feat: add 19 new GPR and consolidate curations between model releases

[cheng-yu-zhang]

Main improvements in this PR:

Add 19 new GPR accoording to SGD and uniprot.

1. new GPRs are in "databasenewGPR.tsv"
2. the proof of the new GPR is in "databasenewGPR_proof.tsv"
3. the detailed new genes are in "databaseNewGPRGenes.tsv"
4. the result of single gene deletion analysis is 0.8989.

This PR is used to demonstrate consolidation of multiple curations in one script, that can convert a previous model release to the next version.

I hereby confirm that I have:

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

[edkerk]

You should make new feature branches of a recent devel branch, this one is derived from a devel commit from last December.

In addition, please do not modify existing curation files, but make new file/folders in code/modelCuration and data/modelCuration. This prevents confusion on what are new curations and old curations.

[edkerk]

I have rebased this onto the most recent devel branch and refactored the datafiles to be contained in their own folder.

Metric	yeast-GEM 8.6.0	this PR
Number of genes	1151	1153
Accuracy	0.8801	0.8810
TP	923	923
TN	61	62
FP	98	97
FN	36	36

[edkerk]

FYI, I'm "hijacking" this PR to demonstrate how to consolidate curation from a particular model version towards the next release. For the moment I've also already merged #305 and #306 to hear, to combine all three curations in one consolidated script.

[edkerk]

Please run /code/modelCuration/v8_6_0.m to test the consolidated curation of #305, #306 and this PR. This new curation pipeline is introduced here, let's test it out for a while to see whether it functions well.

Otherwise, there are a few concerns to look at, @cheng-yu-zhang @feiranl.

[cheng-yu-zhang]

@edkerk When I run "/code/modelCuration/v8_6_0.m", I find that there is a extra parameter "grRatioMuts" in line 44 of the "essentialGenes.m", which may cause some issues.
[genes, fluxes, originalGenes, details, grRatioMuts]=findGeneDeletions(model,'sgd','fba');
[genes, fluxes, originalGenes, details]=findGeneDeletions(model,testType,analysisType,refModel,oeFactor)
Apart from that, this pipeline works well.

[edkerk]

When I run "/code/modelCuration/v8_6_0.m", I find that there is a extra parameter "grRatioMuts" in line 44 of the "essentialGenes.m", which may cause some issues. [genes, fluxes, originalGenes, details, grRatioMuts]=findGeneDeletions(model,'sgd','fba'); [genes, fluxes, originalGenes, details]=findGeneDeletions(model,testType,analysisType,refModel,oeFactor) Apart from that, this pipeline works well.

Great, this behaviour of essentialGenes is expected as long as SysBioChalmers/RAVEN#421 is not merged.

[edkerk]

• Note that all changes should be documented in a script, see for instance:

  yeast-GEM/code/modelCuration/v8_6_0.m

  Lines 55 to 57 in 43d4d14

  	model = setParam(model,'lb','r_4232',-1000);
  	model = setParam(model,'rev','r_4232',1);
  	model = removeReactions(model,'r_4566',true,true,true);

• Note that removal of a reaction remains complete removal, not just blocking by setting LB and UB to 0, so not:

  yeast-GEM/model/yeast-GEM.txt

  Line 3927 in eab45b9

  r_4566 6-phospho-D-gluconate[c] + ADP[c] + H+[c] => ATP[c] + D-gluconate[c] YDR248C 0.00 0.00 0.00