fix-rxn-prop:addNewGPRrelations

[feiranl]

Main improvements in this PR:

• This improvement is based on genome annotation for Saccharomyces cerevisiae S288c from five databases (SGD, Uniprot, KEGG, Biocyc and Reactome). Reactions linked to these new annotated genes were extracted from those databases (Uniprot, KEGG, Biocyc and Reactome) and by searching annotated EC numbers in different databases (Rhea and Brenda).
• Add database new annotation detailed information in ComplementaryData/databases/DBnewGeneAnnotation.tsv.
• Add new GPR relations for existing reactions according to database new annotation.

Addresses issue #60

I hereby confirm that I have:

• Tested my code with all requirements for running the model
• Selected devel as a target branch (top left drop-down menu)
• If needed, asked first in the Gitter chat room about this PR

[edkerk]

Structurally it looks fine, but it would good to see a brief description on how these GPRs were decided. Doesn't have to be very detailed, but now this is entirely unclear. Can be mentioned in this PR, or could have been in commit messages, but now it is not mentioned anywhere.

[BenjaSanchez]

@edkerk the reasoning behind each change can be found in DBnewGeneAnnotation.tsv (sadly too big to be properly seen on Github, but you can open it locally with Excel), which contains all new genes added. For instance, rxn r_0005 has an additional gene YMR306W in the gene rule. If you go to DBnewGeneAnnotation.tsv and search for YMR306W, you'll find that it catalyzes indeed that reaction according to all databases used. The same can be done for all other changes.

[edkerk]

As discussed, please provide a short description of where the information regarding gene annotations is coming from, by editing the original pull request message.

[hongzhonglu]

@feiranl could you check 'YAR073W', which may be pseudogene? We should remove gene like this to make sure the quality.

[BenjaSanchez]

@feiranl @hongzhonglu any remaining changes? if none I will merge in the afternoon.

[hongzhonglu]

@BenjaSanchez No changes from my side.

[feiranl]

@BenjaSanchez No changes from my side.