obo-relations
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oborel
Add several post-translational modification relations under RO:0002436
As an addition to RO:0002447 (phosphorylates) and RO:0002480 (ubiquitinates), that occur under RO:0002436 (molecularly interacts with), I would suggest adding relationships for the following post-translational modifications, which all have corresponding functions with the Biological Expression Language (BEL) as well as corresponding Gene Ontology terms in the molecular function namespace:
| BEL Name | GO | GO Label |
|---|---|---|
| chap | GO:0044183 | protein binding involved in protein folding |
| gtp | GO:0005525 | GTP binding |
| kin (already present) | GO:0016301 | kinase activity |
| pep | GO:0008233 | peptidase activity |
| phos | GO:0016791 | phosphatase activity |
| ribo | GO:0003956 | NAD(P)+-protein-arginine ADP-ribosyltransferase activity |
| tscript | GO:0001071 | nucleic acid binding transcription factor activity |
| tport | GO:0005215 | transporter activity |
| gef | GO:0005085 | guanyl-nucleotide exchange factor activity |
| gap | GO:0032794 | GTPase activating protein binding |
There are also several other entries in cellular protein modification process (e.g., amination, nitration, polyamination, nitrosylation, neddylation, sumoylation, etc.) but let's just start by thinking about a couple concrete ones :)
I think many of these make sense following the form proposed by @cmungall (see: https://github.com/oborel/obo-relations/issues/259#issuecomment-424472190) with the addition of mf to represent one of these molecular functions that are a cellular protein modification process:
?a1 enabled_by ?gp1
?gp1 a ?mf
?mf a GO:'cellular protein modification process'
?a1 directly-regulates ?a2
?a2 enabled-by ?gp2
->
?gp1 XXX ?gp2
One caveat: a couple of these aren't "activities" but come from the "binding" tree. I'm also curious how one would handle those.
Yes I'm still interested in adding additional relationships (and reverse relationships). I'll update the issue header with some more information
It appears there are some issues with the build and these new terms are not being propagated. Unfortunately, of the issues/PRs/commits that were a follow-up to #521 are very cryptic:
- #586
- #587
- c2157c9f6a9e885bfe619196bee298066ec77edd
The new termsin the ro-edit.owl don't appear to be in the release files. e.g., a search in https://github.com/oborel/obo-relations/blob/master/ro.obo for myristolates currently shows nothing. Does this also means there's an overall problem with the build?
I'll look into the ODK migration branch I've been working on if the issue is still there.
@cthoyt I checked the IDs created in PR #586 and I could found in the last RO release. Try to search for myristoylates.
Yes, but that one was done by hand - I mean the remaining ones that we curated in https://github.com/oborel/obo-relations/blob/master/src/patterns/ro-interaction-relations-src.yaml to be generated via template are not getting propogated
Ok, I see it's a LinkML template, which we don't have in ODK. I could move the targets in the src/patterns/Makefile to ro.Makefile and generate the component. What do you think, @matentzn?
In case you missed it, the components are already generated in https://github.com/oborel/obo-relations/blob/master/src/patterns/ro-interaction-relations.ofn and https://github.com/oborel/obo-relations/blob/master/src/patterns/ro-interaction-relations.owl as an example