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#11766 Add do_not_manually_annotate tag to metabolic process
Most direct annotations are either
- GOC (ie inferred from catalytic activity -> metabolic process)
- IEA
- RCA
I see no reason for a curator to manually annotate to as high level as metabolic process. We should add the tag (which should also prevent the GAF inferences).
What level was discussed as "high level"?
This is a subjective call on my part
The original driver for this request was propagation from catalytic activity -> metabolic process via part_of
Maybe this link should be removed?
Hi Chris,
I also agree that metabolic process is high level but of course everything is subjective. The definition of metabolic process is very large "The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation. "
I would say that not all catalytic reactions contribute to metabolic process; does that sound right ?
Pascale
Functions like the activity of nucleases on DNA substrates or kinases on protein substrates certainly stretch the classic biochemistry definition of metabolism, I don't see (full disclosure: am funded not to see) a clear, qualitative distinction between glycolysis and FGFR-mediated signaling.
Going in another direction, though, it's hard to imagine a case where there is solid experimental data to show that a protein is an enzyme but yet no usable data about the domain of biology where it functions, so it's hard to imagine why a curator would need to go to this level of abstraction.
Peter,
Just so I am clear: are you saying there is no need to annotate manually to metabolic process ?
I can't think of an example (but others have done a lot more annotation than I have).
My initial comment was made before my coffee had kicked in and I was thinking you meant high level metabolic process terms, vs. the specific term GO:0008152 ! metabolic process. For the latter, yes, do not annotate, and there are probably children that should also be do not annotate, such as GO:0044237 ! cellular metabolic process. I'm not sure whether one can distinguish catabolic vs biosynthetic processes without being able to assign a more specific child. My question was where to draw the lines.
Peter, I can think of cases where enzyme activities are known but the biological process is unclear. For example, my colleague Margy Glasner works on a family of proteins that include o-succinylbenzoate synthase (OSBS) activities involved in menaquinone (vitamin K) biosynthesis. But members of the same family, and sometimes the same enzymes also catalyze N-succinylamino acid racemization (NSAR). In some cases the relevant activity is inferred from genomic context, but in other cases activity is known from the purified protein, but evidence is lacking about the biological role. Moreover, what the NSAR is for is not clear.
There are other examples that are related to the way enzymologists work, especially from how enzymes were chosen for study in the early days. In some cases proteins were purified based on things like the color of specific cofactors. For example, S. cerevisiae OYE2 encodes Old Yellow Enzyme, which is annotated in SGD to apoptotic process. The physiological role of OYE is still unclear, despite being studied by enzymologists for many years.
Hi Jim,
Thanks for the caffeinated comments !
Maybe that was implied, but : One last thing: even in a case like you describe, where the general process of an enzymatic activity is not known, you wouldn't annotate to metabolic process or cellular metabolic process, would you ?
Thanks,
Pascale
Pascale, you are correct that I would not. Just addressing Peter's comment above about whether it might arise during curation.
Added the do not annotate tag.
I agree, we never use "metabolic process" .....and have it flagged internally as "do not annotate"