if no action is taken.

tgbugs commented 1 year ago

Pinging here since we have updated the pull request from draft state #1606 has been updated and is ready for review.

github-actions[bot] commented 9 months ago

This issue has not seen any activity in the past 6 months; it will be closed automatically one year from now if no action is taken.