UBERON:0004122 genitourinary system and UBERON:0001008 renal system

[paolaroncaglia]

Hi, UBERON:0004122 genitourinary system has_part UBERON:0001008 renal system, but UBERON:0001008 renal system is not part_of UBERON:0004122 genitourinary system. This is causing issues for disease ontologies: in Mondo and EFO, 'disease of genitourinary system' and 'urinary system disease' are siblings instead of parent-child. Could you add the part_of axiom, please? Or are ther species in the Uberon space with a renal system but without a genitourinary one? If so, we may want to assert 'urinary system disease' subclass of 'disease of genitourinary system', because in the species where we typically look at diseases this is always true afaik. Tagging @cmungall and @nicolevasilevsky because it'd be great if this could be fixed sooner rather than later please :-) and tagging @zoependlington for her reference. Thanks!

[cmungall]

The reason is that renal system is taxonomically quite general, and not all species have a genitourinary system as a distinct unit. However, this may be being too particular and the simplest thing may be make the part-of, and treat GU as being a simple mereological sum.

See also #1450

[nicolevasilevsky]

I just tried to make this edit on a branch and I am getting a huge, messy diff. I've never actually edited Uberon before.

@cmungall would you mind doing this edit?

[balhoff]

I was trying to clean things up for this reason, but not sure what to do with the failing check: #1526

[paolaroncaglia]

@nicolevasilevsky @cmungall @balhoff Thank you all for looking into this!

[RDruzinsky]

The genital and urinary systems should be separate and distinct. We could add some in_taxon statements to clarify their interconnected anatomy in mammals and other taxonomic groups, and specify differences in males and females.

Robert E. Druzinsky, Ph.D. Clinical Associate Professor Dept. of Oral Biology College of Dentistry University of Illinois at Chicago 801 S. Paulina Chicago, IL 60612 druzinsk@uic.edu

Office: 312-996-0406 Lab: 312-996-0629 Website: www.peerj.com/RobertDruzinsky

On Tue, Nov 26, 2019 at 8:52 AM paolaroncaglia notifications@github.com wrote:

@nicolevasilevsky https://github.com/nicolevasilevsky @cmungall https://github.com/cmungall @balhoff https://github.com/balhoff Thank you all for looking into this!

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[nicolevasilevsky]

Thanks @RDruzinsky.

@paolaroncaglia if @RDruzinsky makes those edits, would that address the issue? Or should we assert 'urinary system disease' as a subclass of 'disease of genitourinary system' in Mondo (too, or instead)?

[paolaroncaglia]

@nicolevasilevsky

@paolaroncaglia if @RDruzinsky makes those edits, would that address the issue?

I think so, thanks. Let's try and see, and then we can evaluate if any extra assertion is needed for diseases, but hopefully not. Best wishes, Paola

[nicolevasilevsky]

@RDruzinsky - I seem to be up and running with Uberon editing now, so I can make these necessary edits (although I am new to editing Uberon, so if you don't mind, I'll ask you some clarifying questions:

is the genitourinary system restricted to mammals? If yes, I could add the subClass Of axiom to genitourinary system: 'in taxon' some Mammalia

What is the difference in males and females? And how do I encode this in the ontology?

Thanks for your help!

[balhoff]

@nicolevasilevsky FYI (in case you do add the taxon restriction), use only_in_taxon rather than its parent in_taxon.

[RDruzinsky]

The differences in males and female are the major reason that the lumping of the genital and urinary systems, called the genitourinary or urogenital system, has gone out of favor is the recognition that in females there is no significant connection between them. The sharing only occurs in males. @cjmungall @jbalhoff It seems to be a bit of a problem to capture this anatomy. In males, the reproductive and urinary structures overlap but not in females.

Robert E. Druzinsky, Ph.D. Clinical Associate Professor Dept. of Oral Biology College of Dentistry University of Illinois at Chicago 801 S. Paulina Chicago, IL 60612 druzinsk@uic.edu

Office: 312-996-0406 Lab: 312-996-0629 Website: www.peerj.com/RobertDruzinsky

On Thu, Dec 12, 2019 at 4:27 PM Jim Balhoff notifications@github.com wrote:

@nicolevasilevsky https://github.com/nicolevasilevsky FYI (in case you do add the taxon restriction), use only_in_taxon rather than its parent in_taxon.

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[paolaroncaglia]

Note to self: see if this is fixed or good as is.

[paolaroncaglia]

Following up on the thorny issue of genitourinary vs renal system. Re-reading this thread and trying to achieve some clarity:

Uberon has separate terms for ‘reproductive system’ and ‘renal system’, plus it has a term for ‘genitourinary system’: “Anatomical system that has as its parts the organs concerned with the production and excretion of urine and those concerned with reproduction.”, equivalent to 'anatomical system' and ('has part' some 'reproductive system') and ('has part' some 'renal system') but we all agree that the reciprocal part-ofs would not be true for all species. ‘genitourinary system’ doesn’t have any taxon restrictions, but has a UBPROP “Kidneys and gonads (of vertebrates) develop from adjacent tissues, and after the excretory or urinary ducts have developed, the reproductive system usually taps into them or their derivatives.[well established][VHOG]”.

As @RDruzinsky pointed out, the reproductive and urinary structures overlap in (human) males, but not in females. So ‘genitourinary system’ as is isn’t applicable to mammals, unless we restrict it to male mammals. We should clarify this in the term, plus make examples of species where the term applies (see below).

The issue is lexical and historical. “The genitourinary system, or urogenital system, are the organs of the reproductive system and the urinary system. These are grouped together because of their proximity to each other, their common embryological origin and the use of common pathways, like the male urethra. Also, because of their proximity, the systems are sometimes imaged together.” (https://en.wikipedia.org/w/index.php?title=Genitourinary_system&oldid=1005882445)

We care about the lexical issue because it’s reflected in Mondo, where 'disease of genitourinary system' and 'urinary system disease' are siblings instead of parent-child, which is ontologically correct but contrary to what a clinician might expect (that's where the whole ticket stemmed from - building a version of EFO to represent therapeutic areas for Open Targets). More worryingly, HP defines HP:0000119 ‘Abnormality of the genitourinary system’ as Equivalent to: has part some (quality and characteristic of part of some genitourinary system and has modifier some abnormal)

Looking at children of ‘genitourinary system’, we should not find terms applicable to (female) mammals.

However, UBERON:3011048 ‘genital system’ is highly ambiguous. It’s undefined and comes from amphibian anatomy. Luckily it’s not used in Mondo or HP (but Ontobee shows that it’s used in the Gender, Sex, and Sexual Orientation (GSSO) ontology, likely in error). Should this amphibian term be ceded to another ontology? If not, we should at least rename it ‘amphibian genital system’ and restrict it to Amphibia. Other part-of children of ‘genitourinary system’ may also be problematic, like ‘gonadal ridge’: it’s applicable to female mammals but its parent isn’t, the way it’s logically defined.

In summary I think if we wish to keep ‘genitourinary system’ because it’s useful and meaningful biomedically and for non-mammalian vertebrates, we should probably revise its equivalence, but I’m not sure what to suggest to ensure sustainable automated classification going forward. @RDruzinsky suggested “The genital and urinary systems should be separate and distinct. We could add some in_taxon statements to clarify their interconnected anatomy in mammals and other taxonomic groups, and specify differences in males and females.”. Based on how we end up modelling ‘genitourinary system’, we can better address its part children, and we may need to revise Mondo and HP. (This is one case where I really wish I'm overlooking a simpler solution.)

[paolaroncaglia]

I've commented on this issue previously. I'll remove my assignment now (as well as @cmungall 's). The ticket now has a "kidney" label (thank you @bvarner-ebi ), so it might be addressed as part of a project looking at other kidney-related issues, current and future.

[rays22]

It seems that the genitourinary system is thought to be a superset of the reproductive and renal systems in HP. In contrast, in Uberon the genitourinary system includes only the overlapping parts of the reproductive and renal systems. See the HP phenotype classes under the Abnormality of the genitourinary system branch. The discrepancy in the interpretation of the genitourinary system is causing some phenotype category misalignments between HP and MP. While keeping the

• reproductive system UBERON:0000990
• renal system UBERON:0001008

separate in Uberon as they are right now, what would argue against making UBERON:0004122 genitourinary system a mereological sum of them (plus the cloaka and other appropriate anatomical entities)?