metabolite Identifiers are not in the COBRApy-parsed Mouse-GEM.xml

gmhhope commented 2 years ago

Description of the issue:

Metabolite Identifiers are not in the COBRApy-parsed Mouse-GEM.xml. The same scenario are in Rat-GEM.xml, Mouse-GEM, Rat-GEM, Worm-GEM and Zebrafish-GEM(also see https://github.com/SysBioChalmers/Zebrafish-GEM/issues/5). In addition, Fruitfly-GEM cannot be parsed using COBRApy(see https://github.com/SysBioChalmers/Fruitfly-GEM/issues/5).

Expected feature/value/output:

Expect to have identifiers in .xml files synchronized with flatfiles metabolite.tsv.

Current feature/value/output:

In humanGEM, everything is nicely showed up:

model.metabolites[25].__dict__

{'_id': 'MAM00009r',
 'name': '(11Z,14Z)-eicosadienoyl-CoA',
 'notes': {},
 '_annotation': {'sbo': 'SBO:0000247',
  'kegg.compound': 'C16180',
  'chebi': 'CHEBI:76410',
  'lipidmaps': 'LMFA07050036',
  'vmhmetabolite': 'CE4843',
  'metanetx.chemical': ['MNXM167435', 'MNXM6496']},
 '_model': <Model HumanGEM at 0x7fcff72836a0>,
 '_reaction': {<Reaction MAR02901 at 0x7fcfec58fe50>,
  <Reaction MAR03002 at 0x7fcfeb423130>,
  <Reaction MAR03492 at 0x7fcffda16e80>,
  <Reaction MAR03681 at 0x7fcfeea65fd0>},
 'formula': 'C41H66N7O17P3S',
 'compartment': 'r',
 'charge': -4,
 '_bound': 0.0}

But in Mouse-GEM, Worm-GEM ...: Same codes result in:

{'_id': 'MAM00012c',
 'name': '(11Z,14Z,17Z)-eicosatrienoyl-CoA',
 'notes': {},
 '_annotation': {'sbo': 'SBO:0000247'},
...,
 'formula': 'C41H64N7O17P3S',
 'compartment': 'c',
 'charge': -4,
 '_bound': 0.0}

I hereby confirm that I have:

[ ] Tested my code with all requirements for running the model
[x] Done this analysis in the master branch of the repository
[x] Checked that a similar issue does not exist already
[ ] If needed, asked first in the Gitter chat room about the issue

haowang-bioinfo commented 2 years ago

@gmhhope thanks for reporting this bug that should be fixed by applying annotateGEM function to Mouse-GEM before exporting as .xml.

gmhhope commented 2 years ago

@gmhhope thanks for reporting this bug that should be fixed by applying annotateGEM function to Mouse-GEM before exporting as .xml.

Dear Haowang,

Thanks for replying me! Could you elaborate on what exactly the function annotateGEM from and how to apply? And I was trying to read your Mouse-GEM.xml file instead of exporting it. So I got confused.

Thanks, Minghao Gong

haowang-bioinfo commented 2 years ago

@gmhhope the annoateGEM function is from Human-GEM and usually applied while releasing new version. We'll incorporate this step to Mouse-GEM in future release.

haowang-bioinfo commented 2 years ago

this has been fixed in v1.3

SysBioChalmers / Mouse-GEM