Make outputs of salvage processes primary outputs

[ukemi]

We noticed this morning that many of the logical definitions of salvage processes have an output of the chemical specified in the term. If we want these to auto-classify correctly in the metabolism branch of the ontology these should be changed to primary outputs. There are also a lot of asserted sub-classifications in this branch of the ontology that I think are unnecessary once the correct logical defs are in place. One question with respect to this is whether all salvage would be considered a subclass of biosynthesis or are only some or are none. This relationship will need to be asserted at the appropriate generic level. @deustp01 I know we had hand-waived and decided that the nucleotide salvage made sense to be a biosynthetic process, but we were a little unsure. This would be the time to nail this down for the various salvage processes.

[deustp01]

I know we had hand-waived

There's a general ontology question here. Can there be metabolism that is neither synthesis nor catabolism?

If not, then salvage has to be biosynthesis because it's always working towards the goal of preserving and reusing an existing molecule, preventing that molecule from entering an irreversible catabolic process.

But if there can be metabolic processes that are neither synthesis nor catabolism, then nucleotide salvage and also the reactions labeled "nucleotide interconversion", e.g., GMP + ATP => GDP+ ADP, could plausibly go in that category.

I think both salvage and interconversion are good enough fits to synthesis so that, if there is not already a category of non-synthetic non-catabolic metabolism, this is not a reason to go and create it now, though. And anyway this is a tangent to the main issue, that specifying primary outputs will be a really useful clean-up for both human and computer users.

[ukemi]

Salvage could be it's own class, distinct from biosynthesis and catabolism. But since it is still metabolic, we would need the 'primary' distinction in the logical defs. We haven't gotten to interconversion yet. I still have questions for you about that for a future Thursday afternoon.

[ukemi]

Thinking about this a bit more, although I think we should discuss it too, it might make sense to have the salvage as separate metabolic processes. This would allow us to distinguish it from 'de novo' biosynthesis. Otherwise things would be lumped together unless we did some trickery to create sibling biosynthetic processes that were distinct. One thing we toyed with was going the old route of 'x biosynthesis from y'. Not sure how well that would be received.

[ukemi]

Plus, keeping them separate would also parallel the arrangement in Reactome: biosynthesis, catabolism, salvage and interconversion are all 'sibs' under metabolism in the hierarchy.

[deustp01]

Combining bits of @ukemi 's last three comments to say it's a hard problem. First, whatever sibling categories we choose, clear boundary conditions are needed, and the salvage / synthesis / interconversion boundaries look tricky. Specifying start and end points, e.g., 'x biosynthesis from y' can do this at the expense of making a structure that is detailed (too granular?) and potentially rigid and complicated to maintain - e.g., how does the structure perform when extended from mammalian metabolism to bacterial?

To be clear - keeping the terms as separate siblings is a good fit to textbook biochemistry and existing Reactome structure, if these other issues can be avoided or handled well.

[hdrabkin]

changed to 'has primary output' for AMP salvage GMP salvage IMP salvage XMP salvage purine nucleotide salvage

[hdrabkin]

@ukemi do the changes I did on Jun 18 sufficient to close this?

[ukemi]

Looks like it.