SPARC term request workflow #1606
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uberon_edit.obo
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| name: urethral seam | ||
| def: "The urethral seam (urseam) (syn: urethral raphe, ventral seam) (TS24-TS28). In the male, growth from mesenchyme ventral to the phallic urethra closes the proximal urethral meatus and septates the epithelium of phallic urethra. This results in the centrally positioned phallic urethra and the ventrally positioned urethral seam. The urethral seam is a solid epithelial cord present underneath the skin along the ventral midline of the penis. Septation moves in a proximal to distal direction along the penis during development and the urethral seam is retained in the adult penis. Part of the genital tubercle of male (TS24), part of the penis (TS25-TS28) and also part of phallic urethra of male (TS24) and penile urethra." [] | ||
| synonym: "urethral raphe" EXACT [] | ||
| synonym: "ventral seam" EXACT [] |
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Hi Tom - we should discuss how to unblock this. |
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I have a couple of commits that I need to make to the code that generates these new classes to make use of the block of UBERON_ identifiers that I reserved for InterLex synchronization, once that is done I should be able to update this PR to a non-draft version. |
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Updated this from master (huge structural changes) and set PR to draft. |
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@MCSZ updated and ready for review. |
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We are missing the subClassOf axioms here. Need to investigate. |
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Moved this to Draft so its clear we cant merge this |
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Minor: run through normalize step or just robot convert to get It looks like only is-a relations are provided, we would need at least part-of; and many of these conform to patterns and should get logical defs. What is the expected workflow here? If I had more time I could open in emacs and quickly go through these (assuming they are one contiguous chunk in the obo file) and make them complete. But I don't have so much time for this any more. If this was a one off I could try and allocate some time to do it. But doing this in a conventional protege setup would be a lot of work. Is there any way you could supply more logical axioms as part of the PR? |
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We can provide more axioms. I wasn't sure whether we wanted them in now as part of this pull request, or whether we wanted to get the identifiers minted now and then add the axioms in a second pull request, but I can see that having the axioms will help. With regard to the Yes, everything is in a single contiguous block. |
src/ontology/uberon-edit.obo
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| synonym: "S2 grey ramus" EXACT [] | ||
| xref: FMA:65987 | ||
| xref: ILX:0793229 | ||
| is_a: UBERON:0017642 |
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looks like the is_a is too granular here, and need partonomy or similar for S2 (etc.) @stappan
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actually can't do partonomy to S2 because there is no existing relation that matches it seems
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Can you elaborate? Do you need to record overlap?
…On Tue, 28 Nov 2023, 23:21 Tom Gillespie, ***@***.***> wrote:
***@***.**** commented on this pull request.
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In src/ontology/uberon-edit.obo
<#1606 (comment)>:
> +def: "The postganglionic nerve fibers from the first sacral sympathetic chain ganglion passing to the first sacral spinal nerve." [http://scicrunch.org/resolver/SCR_018709, https://www.sciencedirect.com/topics/veterinary-science-and-veterinary-medicine/gray-ramus-communicans]
+synonym: "S1 gray ramus" EXACT []
+synonym: "S1 grey ramus" EXACT []
+xref: FMA:65986
+xref: ILX:0793228
+is_a: UBERON:0017642
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+[Term]
+id: UBERON:8310101
+name: gray communicating ramus of second sacral nerve
+def: "The postganglionic nerve fibers from the second sacral sympathetic chain ganglion passing to the second sacral spinal nerve." [http://scicrunch.org/resolver/SCR_018709, https://www.sciencedirect.com/topics/veterinary-science-and-veterinary-medicine/gray-ramus-communicans]
+synonym: "S2 gray ramus" EXACT []
+synonym: "S2 grey ramus" EXACT []
+xref: FMA:65987
+xref: ILX:0793229
+is_a: UBERON:0017642
actually can't do partonomy to S2 because there is no existing relation
that matches it seems
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@dosumis I'm planning to open a dedicated issue to discuss this, but in brief the naming conventions for structures along the spinal cord tend to include a reference to the anatomical segment (e.g. C1 ... T1 ... L1 ... S1 ... Cx1 ...) they are close to/communicate with/are derived from the same development structure as, etc. I can imagine a number of ways that this might be done in the ontology and we need to figure out if there is a consistent anatomical relationship that we could use instead of e.g. trying for a developmental relationship which might not actually be factually correct. |
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#gogoeditdiff |
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Plan for review:
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#gogoeditdiff |
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Decision on how to proceed:
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@aleixpuigb - may also be interesting to check whether this fixes any missing Uberon terms in PNS ASCT+B table - submitted by SPARC. @tgbugs would you be able to let is know if this is the case? |
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@stappan @smtifahim can you comment re: the ASCT+B tables? |
…g ramus spinal nerves
…type/uberon into sparc-term-request-flow
| def: "The most caudal segment of the spinal cord, which gives rise to the coccygeal dorsal and ventral roots." [PMID:31751060, RRID:SCR_018709] | ||
| synonym: "coccygeal spinal cord segment" EXACT [] | ||
| xref: ILX:0740051 | ||
| xref: ilx:swanson/uris/neuroanatomical-terminology/terms/56 |
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I am not sure how to change this, would it be possible to have the URL? That might help. Thanks!
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I can expand all these curies to iris, if that would help.
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Thank you, only this one please, all the others are fine.
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With regard to the ASCT+B tables, there are a number of interganglionic segments that are used in the tables that are not in this pull request. It is just a matter of changing a check box to have them included in this pull request if you would like them. |
That would be great, thank you! |
As this PR has been around for a while, it ight be worth merging it and create a new PR for the ASCT+B terms. |
I think we should do that. @tgbugs - any ETA on additional terms? |
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We are in the process of checking over the additional terms we need for this PR, I think without the ASCT+B tables. This PR isn't quite ready because we are missing some important subClassOf axioms, but should have a new iteration later this week. |
DO NOT MERGE
This is a first pass at a pull request generated by a semi-automated
workflow from InterLex and the SPARC term request pipeline. This is a
starting point for figuring out the next steps for being able to
transition to a fully automated pull request pipeline. One of those next
steps will be to reserve an id block for requests coming from
tgbugs/NIFSTD/InterLex. We also need to review what information is
currently missing from what we collect as part of the SPARC pipeline.
@memartone
@MCSZ We need to review the output of the conversion because a number of things are missing (e.g. sources for the definitions) and/or incorrect (e.g.
ventral seamcannot be an exact synonym, but I'm not entirely sure what kind of synonym it actually is).