TPV - GO:0042450 'arginine biosynthetic process...'

[gocentral]

GO:0042450 'arginine biosynthetic process via ornithine' is_a GO:0006591 'ornithine metabolic process' is_a GO:0000051 'urea cycle intermediate biosynthetic process'. That path is true for ureotelic (urea-synthesizing and -excreting) organisms like humans and mice, but is false for uricotelic (uric acid-synthesizing and -excreting) organisms like reptiles and birds. The latter (at least, chickens) have the enzymes needed to synthesize arginine via ornithine, but lack functional cytosolic arginase and do not cleave the arginine to generate urea. GO:0006525 'arginine metabolic process' is a sibling of GO:0006591 and has the same true-pathway problem for the same reason.

Possible straightforward fix: delete the parent-child relationships between GO:0000051 (urea cycle) and its current children GO:0006525 (arginine metabolism) and GO:0006591 (ornithine metabolism).

More elaborate fix: make a new trio of sibs fairly high in the metabolism tree, "ureotelic nitrogen metabolic process", "uricotelic nitrogen metabolic process", and, for completeness, to include fish that simply excrete ammonia, "ammoniotelic metabolic process". This fix is certainly complicated and I'm not sure I can clearly see all of its consequences.

Peter

Reported by: deustp01

Original Ticket: "geneontology/ontology-requests/5210":https://sourceforge.net/p/geneontology/ontology-requests/5210

[gocentral]

Logged In: YES user_id=1101528 Originator: YES

A second thought about the possible simple fix. The urea cycle term (GO:0000051) has always looked too far up in the pathway hierarchy. For humans and chickens, it might make biological sense to make it an is_a child of GO:0042450 'arginine biosynthetic process via ornithine'. The idea is that urea synthesis is a special case of GO:0042450 - the synthesis of arginine via ornithine is a very well-conserved process among eukaryotes; some organisms (the ureotelic animals) carry out the additional step of hydrolyzing arginine to urea and ornithine on a large scale. (So the rearrangement may be OK more generally - fungi, etc.)

Note that, despite its place at the top of hierarchy, GO:0000051 has very few children, and all are closely related, so this rearrangement seems safe - unlikely to have unexpected cascading consequences throughout the biological_process ontology.

Peter

Original comment by: deustp01

[gocentral]

Logged In: YES user_id=436423 Originator: NO

Now that I'm looking at this closely, it occurs to me that GO:0000051 is analogous to the TCA cycle intermediate metabolism term (GO:0006100), which we made obsolete.

If we move GO:0000051 as you suggest, we would first have to move the child terms elsewhere, to avoid introducing different TPVs. All except GO:0000053, argininosuccinate metabolic process, already have another parent, so they pose no problem; I could easily re-home GO:0000053. But given the similarity to the TCA cycle case, do we really need GO:0000051 at all? Nothing is annotated directly to it, and, oddly, there's no relationship between it and 'urea cycle' (GO:0000050).

As for adding new terms, we would do so if annotators such as yourself would find them useful; otherwise, we probably won't bother. If you want them, I'll almost certainly come running for help crafting definitions.

midori

Original comment by: mah11

[gocentral]

Logged In: YES user_id=1101528 Originator: YES

For what I know about human and chicken, obsoletion of GO:0000051 (with the suggestion that GO:0000050 or the current children of GO:0000051 are better alternatives) solves the path problem; no new terms are needed.

Thanks.

Peter

Original comment by: deustp01

[gocentral]

Logged In: YES user_id=436423 Originator: NO

If obsoletion works for you, I'll set the process in motion.

m

Original comment by: mah11

[gocentral]

• assigned_to: nobody --> gomidori

Original comment by: mah11

[gocentral]

Logged In: YES user_id=436423 Originator: NO

email sent

Original comment by: mah11

[gocentral]

Logged In: YES user_id=436423 Originator: NO

GO:0000051 now obsolete

Original comment by: mah11

[gocentral]

• status: open --> closed-fixed

Original comment by: mah11