Fix GPRs of mitochondrial beta-oxidation reactions with peroxisomal genes

[Devlin-Moyer]

Main improvements in this PR:

Updates all GPRs mentioned in #634
Since those GPR changes would leave ACAD11 (ENSG00000240303) associated with no reactions, also:

• Adds ACAD11 to GPRs of MAR03107 and MAR03111
• Adds PMID:21237683 to lists of references for MAR03107 and MAR03111

I hereby confirm that I have:

• Tested my code on my own computer for running the model
• Selected develop as a target branch
• Any removed reactions and metabolites have been moved to the corresponding deprecated identifier lists

[Devlin-Moyer]

Tests are failing cuz after changing all of those GPRs, ACAD10 (ENSG00000111271) and ACAD11 (ENSG00000240303) are no longer associated with any reactions.

According to Uniprot, ACAD11 is known to catalyze MAR03107 and MAR03111, so I'm just gonna add it to those GPRs to stop the error

Uniprot says ACAD10 can only act on (R)- and (S)-2-methyl-pentadecanoyl-CoA, citing this paper, which clarified that, while those were the only substrates they observed ACAD10 to act on, the activity was low enough that they doubted either was the main substrate in vivo. I can't seem to find any other papers that ever showed that ACAD10 can act on anything else; should I just remove it from the model altogether, or figure out how many other reactions I'd need to add to connect 2-methyl-pentadecanoyl-CoA to the rest of the network?

[haowang-bioinfo]

Uniprot says ACAD10 can only act on (R)- and (S)-2-methyl-pentadecanoyl-CoA, citing this paper, which clarified that, while those were the only substrates they observed ACAD10 to act on, the activity was low enough that they doubted either was the main substrate in vivo. I can't seem to find any other papers that ever showed that ACAD10 can act on anything else; should I just remove it from the model altogether, or figure out how many other reactions I'd need to add to connect 2-methyl-pentadecanoyl-CoA to the rest of the network?

based on the evidence provided, it seems that ACAD10 should be removed from the model

[haowang-bioinfo]

Modification of 100+ GPRs is too big to be implemented at once, because it is error-prone in making changes and hard to review, and should be avoided in future.

[pranasag]

Tremendous work @Devlin-Moyer! I will have a look at this in the following days (and agree with @haowang-bioinfo, a big chunk to digest at once), but maybe let's start with moving ENSG00000111271 to the deprecated genes' list so the sanity checks from the Actions can proceed

[haowang-bioinfo]

I believe the work of this PR is commendable and truly impressive, yet I must express some concerns regarding the current state. As it stands, the PR appears quite extensive and complex, posing a challenge for effective review and integration in a single session.

As reviewers, we have a responsibility to the community to uphold the quality of the model. Over time, without thorough checks, the model could degrade from unchecked changes. To facilitate a more effective and pragmatic review process for this PR, there might be two possible options:

1. Enhance the PR by including the code with detailed comments should clearly articulate the rationale and specifics of the changes implemented. This approach allows for a more informed and thorough review.

2. Alternatively, consider closing this PR and dividing it into several smaller, more manageable segments. Each segment should be self-contained and straightforward enough to undergo manual inspection. This method would simplify the review process, ensuring each change is meticulously examined and validated.

[Devlin-Moyer]

I went back through all of the reactions whose GPRs I edited here and I found that a lot of them had other problems that seemed like they merited separate issues, so I've updated #634 to have a much shorter list of reactions and also tried to add a bit more information that hopefully makes it easier for y'all to fact check it; I'm gonna close this PR now

[haowang-bioinfo]

I went back through all of the reactions whose GPRs I edited here and I found that a lot of them had other problems that seemed like they merited separate issues, so I've updated #634 to have a much shorter list of reactions and also tried to add a bit more information that hopefully makes it easier for y'all to fact check itI went back through all of the reactions whose GPRs I edited here and I found that a lot of them had other problems that seemed like they merited separate issues, so I've updated #634 to have a much shorter list of reactions and also tried to add a bit more information that hopefully makes it easier for y'all to fact check it

thanks