Fix: GPR curation for Leukotriene metabolism

[JHL-452b]

Main improvements in this PR:

As proposed in #867 #868 #869 #870

• Remove ENSG00000186908, ENSG00000172197, ENSG00000174165, ENSG00000171307, ENSG00000123684, ENSG00000135372, ENSG00000100344, ENSG00000173418, ENSG00000176454, ENSG00000243477, ENSG00000163958, ENSG00000023041, ENSG00000184307, ENSG00000121579, ENSG00000103066, ENSG00000144035, ENSG00000054392, ENSG00000184210, ENSG00000177108, ENSG00000204160, ENSG00000143797, ENSG00000102312, ENSG00000180776, ENSG00000203972 from MAR01088;
• Remove ENSG00000172954, ENSG00000110583, ENSG00000184210, ENSG00000111684, ENSG00000184307, ENSG00000171307, ENSG00000203972, ENSG00000204160, ENSG00000123684, ENSG00000100344, ENSG00000109065, ENSG00000177669, ENSG00000180776, ENSG00000156599, ENSG00000136247, ENSG00000171320, ENSG00000160446, ENSG00000054392, ENSG00000173418, ENSG00000176454, ENSG00000125505 from MAR01091;
• Remove ENSG00000121039, ENSG00000176387, ENSG00000087076, ENSG00000160439 from MAR01098;
• Remove ENSG00000159228 from MAR01103;
• Remove ENSG00000148344 from MAR01119;
• Remove ENSG00000196616 from MAR01129;
• Remove ENSG00000196616 from MAR01130;
• Remove ENSG00000137869, ENSG00000108242, ENSG00000186526 from MAR01149;
• Remove ENSG00000106258, ENSG00000186377, ENSG00000100197 from MAR01150;
• Remove ENSG00000160870, ENSG00000137869, ENSG00000108242, ENSG00000197408 from MAR01151;
• Remove ENSG00000137869 from MAR01152;
• Remove ENSG00000100197, ENSG00000137869, ENSG00000108242, ENSG00000186204 from MAR01154;
• Remove ENSG00000160870, ENSG00000137869, ENSG00000186204, ENSG00000186526 from MAR01155;
• Remove ENSG00000160870, ENSG00000138109, ENSG00000186526 from MAR01156;
• Remove ENSG00000108242, ENSG00000137869 from MAR01193;
• Remove ENSG00000108242 from MAR01195;
• Remove ENSG00000196616 from MAR01288;
• Remove ENSG00000141096 from MAR01085;
• Remove ENSG00000196616, ENSG00000147576 from MAR01131;
• Remove ENSG00000186160, ENSG00000137869, ENSG00000186204 from MAR01153;
• Remove ENSG00000108242 from MAR01194;
• Remove ENSG00000159228 from MAR01106;
• Remove ENSG00000186526, ENSG00000138109 from MAR01196;
• Remove ENSG00000161533 from MAR01205;
• Remove ENSG00000159228 from MAR01101;
• Remove ENSG00000054392, ENSG00000141096, ENSG00000171307, ENSG00000173418, ENSG00000180776, ENSG00000184210, ENSG00000184307, ENSG00000203972, ENSG00000204160 from the model as they are connected no reaction after this curation.

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

[github-actions]

This PR has been automatically tested with GH Actions. Here is the output of the MACAW test:

Starting dead-end test...
 - Found 1523 dead-end metabolites.
 - Found 1328 reactions incapable of sustaining steady-state fluxes in either direction due to these dead-ends.
 - Found 1975 reversible reactions that can only carry steady-state fluxes in a single direction due to dead-ends.
Starting duplicate test...
 - Skipping redox duplicates because no redox_pairs and/or proton_ids were provided.
 - Found 447 reactions that were some type of duplicate:
   - 0 were completely identical to at least one other reaction.
   - 13 involve the same metabolites but go in the opposite direction or have the opposite reversibility as at least one other reaction.
   - 447 involve the same metabolites but with different coefficients as at least one other reaction.

This and a more detailed output from MACAW are also committed to data/macawResults/.

Note: In the case of multiple test runs, this post will be edited.

[hhl-24]

Remove ENSG00000159228 from MAR01103; Remove ENSG00000159228 from MAR01101;

as proposed in 868, since ENSG00000159228 and ENSG00000159231 are located in the cytosol, and ENSG00000157326 is in the nucleus and peroxisome, they should be removed from MAR01101 [m] and MAR01103 [r]. Others look good to me.

[JHL-452b]

Yes, because these weren't caught by GPT. My idea is to fix them in another PR.

[hhl-24]

Yes, because these weren't caught by GPT. My idea is to fix them in another PR.

I see.

[hhl-24]

LGTM!