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Fix: GPR curation of Bile_acid_biosynthesis/recycling #930

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merged 3 commits into from
Dec 17, 2024

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JHL-452b
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@JHL-452b JHL-452b commented Dec 5, 2024

Main improvements in this PR:

As proposed in #856

  • Remove ENSG00000130822, ENSG00000130821 from MAR01659;
  • Change the GPR of MAR01716 into ENSG00000184227 or ENSG00000097021 or ENSG00000136881;
  • Change the GPR of MAR01718 into ENSG00000177465 or ENSG00000101473 or ENSG00000136881;
  • Remove ENSG00000140284 from MAR01726;
  • Remove ENSG00000170786, ENSG00000160439 from MAR01813;
  • Remove ENSG00000136750 from MAR03910;
  • Remove ENSG00000128683, ENSG00000136750 from MAR08065;
  • Change the GPR of MAR01786 into ENSG00000135929;
  • Remove ENSG00000021488 from MAR01875;
  • Remove ENSG00000021488 from MAR01877;
  • Remove ENSG00000021488 from MAR01880;
  • Remove ENSG00000021488 from MAR01881;
  • Remove ENSG00000021488 from MAR01882;
  • Remove ENSG00000021488 from MAR01883;
  • Remove ENSG00000021488 from MAR01885;
  • Remove ENSG00000021488 from MAR01886;
  • Remove ENSG00000021488 from MAR01887;
  • Remove ENSG00000021488 from MAR01889;
  • Remove ENSG00000021488 from MAR01890;
  • Remove ENSG00000021488 from MAR01891;
  • Remove ENSG00000021488 from MAR01894;
  • Remove ENSG00000021488 from MAR01876;
  • Remove ENSG00000021488 from MAR01884;
  • Remove ENSG00000021488 from MAR01888.

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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github-actions bot commented Dec 5, 2024

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.

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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@feiranl feiranl left a comment

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LGTM!

…ynthesis_and-recycling

# Conflicts:
#	data/testResults/README.md
@edkerk edkerk merged commit d3472ad into develop Dec 17, 2024
0 of 4 checks passed
@edkerk edkerk deleted the Fix-Bile_acid_biosynthesis_and-recycling branch December 17, 2024 00:59
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3 participants