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Fix-GPR curation for Galactose, Fructose and mannose metabolism #886

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Main improvements in this PR:

As proposed in #849

  • Remove ENSG00000171298 from MAR04303;
  • Remove ENSG00000198074 from MAR04316;
  • Remove ENSG00000141560, ENSG00000172456, ENSG00000167363, ENSG00000162408 from MAR04317;
  • Remove ENSG00000141560, ENSG00000162408, ENSG00000116199 from MAR04318;
  • Remove ENSG00000141560, ENSG00000172456, ENSG00000167363, ENSG00000162408 from MAR04320;
  • Remove ENSG00000100413 from MAR04385;
  • Remove ENSG00000164068 from MAR04386;
  • Remove ENSG00000116783 from MAR04401;
  • Remove ENSG00000241343 from MAR04416;
  • Remove ENSG00000198074 from MAR08766;
  • Remove ENSG00000116783 and ENSG00000241343 from model as they are not connected to any reactions after this curation.
  • Add PMID:2469615;PMID:19158351 to the references of MAR08761 and MAR01472.

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 1514 dead-end metabolites.
- Found 1319 reactions incapable of sustaining steady-state fluxes in either direction due to these dead-ends.
- Found 1977 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.

A more detailed output from this test run is also committed to data/macawResults/macaw_results.csv.

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

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