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SPARC term request workflow

Open tgbugs opened this issue 5 years ago • 22 comments

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 seam cannot be an exact synonym, but I'm not entirely sure what kind of synonym it actually is).

tgbugs avatar May 26 '20 06:05 tgbugs

Hi Tom - we should discuss how to unblock this.

dosumis avatar Jan 13 '21 15:01 dosumis

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.

tgbugs avatar Jan 13 '21 17:01 tgbugs

Updated this from master (huge structural changes) and set PR to draft.

matentzn avatar Jul 21 '21 10:07 matentzn

@MCSZ updated and ready for review.

tgbugs avatar Nov 04 '21 00:11 tgbugs

We are missing the subClassOf axioms here. Need to investigate.

tgbugs avatar Nov 04 '21 01:11 tgbugs

Moved this to Draft so its clear we cant merge this

matentzn avatar Jan 31 '22 14:01 matentzn

Minor: run through normalize step or just robot convert to get ! comments to make the PR more understandable.

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?

cmungall avatar Aug 01 '23 18:08 cmungall

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 ! comments, I thought I had those in already, but clearly not. I'll make sure they are added to simplify things.

Yes, everything is in a single contiguous block.

tgbugs avatar Aug 03 '23 19:08 tgbugs

Can you elaborate? Do you need to record overlap?

On Tue, 28 Nov 2023, 23:21 Tom Gillespie, @.***> wrote:

@.**** commented on this pull request.

In src/ontology/uberon-edit.obo https://github.com/obophenotype/uberon/pull/1606#discussion_r1408531226:

+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

+[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 avatar Nov 29 '23 08:11 dosumis

@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.

tgbugs avatar Dec 01 '23 23:12 tgbugs

#gogoeditdiff

dosumis avatar Dec 18 '23 17:12 dosumis

Plan for review:

  • [ ] 1. Review classifications
  • [ ] 2. Look into adding at least some location/connectivity relationships for all - where the classifications do not already give us that.
  • [x] 3. Fix def xrefs to be known CURIES (they are currently bare URLs).

dosumis avatar Dec 18 '23 17:12 dosumis

#gogoeditdiff

anitacaron avatar Jan 02 '24 20:01 anitacaron

Here's a diff of how these changes impact the classified ontology (on -simple file):

Ontology comparison

Left

  • Ontology IRI: http://purl.obolibrary.org/obo/uberon/uberon-simple.owl
  • Version IRI: http://purl.obolibrary.org/obo/uberon/releases/2024-01-02/uberon-simple.owl
  • Loaded from: file:/work/src/ontology/../../master/src/ontology/uberon-simple.owl

Right

  • Ontology IRI: http://purl.obolibrary.org/obo/uberon/uberon-simple.owl
  • Version IRI: http://purl.obolibrary.org/obo/uberon/releases/2024-01-02/uberon-simple.owl
  • Loaded from: file:/work/src/ontology/uberon-simple.owl

Ontology imports

Ontology annotations

ansa subclavia http://purl.obolibrary.org/obo/UBERON_8310005

Added

anterior subdiaphragmatic vagus nerve http://purl.obolibrary.org/obo/UBERON_8310003

Added

coccygeal dorsal root ganglion http://purl.obolibrary.org/obo/UBERON_8310013

Added

coccygeal nerve trunk http://purl.obolibrary.org/obo/UBERON_8310012

Added

coccygeal spinal cord http://purl.obolibrary.org/obo/UBERON_8310009

Added

dorsal root of coccygeal nerve http://purl.obolibrary.org/obo/UBERON_8310010

Added

first coccygeal dorsal root ganglion http://purl.obolibrary.org/obo/UBERON_8310017

Added

gray communicating ramus of eighth thoracic nerve http://purl.obolibrary.org/obo/UBERON_8310087

Added

gray communicating ramus of eleventh thoracic nerve http://purl.obolibrary.org/obo/UBERON_8310090

Added

gray communicating ramus of fifth lumbar nerve http://purl.obolibrary.org/obo/UBERON_8310097

Added

gray communicating ramus of fifth sacral nerve http://purl.obolibrary.org/obo/UBERON_8310104

Added

gray communicating ramus of first coccygeal nerve http://purl.obolibrary.org/obo/UBERON_8310105

Added

gray communicating ramus of first lumbar nerve http://purl.obolibrary.org/obo/UBERON_8310093

Added

gray communicating ramus of first sacral nerve http://purl.obolibrary.org/obo/UBERON_8310100

Added

gray communicating ramus of fourth lumbar nerve http://purl.obolibrary.org/obo/UBERON_8310096

Added

gray communicating ramus of fourth sacral nerve http://purl.obolibrary.org/obo/UBERON_8310103

Added

gray communicating ramus of ninth thoracic nerve http://purl.obolibrary.org/obo/UBERON_8310088

Added

gray communicating ramus of second coccygeal nerve http://purl.obolibrary.org/obo/UBERON_8310106

Added

gray communicating ramus of second lumbar nerve http://purl.obolibrary.org/obo/UBERON_8310094

Added

gray communicating ramus of second sacral nerve http://purl.obolibrary.org/obo/UBERON_8310101

Added

gray communicating ramus of seventh lumbar nerve http://purl.obolibrary.org/obo/UBERON_8310099

Added

gray communicating ramus of seventh thoracic nerve http://purl.obolibrary.org/obo/UBERON_8310086

Added

gray communicating ramus of sixth lumbar nerve http://purl.obolibrary.org/obo/UBERON_8310098

Added

gray communicating ramus of sixth thoracic nerve http://purl.obolibrary.org/obo/UBERON_8310085

Added

gray communicating ramus of tenth thoracic nerve http://purl.obolibrary.org/obo/UBERON_8310089

Added

gray communicating ramus of the eighth cervical nerve http://purl.obolibrary.org/obo/UBERON_8310079

Added

gray communicating ramus of the fifth cervical nerve http://purl.obolibrary.org/obo/UBERON_8310076

Added

gray communicating ramus of the fifth thoracic nerve http://purl.obolibrary.org/obo/UBERON_8310084

Added

gray communicating ramus of the first cervical nerve http://purl.obolibrary.org/obo/UBERON_8310072

Added

gray communicating ramus of the first thoracic nerve http://purl.obolibrary.org/obo/UBERON_8310080

Added

gray communicating ramus of the fourth cervical nerve http://purl.obolibrary.org/obo/UBERON_8310075

Added

gray communicating ramus of the fourth thoracic nerve http://purl.obolibrary.org/obo/UBERON_8310083

Added

gray communicating ramus of the second cervical nerve http://purl.obolibrary.org/obo/UBERON_8310073

Added

gray communicating ramus of the second thoracic nerve http://purl.obolibrary.org/obo/UBERON_8310081

Added

gray communicating ramus of the seventh cervical nerve http://purl.obolibrary.org/obo/UBERON_8310078

Added

gray communicating ramus of the sixth cervical nerve http://purl.obolibrary.org/obo/UBERON_8310077

Added

gray communicating ramus of the third cervical nerve http://purl.obolibrary.org/obo/UBERON_8310074

Added

gray communicating ramus of the third thoracic nerve http://purl.obolibrary.org/obo/UBERON_8310082

Added

gray communicating ramus of third coccygeal nerve http://purl.obolibrary.org/obo/UBERON_8310107

Added

gray communicating ramus of third lumbar nerve http://purl.obolibrary.org/obo/UBERON_8310095

Added

gray communicating ramus of third sacral nerve http://purl.obolibrary.org/obo/UBERON_8310102

Added

gray communicating ramus of thirteenth thoracic nerve http://purl.obolibrary.org/obo/UBERON_8310092

Added

gray communicating ramus of thoracic nerve http://purl.obolibrary.org/obo/UBERON_8310091

Added

inner submucosal nerve plexus http://purl.obolibrary.org/obo/UBERON_8310006

Added

interscapular brown adipose tissue http://purl.obolibrary.org/obo/UBERON_8310004

Added

outer submucosal nerve plexus http://purl.obolibrary.org/obo/UBERON_8310007

Added

second coccygeal dorsal root ganglion http://purl.obolibrary.org/obo/UBERON_8310018

Added

seventh lumbar dorsal root ganglion http://purl.obolibrary.org/obo/UBERON_8310016

Added

seventh lumbar spinal cord segment http://purl.obolibrary.org/obo/UBERON_8310008

Added

sixth lumbar dorsal root ganglion http://purl.obolibrary.org/obo/UBERON_8310015

Added

third coccygeal dorsal root ganglion http://purl.obolibrary.org/obo/UBERON_8310019

Added

thirteenth thoracic dorsal root ganglion http://purl.obolibrary.org/obo/UBERON_8310014

Added

ureter junction of bladder trigone http://purl.obolibrary.org/obo/UBERON_8310000

Added

urethra junction with bladder trigone http://purl.obolibrary.org/obo/UBERON_8310001

Added

urethral seam http://purl.obolibrary.org/obo/UBERON_8310002

Added

ventral root of coccygeal nerve http://purl.obolibrary.org/obo/UBERON_8310011

Added

ventral root of the eighth cervical spinal cord segment http://purl.obolibrary.org/obo/UBERON_8310027

Added

ventral root of the eighth thoracic spinal cord segment http://purl.obolibrary.org/obo/UBERON_8310035

Added

ventral root of the eleventh thoracic spinal cord segment http://purl.obolibrary.org/obo/UBERON_8310038

Added

ventral root of the fifth cervical spinal cord segment http://purl.obolibrary.org/obo/UBERON_8310024

Added

ventral root of the fifth lumbar spinal cord segment http://purl.obolibrary.org/obo/UBERON_8310045

Added

ventral root of the fifth sacral spinal cord segment http://purl.obolibrary.org/obo/UBERON_8310052

Added

ventral root of the fifth thoracic spinal cord segment http://purl.obolibrary.org/obo/UBERON_8310032

Added

ventral root of the first coccygeal spinal cord segment http://purl.obolibrary.org/obo/UBERON_8310053

Added

ventral root of the first lumbar spinal cord segment http://purl.obolibrary.org/obo/UBERON_8310041

Added

ventral root of the first sacral spinal cord segment http://purl.obolibrary.org/obo/UBERON_8310048

Added

ventral root of the first spinal cord segment http://purl.obolibrary.org/obo/UBERON_8310020

Added

ventral root of the first thoracic spinal cord segment http://purl.obolibrary.org/obo/UBERON_8310028

Added

ventral root of the fourth cervical spinal cord segment http://purl.obolibrary.org/obo/UBERON_8310023

Added

ventral root of the fourth lumbar spinal cord segment http://purl.obolibrary.org/obo/UBERON_8310044

Added

ventral root of the fourth sacral spinal cord segment http://purl.obolibrary.org/obo/UBERON_8310051

Added

ventral root of the fourth thoracic spinal cord segment http://purl.obolibrary.org/obo/UBERON_8310031

Added

ventral root of the ninth thoracic spinal cord segment http://purl.obolibrary.org/obo/UBERON_8310036

Added

ventral root of the second cervical spinal cord segment http://purl.obolibrary.org/obo/UBERON_8310021

Added

ventral root of the second coccygeal spinal cord segment http://purl.obolibrary.org/obo/UBERON_8310054

Added

ventral root of the second lumbar spinal cord segment http://purl.obolibrary.org/obo/UBERON_8310042

Added

ventral root of the second sacral spinal cord segment http://purl.obolibrary.org/obo/UBERON_8310049

Added

ventral root of the second thoracic spinal cord segment http://purl.obolibrary.org/obo/UBERON_8310029

Added

ventral root of the seventh cervical spinal cord segment http://purl.obolibrary.org/obo/UBERON_8310026

Added

ventral root of the seventh lumbar spinal cord segment http://purl.obolibrary.org/obo/UBERON_8310047

Added

ventral root of the seventh thoracic spinal cord segment http://purl.obolibrary.org/obo/UBERON_8310034

Added

ventral root of the sixth cervical spinal cord segment http://purl.obolibrary.org/obo/UBERON_8310025

Added

ventral root of the sixth lumbar spinal cord segment http://purl.obolibrary.org/obo/UBERON_8310046

Added

ventral root of the sixth thoracic spinal cord segment http://purl.obolibrary.org/obo/UBERON_8310033

Added

ventral root of the tenth thoracic spinal cord segment http://purl.obolibrary.org/obo/UBERON_8310037

Added

ventral root of the third cervical spinal cord segment http://purl.obolibrary.org/obo/UBERON_8310022

Added

ventral root of the third coccygeal spinal cord segment http://purl.obolibrary.org/obo/UBERON_8310055

Added

ventral root of the third lumbar spinal cord segment http://purl.obolibrary.org/obo/UBERON_8310043

Added

ventral root of the third sacral spinal cord segment http://purl.obolibrary.org/obo/UBERON_8310050

Added

ventral root of the third thoracic spinal cord segment http://purl.obolibrary.org/obo/UBERON_8310030

Added

ventral root of the thirteenth thoracic spinal cord segment http://purl.obolibrary.org/obo/UBERON_8310040

Added

ventral root of the twelveth thoracic spinal cord segment http://purl.obolibrary.org/obo/UBERON_8310039

Added

white communicating ramus of eighth thoracic spinal nerve http://purl.obolibrary.org/obo/UBERON_8310063

Added

white communicating ramus of eleventh thoracic spinal nerve http://purl.obolibrary.org/obo/UBERON_8310066

Added

white communicating ramus of fifth thoracic spinal nerve http://purl.obolibrary.org/obo/UBERON_8310060

Added

white communicating ramus of first lumbar spinal nerve http://purl.obolibrary.org/obo/UBERON_8310069

Added

white communicating ramus of first thoracic spinal nerve http://purl.obolibrary.org/obo/UBERON_8310056

Added

white communicating ramus of fourth thoracic spinal nerve http://purl.obolibrary.org/obo/UBERON_8310059

Added

white communicating ramus of ninth thoracic spinal nerve http://purl.obolibrary.org/obo/UBERON_8310064

Added

white communicating ramus of second lumbar spinal nerve http://purl.obolibrary.org/obo/UBERON_8310070

Added

white communicating ramus of second thoracic spinal nerve http://purl.obolibrary.org/obo/UBERON_8310057

Added

white communicating ramus of seventh thoracic spinal nerve http://purl.obolibrary.org/obo/UBERON_8310062

Added

white communicating ramus of sixth thoracic spinal nerve http://purl.obolibrary.org/obo/UBERON_8310061

Added

white communicating ramus of tenth thoracic spinal nerve http://purl.obolibrary.org/obo/UBERON_8310065

Added

white communicating ramus of third lumbar spinal nerve http://purl.obolibrary.org/obo/UBERON_8310071

Added

white communicating ramus of third thoracic spinal nerve http://purl.obolibrary.org/obo/UBERON_8310058

Added

white communicating ramus of thirteenth thoracic spinal nerve http://purl.obolibrary.org/obo/UBERON_8310068

Added

white communicating ramus of twelfth thoracic spinal nerve http://purl.obolibrary.org/obo/UBERON_8310067

Added

github-actions[bot] avatar Jan 02 '24 21:01 github-actions[bot]

Decision on how to proceed:

  • [x] Fix curies & merge
    • https://scicrunch.org/resolver/SCR_018709 --> RRID:SCR_018709
    • Sciencedirect refs: https://www.sciencedirect.com/topics/veterinary-science-and-veterinary-medicine/gray-ramus-communicans & https://www.sciencedirect.com/topics/veterinary-science-and-veterinary-medicine/white-ramus-communicans. Review papers on these pages for ones which clearly describe nerves. Add all of these DOIs to all terms with the URL xref. Retain URL in seeAlso link.
  • [ ] Make a new ticket to review classifications and connectivity relationships for all terms in this PR. Getting to this will depend on funding and priorities of collaborative projects. This PR should list all terms to be reviewed by name and ID.

dosumis avatar Jan 29 '24 15:01 dosumis

@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?

dosumis avatar Jan 29 '24 17:01 dosumis

@stappan @smtifahim can you comment re: the ASCT+B tables?

tgbugs avatar Jan 29 '24 21:01 tgbugs

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.

tgbugs avatar Jan 30 '24 22:01 tgbugs

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!

aleixpuigb avatar Jan 31 '24 15:01 aleixpuigb

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.

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.

aleixpuigb avatar Apr 22 '24 12:04 aleixpuigb

As this PR has been around for a while, it might 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?

dosumis avatar Apr 22 '24 12:04 dosumis

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.

tgbugs avatar Apr 22 '24 17:04 tgbugs