duplicated reactions

[snmendoz]

Description of the issue:

@BenjaSanchez I found 5 duplicated reactions. They are the same but written in the opposite direction.

1) 'r_2115' 'r_0163' '1 s_0359[c] + 1 s_0794[c] + 1 s_1203[c] -> 1 s_0680[c] + 1 s_1198[c]'
'1 s_0680[c] + 1 s_1198[c] -> 1 s_0359[c] + 1 s_0794[c] + 1 s_1203[c]'

2) 'r_0919' 'r_0342' '1 s_1085[er] + 1 s_1366[er] -> 1 s_0481[er]'
'1 s_0481[er] -> 1 s_1085[er] + 1 s_1366[er]'

3) 'r_0920' 'r_0343' '1 s_0507[er] + 1 s_1366[er] -> 1 s_0484[er]'
'1 s_0484[er] -> 1 s_0507[er] + 1 s_1366[er]'

4) 'r_1760' 'r_1148' '1 s_0666[c] <=> 1 s_0665[ce]'
'1 s_0665[ce] <=> 1 s_0666[c]'

5) 'r_4566' 'r_4232' '1 s_0340[c] + 1 s_0394[c] + 1 s_0794[c] -> 1 s_0434[c] + 1 s_3875[c]'
'1 s_0434[c] + 1 s_3875[c] -> 1 s_0340[c] + 1 s_0394[c] + 1 s_0794[c]'

I would suggest to remove one of each pair of duplicated reactions and change to reversible the reaction that is kept.

This new issue is in relation with the issue #172. It is important to avoid duplicated reactions because it would facilites the translation of the model to BIGG identifiers.

If there is a particular reason to keep these duplicated reactions? If there is can handle them for the translation to BIGG identifiers (#172). Please, tell me what you think or decide.

If you agree, please assign this task to me

I hereby confirm that I have:

• [X] Tested my code with all requirements for running the model
• [X] Done this analysis in the master branch of the repository
• [X] Checked that a similar issue does not exist already
• [X] If needed, asked first in the Gitter chat room about the issue

[BenjaSanchez]

@snmendoz no need imo to keep these duplicated rxns, any thoughts @hongzhonglu @feiranl?

[hongzhonglu]

@snmendoz @BenjaSanchez Are the enzymes ( or genes) same for these duplicated reactions?

[snmendoz]

@BenjaSanchez @hongzhonglu

No, they have different gene-associations. Maybe that's why they were included in this way in the first place.

[BenjaSanchez]

@snmendoz @hongzhonglu then when merging remember to also combine both grRules with "or" associations

[hongzhonglu]

@snmendoz @BenjaSanchez Not sure whether they can merged as different genes were connected for these duplicated reactions.

[BenjaSanchez]

adding to this discussion other duplicate rxns found by @hvdinh16

r_4235: duplicate of r_0534 r_4236: lumped reaction, duplicate of r_0697 + r_0553 r_4264: potential duplicate of r_0454

[BenjaSanchez]

Coming back to this, wrt to the 5 cases that @snmendoz pointed out, I agree with @hongzhonglu that if they have different gene rules then both of them should stay. From all 5 reactions, only 1 of them is a true duplicate, see below all info available for each one in the .yml file: So I think we can delete r_1760 from the model, will do that in PR #188. @hongzhonglu let me know what you think.

wrt to the 3 cases that @hvdinh16 pointed out:

• r_4235/r_0534: This one indeed seems to be a duplicate, the only stoichiometric difference is in that r_0534 is mass balanced so it has a proton (s_0794): so I can just add YDR516C to the gene rule of r_0534 and then delete r_4235, also in PR #188. @feiranl @hongzhonglu thoughts?

• r_4236/r_0697+r_0553: Here for simplicity I would keep all three, as the lumped one has several genes that otherwise we would loose, but as far as I could tell those genes were not associated to any of the two steps of the reaction, e.g. YDR533C (part of the r_4236 gene rule) is just described as "Methylglyoxalase that converts methylglyoxal to D-lactate", whereas [YML004C]() (controling r_0697) is described as "Monomeric glyoxalase I; catalyzes the detoxification of methylglyoxal (a by-product of glycolysis) via condensation with glutathione to produce S-D-lactoylglutathione".

• r_4264/r_0454: These are different reactions entirely, as one uses NADH as cofactor and the other one FADH2. So both should stay.

@snmendoz @hvdinh16 thanks for pointing these cases out!