Obsoletion request: hypoxanthine salvage GO:0043103

[ValWood]

Please provide as much information as you can:

• GO term ID and Label

GO:0043103 hypoxanthine salvage

• Reason for deprecation Put an x in the appropriate box:

• The reason for obsoletion is that this term was an unnecessary grouping term.

I'm not sure that we need this term. hypoxanthine appears to be an intermediate in IMP salvage. We noticed when modelling nucleotide metabolism, that this BP term was only used for 2 steps in the the IMP salvage pathway.

See
http://noctua.geneontology.org/workbench/noctua-visual-pathway-editor/?barista_token=b9lbuk0h1mdk0h925a9l&model_id=gomodel:663d668500001911

@pgaudet @deustp01 do you agree?

• "Replace by" term (ID and label)
  If all annotations can safely be moved to that term

IMP salvage

• Are there annotations to this term?

• How many EXP: 6

PomBase 2
SGD 2
UniProt 1
E coli wiki 1

• Are there mappings and cross references to this term? (InterPro, Keywords; check QuickGO cross-references section)

• Is this term in a subset? (check the AmiGO page for that term)

• Any other information

---

CC @PCarme

[deustp01]

do you agree?

We don't subdivide the process of purine catabolism, seeing it as an interconnected single process, so the obsoletion looks fine to me, but also ask David @ukemi - he's the local expert.

[ValWood]

It seems to be used for Aah1/Dea2, Hpt1/HPRT1 which have hypoxanthine as input/output

[ukemi]

I suspect it is there because of clinical significance. eg. PMID:3818951

[ValWood]

Is that a reason to include it as a term? The activities will be there and the overall process.

We could add "hypoxanthine salvage" as a related synonym for "IMP salvage" and any other end points?

@pgaudet

[ValWood]

@pgaudet do you agree with this change?

[pgaudet]

I dont know, you write that it's an unnecessary grouping term, but I dont see any children.

[ValWood]

I mean it's an unecessary intermediate, I don't know what we call that. It's an intermediate in IMP salvage (and possibly othernucleotide salvage pathways)

[pgaudet]

Is it? Here it seems to be an 'input' :
2023 review:
https://www.sciencedirect.com/science/article/pii/S0028390822004294

[pgaudet]

Granted, it's quite underannotated. What we need to think about how to clearly define this pathway with a start and end. In this case hypoxanthine may be the start of some purine salvage pathway.

[ValWood]

The pathway begins with adenine
It is an input.

So, we have
dea2 an adenine deaminase annotated to IMP salvage and hypoxanthine salvage

Then the next step
hpt1 hypoxanthine phosphoribosyltransferase activity
creates IMP from hypoxanthine

the hypoxanthine salvage seems unnecessary if it isn't an endpoint.

[ValWood]

There may be other starting points but hypoxanthine isn't the end point?

[deustp01]

this case hypoxanthine may be the start of some purine salvage pathway.

For what it's worth, here is our view of the purine salvage and catabolism processes in humans. We treat hypoxanthine as one of the start points for catabolism and it is one of the molecules generated by salvage so it could be an end point there.

[ValWood]

I'm happy to close this one.

A couple of weeks ago, instead of opening tickets, I began a list of process terms that seemed superfluous to the GO-CAM models (i.e. because they seemed like an intermediate step rather than a start point or end point)
When I began opening tickets I didn't think there would be so many.

It will probably be better to review these at the end in case we missed something or if there are organism-specific differences.

I will continue to open tickets if there is a clear-cut case, but this one seems more cpmplicated

@deustp01 I tried to look at
https://reactome.org/PathwayBrowser/#/R-HSA-74217 but I could not get it to load. Is that just me?

[deustp01]

I could not get it to load.

It worked for me when I was composing the message, and also just now. We have been having intermittent loading problems, though, so try again and if the problem persists send a message to help@reactome.org. Thanks