SysBioChalmers
Many reactions have GPRs but not EC number. Is it possible to fill them in somehow?
Description of the issue:
I'm currently working with GECKO3, and one of the ideas there is to work with the EC field in the model directly instead of identifying the EC. For Human-GEM, many reactions with GPRs have an empty EC field. Perhaps we could use getEnzymeCodes in GECKO2 to fill them in? Or has this been tried already?
I hereby confirm that I have:
- [ ] Tested my code on my own computer for running the model
- [ ] Done this analysis in the
mainbranch of the repository - [X] Checked that a similar issue does not exist already
I'm thinking we only replace the empty ones to stay on the safe side, right?
Another interesting thing - it seems that some reactions also have EC numbers but no GPRS - I'm thinking that filling in the GPRs for those may be possible? If we don't have the GPRs, ftINIT cannot use them, and GECKO will also have problems, at least if we want to use dlkcat.
I'm thinking we only replace the empty ones to stay on the safe side, right?
Yes, I agree
filling in the GPRs for those may be possible?
To me this sounds like a lot more work, and likely much less automatic unless one would use a tool such as GPRuler (which may take hundreds of hours on the cluster to run). From what I noticed, there isn't a general issue for GPR curation in this repo. My suggestion would then be to restrict the current issue to fill in missing ECs with GECKO, and open a new one for GPR curation.
@IVANDOMENZAIN Have you had time to look at this? I'm just thinking that for GECKO3 to work properly with Human-GEM, this needs to be fixed. It sounds like a quick thing to do, or did you run into trouble?