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Fix: GPR curation for Estrogen and Steroid metabolism #948

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Main improvements in this PR:

As proposed in #851 :

  • Change the GPR of MAR01927 as ENSG00000140459 or ENSG00000138061, and add PMID:39395524 as additional references;
  • Change the GPR of MAR02029 as ENSG00000137869, and add PMID:34095690 as additional references;
  • Change the GPR of MAR02030 as ENSG00000137869, and add PMID:34095690 as additional references;
  • Change the GPR of MAR02031 as ENSG00000137869, and add PMID:34095690 as additional references;
  • Change the GPR of MAR02032 as ENSG00000137869, and add PMID:34095690 as additional references;
  • Change the GPR of MAR02033 as ENSG00000137869, and add PMID:34095690 as additional references;
  • Change the GPR of MAR02034 as ENSG00000137869, and add PMID:34095690 as additional references;
  • Change the GPR of MAR02038 as ENSG00000101846, and add PMID:37951289 as additional references;
  • Change the GPR of MAR07940 as ENSG00000137869, and add PMID:34095690 as additional references;
  • Change the GPR of MAR07941 as ENSG00000137869, and add PMID:34095690 as additional references;
  • Change the GPR of MAR07957 as ENSG00000137869, and add PMID:34095690 as additional references;
  • Remove ENSG00000155016, ENSG00000186377, ENSG00000186526 from MAR02042;
  • Remove ENSG00000108242, ENSG00000134716, ENSG00000186377 from MAR02043;
  • Remove ENSG00000186377, ENSG00000186160, ENSG00000186204, ENSG00000108242 from MAR02053;
  • Remove ENSG00000186204, ENSG00000155016, ENSG00000186377, ENSG00000186526 from MAR02054;
  • Remove ENSG00000115705 from MAR02077;
  • Remove ENSG00000115705 from MAR02089;
  • Remove ENSG00000137869 from MAR02458, MAR00947, MAR01156, MAR01155, MAR04051, MAR00994, MAR01196, MAR04055, MAR00950, MAR01154, MAR00955, MAR00942, MAR01149, MAR00931, MAR00954, MAR00937, MAR00935, MAR06658, MAR04090, MAR00951, MAR02457, MAR01150, MAR01193, MAR00992, MAR00938, MAR02456, MAR01152, MAR03788, MAR01195, MAR00934, MAR00936, MAR00991, MAR00948, MAR00993, MAR02455, MAR01194, MAR00933, MAR00944, MAR00940, MAR00943, MAR04041, MAR00939, MAR00946, MAR00956, MAR01151, MAR01153, MAR00932.

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

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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.

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LGTM!

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