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SysBioChalmers / Human-GEM

The generic genome-scale metabolic model of Homo sapiens
https://sysbiochalmers.github.io/Human-GEM-guide/
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MAM01026 and MAM00348 have the same name, an issue for VMH #375

Open ANiknejad opened 2 years ago

ANiknejad commented 2 years ago

hello,

Could you please have a look at the '2 metabolites found' here: https://www.vmh.life/#allsearch/oretn

MAM01026 4-oxo-13-cis-retinoate is 'oretn' MAM00348 13-cis-oxo-retinoate is '13_cis_oretn'

the name is similar/identical but only MAM00348 corresponds to the -cis stereo form at carbon 13 (I recently created the corresponding chebi for that chemical, should hopefully be validated soon as CHEBI:190136) MAM01026 is the compound that can be mapped to CHEBI:134186 all-trans-4-oxoretinoate, both have the same mol file actually

As a consequence, I send this message to VMH via their contact form, and I hope you agree

Hello Team,

I am currently doing chemical curation work for MetaNetX.org.
It sounds like the compounds with abbreviation '13_cis_oretn' and 'oretn' have the same name (13-Cis-Oxo-Retinoic Acid, and 4-Oxo-13-Cis-Retinoate), while only '13_cis_oretn' corresponds to the structure with a -cis stereo at carbone 13. 'oretn' should maybe be redefined as 'all-trans-4-oxoretinoate' such as CHEBI:134186, right?

Thank you in advance and best regards,

Anne

Anne Niknejad
Senior biocurator
SIB | Swiss Institute of Bioinformatics Unil, Department of Ecology and Evolution - Quartier Sorge, bâtiment Biophore - 1015 Lausanne t: +41 21 692 42 21 - f: +41 21 692 41 65 Anne.Niknejad@sib.swiss - https://www.sib.swiss

I hereby confirm that I have:

JonathanRob commented 2 years ago

Thanks @ANiknejad for identifying this. It seems that both metabolites (MAM01026 and MAM00348) are supposed to correspond to the same 4-oxo-13-cis form, though some of the reactions in which they are involved in Human-GEM may need to be investigated (e.g. MAR08703). The all-trans-4-oxo form is actually already present in the model as the MAM01031 metabolite.

Therefore, to address this issue, I suspect that we will need to do the following:

  1. Merge the MAM01026 and MAM00348 metabolites (remove one from the model).
  2. Evaluate the reactions in which these metabolites are involved to determine if instead the all-trans metabolite MAM01031 should be used instead.
  3. Update cross references (i.e. ChEBI IDs) of these metabolites accordingly.