fix: remove genes not found in S288C annotation

[BenjaSanchez]

Description of the issue:

I was contacted by @snmendoz who pointed out that 2 of the current genes in the model cannot be found in the annotation of strain S288C, according to NCBI: YAR069W-A and YHR214W-F. @hongzhonglu do you see these genes in any of the newly added annotations? If so, are the annotations of those genes publicly available somewhere?

I hereby confirm that I have:

• Done this analysis in the master branch of the repository
• Checked that a similar issue does not exist already
• If needed, asked first in the Gitter chat room about the issue

[hongzhonglu]

@BenjaSanchez
These two genes could be found from SGD
https://www.yeastgenome.org/locus/S000125021
https://www.yeastgenome.org/locus/S000029723
They are not belong to S288c, but also for the yeast. These two genes are from iSce926.

[BenjaSanchez]

@hongzhonglu should then be removed? We should only keep genes belonging to the strain of the model I think.

[hongzhonglu]

@BenjaSanchez As we discussed in last meeting, the present yeast-GEM will be developed as pan-model of Saccharomyces cerevisiae. The strain specific model will be obtained based on yeast-GEM. In this case, it is OK to include these two genes.

[edkerk]

@BenjaSanchez @hongzhonglu The general yeast-GEM consensus model should describe one species also due to strain-specific gapfilling and curation, and s288c has been the standard for S .cerevisiae models. We schould schedule a meeting to brainstorm and formalize how to deal with non-S288c genes and reactions, I already have some ideas, and then decide on how to deal with these two genes and similar instances.

[hongzhonglu]

@edkerk @BenjaSanchez Great! We are also thinking about it. So when are you free?

[edkerk]

During our offline discussion on Monday we decided that yeast-GEM should remain S288c-specific, to stick with the long-running consensus that the S. cerevisiae GEMs are based on this strain. So non-S288c genes should be removed from this model.

[snmendoz]

Thanks a lot, @edkerk, @BenjaSanchez and @hongzhonglu . Now, my life is easier.