Taxon rule for 'urinary bladder' #454

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paolaroncaglia opened this Issue May 20, 2014 · 2 comments

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@paolaroncaglia

Hi,

Stemming from a user's request on the GO SourceForge tracker:
is the 'urinary bladder' found in Paleognathae birds such as ostriches and rhea (but not in Neognathae birds such as chicken or turkey) a 'real' urinary bladder, i.e. developed from the cloaca into a separate anatomical structures? Or is it rather an 'undifferentiated' portion of the cloaca?

The uncertainty comes from these statements:

"homology_notes: In tetrapods, the urinary bladder arises as an outpocketing of the cloaca. (...) The tetrapod urinary bladder appears first among amphibians and is present in Sphenodon, turtles, most lizards, ostriches among birds, and all mammals.[well established][VHOG]"
(http://www.ontobee.org/browser/rdf.php?o=UBERON&iri=http://purl.obolibrary.org/obo/UBERON_0001255)

However, the references that the GO user provided say that ostrich and rhea don't have a proper urinary bladder, but, differently from other birds, they store urine separately in an expansion of the cloaca.
(See e.g. http://en.wikipedia.org/wiki/Rhea_(bird)#Description)

The ultimate question for GO is whether we should restrict the terms 'urinary bladder development' and 'urinary bladder smooth muscle contraction' to never_in_taxon Aves (i.e. both Paleognathae and Neognathae) or just to Neognathae.

GO SF ticket for reference:
https://sourceforge.net/p/geneontology/ontology-requests/10840/

Thanks,
Paola

@ANiknejad

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ANiknejad May 21, 2014

Hi Paula,

For urinary bladder, we report the following assertions:
(This one is the one you mentioned, currently reported in Uberon as 'homology notes)

ISBN:978-0072528305 "Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.577-78"
ECO:issue22 phylogenetic distribution
CONF:0000004 Medium confidence assertion
32523 Tetrapoda
"In tetrapods, the urinary bladder arises as an outpocketing of the cloaca. (...) The tetrapod urinary bladder appears first among amphibians and is present in Sphenodon, turtles, most lizards, ostriches among birds, and all mammals."

In our new process to expand and annotate an homology assertion by linking to a defined taxonomy, we also report this reference (PMID:538956 "Bentley PJ, The vertebrate urinary bladder: osmoregulatory and other uses. Yale J Biol Med (1979)"9

"Urinary bladders appear to have evolved in vertebrates at least twice, which suggests that they are useful. In tetrapods the bladder is an endodermal structure which arises as an outgrowth of the cloaca. In amniotes it gives rise to the embryonic allantoic membrane, part of which may persist as the bladder in the adult. While a bladder does not occur in birds the allantois remains an important organ during its development in the egg. The fish bladder is embryologically quite different to the tetrapod bladder and is mesodermal in origin, arising as an expansion of the mesonephoric ducts. It is thus really an extension of the kidney."

From this assertion we capture the 'urinary bladder' as an organ potentially already present into the ancestor of Tetrapoda (taxon ID 32523) , but also as an organ that potentially evolves into a more specific organ in Amniota (taxon ID 32524).

Current structures in living animals do not necessary have the same shape than the homologous one in their common ancestor. However regarding the definition of GO terms 'urinary bladder development' and 'urinary bladder smooth muscle contraction', I would say that
'urinary bladder development' and 'urinary bladder smooth muscle contraction' will be linked to Amniota taxon and restricted by 'never_in_taxon Aves (taxon ID 8782)

Hope these comments help.

Anne

Biocurator
Bgee team (http://bgee.unil.ch)
SIB Swiss Institute of Bioinformatics
Dept Ecology & Evolution
Biophore, UNIL-Sorge
UNIL-CH-1015 Lausanne
Switzerland

Hi Paula,

For urinary bladder, we report the following assertions:
(This one is the one you mentioned, currently reported in Uberon as 'homology notes)

ISBN:978-0072528305 "Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.577-78"
ECO:issue22 phylogenetic distribution
CONF:0000004 Medium confidence assertion
32523 Tetrapoda
"In tetrapods, the urinary bladder arises as an outpocketing of the cloaca. (...) The tetrapod urinary bladder appears first among amphibians and is present in Sphenodon, turtles, most lizards, ostriches among birds, and all mammals."

In our new process to expand and annotate an homology assertion by linking to a defined taxonomy, we also report this reference (PMID:538956 "Bentley PJ, The vertebrate urinary bladder: osmoregulatory and other uses. Yale J Biol Med (1979)"9

"Urinary bladders appear to have evolved in vertebrates at least twice, which suggests that they are useful. In tetrapods the bladder is an endodermal structure which arises as an outgrowth of the cloaca. In amniotes it gives rise to the embryonic allantoic membrane, part of which may persist as the bladder in the adult. While a bladder does not occur in birds the allantois remains an important organ during its development in the egg. The fish bladder is embryologically quite different to the tetrapod bladder and is mesodermal in origin, arising as an expansion of the mesonephoric ducts. It is thus really an extension of the kidney."

From this assertion we capture the 'urinary bladder' as an organ potentially already present into the ancestor of Tetrapoda (taxon ID 32523) , but also as an organ that potentially evolves into a more specific organ in Amniota (taxon ID 32524).

Current structures in living animals do not necessary have the same shape than the homologous one in their common ancestor. However regarding the definition of GO terms 'urinary bladder development' and 'urinary bladder smooth muscle contraction', I would say that
'urinary bladder development' and 'urinary bladder smooth muscle contraction' will be linked to Amniota taxon and restricted by 'never_in_taxon Aves (taxon ID 8782)

Hope these comments help.

Anne

Biocurator
Bgee team (http://bgee.unil.ch)
SIB Swiss Institute of Bioinformatics
Dept Ecology & Evolution
Biophore, UNIL-Sorge
UNIL-CH-1015 Lausanne
Switzerland

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paolaroncaglia Jun 16, 2014

Hi Anne,
Many thanks for your very useful feedback, and sorry for the delay!
Best,
Paola.

Hi Anne,
Many thanks for your very useful feedback, and sorry for the delay!
Best,
Paola.

@gocentral gocentral referenced this issue in geneontology/go-ontology Jul 25, 2015

Closed

Taxon rules for several terms #11025

@cmungall cmungall closed this in b4f0292 Sep 22, 2015

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