I was resolving the yeastGEM against MetaNetX v4.4 and found some collisions.
Most that I found I think were mistakes in MetaNetX, but some I think are mistakes in the identifiers in the yeastGEM.
I list the collisions below headed by the metanetx name and URL, and below that the info from all colliding molecules in the GEM, I bold the section I think is wrong or dubious:
- alpha-D-ribose 5-phosphate (https://www.metanetx.org/chem_info/MNXM1104056)
- s_1408 (ribose-5-phosphate [c])
- sbo: SBO:0000247
- bigg.metabolite: r5p
- chebi: CHEBI:18189
- kegg.compound: C03736
- metanetx.chemical: MNXM15900
- s_3768 (D-ribofuranose 5-phosphate [c])
- sbo: SBO:0000247
- chebi: CHEBI:78346
- kegg.compound: C00117
- metanetx.chemical: MNXM722712
- s_3852 (aldehydo-D-ribose 5-phosphate [c])
- sbo: SBO:0000247
- chebi: CHEBI:58273
- kegg.compound: C00117
- metanetx.chemical: MNXM722712
- taurocholate (https://www.metanetx.org/chem_info/MNXM1104296)
- s_1473 (taurocholic acid [c])
- sbo: SBO:0000247
- bigg.metabolite: tchola
- chebi: CHEBI:36257
- kegg.compound: C05122
- metanetx.chemical: MNXM2288
- s_4267 (taurocholate [c])
- sbo: SBO:0000247
- bigg.metabolite: tchola
- biocyc: CPD-3743
- chebi: CHEBI:28865
- kegg.compound: C05122
- metanetx.chemical: MNXM1104296
- 6-(N-acetyl-alpha-D-glucosaminyl)-1-phosphatidyl-1D-myo-inositol (https://www.metanetx.org/chem_info/MNXM1104777)
- s_0331 (6-(N-acetyl-alpha-D-glucosaminyl)-1-phosphatidyl-1D-myo-inositol [er])
- sbo: SBO:0000247
- bigg.metabolite: acgpail_hs
- chebi: CHEBI:57265
- kegg.compound: C01288
- metanetx.chemical: MNXM999
- s_3879 (G00143 [er])
- sbo: SBO:0000247
- chebi: CHEBI:57265
- metanetx.chemical: MNXM92477
- alpha-D-galactose (https://www.metanetx.org/chem_info/MNXM1108175)
- s_0558 (D-galactose [c])
- sbo: SBO:0000247
- bigg.metabolite: gal
- chebi: CHEBI:12936
- kegg.compound: C00124
- metanetx.chemical: MNXM390
- s_3862 (alpha-D-Galactose [c])
- sbo: SBO:0000247
- bigg.metabolite: a_gal__D
- chebi: CHEBI:28061
- kegg.compound: C00984
- metanetx.chemical: MNXM390
- raffinose (https://www.metanetx.org/chem_info/MNXM1108339)
- s_3717 (protein [c])
- sbo: SBO:0000649
- bigg.metabolite: protein
- kegg.compound: C00492
- metanetx.chemical: MNXM621
- s_4193 (raffinose [c])
- sbo: SBO:0000247
- bigg.metabolite: raffin
- chebi: CHEBI:16634
- kegg.compound: C00492
- metanetx.chemical: MNXM621
- succinate (https://www.metanetx.org/chem_info/MNXM25)
- s_1460 (succinate [m])
- sbo: SBO:0000247
- bigg.metabolite: succ
- chebi: CHEBI:30031
- kegg.compound: C00042
- metanetx.chemical: MNXM25
- s_4313 (ITP [m])
- sbo: SBO:0000247
- bigg.metabolite: succ
- biocyc: SUC
- chebi: CHEBI:61402
- kegg.compound: C00081
- metanetx.chemical: MNXM25
- pubchem.compound: 160419
- seed.compound: cpd00036
I am not sure though i have bolded the right bits as errors.
Especially for taurocholate which kegg does indeed list as an alias for taurocholic acid
The total affected ID are:
['s_1408', 's_3768', 's_3852', 's_1473', 's_4267', 's_0331', 's_3879', 's_0558', 's_3862', 's_3717', 's_4193', 's_1460', 's_4313']
but as you can see the problems are probably only in about half of them
I actually ran this against v9.0.0, but i have checked the release notes and the diffs of PRs that were merged and I don't see these sections as changed. I might have missed though.
Related issues:
I was resolving the yeastGEM against MetaNetX v4.4 and found some collisions.
Most that I found I think were mistakes in MetaNetX, but some I think are mistakes in the identifiers in the yeastGEM.
I list the collisions below headed by the metanetx name and URL, and below that the info from all colliding molecules in the GEM, I bold the section I think is wrong or dubious:
I am not sure though i have bolded the right bits as errors.
Especially for taurocholate which kegg does indeed list as an alias for taurocholic acid
The total affected ID are:
but as you can see the problems are probably only in about half of them
I actually ran this against v9.0.0, but i have checked the release notes and the diffs of PRs that were merged and I don't see these sections as changed. I might have missed though.
Related issues: