Query UBERON_0006174 pronephric sinus

[pgaudet]

Uberon term
UBERON_0006174 pronephric sinus

Bug description
UBERON_0006174 pronephric sinus is causing some reasoning problems in GO (geneontology/go-ontology#16524; GO:0039012 pronephric sinus development ), since it is classified as a space; however the definition, as well as the paper cited in GO (https://pubmed.ncbi.nlm.nih.gov/10535314/), describes a network of capillaries. Can the definition and the placement in the ontology be made consistent? It looks like the name 'sinus' is confusing the classification.

Thanks, Pascale

[shawntanzk]

@bvarner-ebi assigning this to you - please bring up in meetings etc. if need be. Thanks

[ghost]

@pgaudet, could you briefly summarise the reasoning problem related to this specific term? I skimmed geneontology/go-ontology#16524, but it's not clear to me what the reasoning problem is that involves 'pronephric sinus'.

Notes:

from https://pubmed.ncbi.nlm.nih.gov/10535314/:

The term in the Xenopus Anatomy Ontology has "system of vessels" in the definition and classifies it as an "anatomical space". This term is cross referenced to UBERON:0006174 'pronephric sinus'.

Full definition from XAO: "A system of vessels that initially swell from where the anterior and posterior cardinal veins meet before draining into the heart via the duct of Cuvier at NF stage 33 and 34, and then continue to narrow and fold into a characteristic S-shape by NF stage 37 and 38. It continues to loop on itself, at first a loose, then a dense knot of many vessels by NF stage 45."

Excerpts from https://pubmed.ncbi.nlm.nih.gov/10535314/:
"The convoluted pronephric tubules are permeated with venous blood vessels that arise in close association with the posterior cardinal vein to form the pronephric sinus (Millard, 1949)."
"Endothelial cells will contribute to the pronephric sinus and the vasculature of the glomus."
"Blood from the posterior cardinal vein flows through the pronephric sinus, an ill-defined capillary network between the tubules, to return resorbed solutes to the circulatory system."

Proposal:

Change EA of 'pronephric sinus' from:

'renal sinus'
and ('part of' some pronephros)

to

'capillary plexus'
and ('part of' some pronephros)

or

'vascular plexus'
and ('part of' some pronephros)

I'm not sure if this is a full solution, but would it at least address the concern of having 'sinus' in the EA?

[balhoff]

@bvarner-ebi I think this issue is subsumed by #2218.

[ghost]

Thank you, @balhoff. In that case, should this issue be closed?

[balhoff]

I think it could be, maybe your solution could be applied to the other issue. Basically we just need the term to be a material structure rather than an immaterial one.

[ghost]

Thank you, @balhoff.
@pgaudet, kindly advise how you would like to proceed.

[pgaudet]

Yes we can close this, thanks.

[cmungall]

The issue was solved in GO by removing the logical definition!

And there is still an issue with Uberon. The definition conflicts with the placement