Fix: subsystem changes and reaction deletion #171
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HMR_3851 is the only reaction in the "Nitrogen metabolism" subsystem, so this change also effectively removes this subsystem from the model.
Subsystem was duplicated with different capitalization
Evidence does not support the existence of this reaction in humans.
JonathanRob
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Note: I suggest we first merge #173 so I can update this branch with the new version of |
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@JonathanRob I agree to first merge #173, which is more heavyweight. |
command: git merge -Xtheirs devel
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The changes have been re-implemented after merging #173, and should now be ready for merge with |
haowang-bioinfo
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Jun 7, 2020
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- Modify rxn JSON file by removing the id that had been deleted in #171
This was referenced Jun 8, 2020
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Main improvements in this PR:
This PR makes a few small changes to address Issues #129 and #153.
Subsystem changes
Addresses Issue #129
Reaction
HMR_5407: CO2[s] + H2O[s] <=> carbonate[s]was the only reaction assigned to theNitrogen metabolismsubsystem. The subsystem for this reaction was changed toMiscellaneous, the same as the other compartment versions of this reaction (HMR_5406andHMR_8751in cytosol and mitochondia, respectively). This effectively removes the one-reactionNitrogen metabolismsubsystem.In addition, the capitalization of the
Metabolism of Other Amino Acidssubsystem was changed toMetabolism of other amino acids, to merge these two subsystems.Reaction deletion
Addresses Issue #153
Based on the provided evidence (see Issue #153) and further searching, the following reaction:
HMR_4362: ATP + H2O + pyruvate => AMP + 2 H+ + PEP + Piis not known to occur in humans (it is microbial), and was therefore removed from the model.
I hereby confirm that I have:
develas a target branch