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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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wrong xref for MAM02679c pantetheine #297

Closed ANiknejad closed 2 years ago

ANiknejad commented 3 years ago

Hi @Hao-Chalmers

https://metabolicatlas.org/explore/Human-GEM/gem-browser/metabolite/MAM02679c

this page talks about 'pantetheine' but displays 'palmitoyl-coA' as in https://metabolicatlas.org/explore/Human-GEM/gem-browser/metabolite/MAM02678c

I guess, there is a typo issue between MAM02678 and MAM02679

there are strange 'Related metabolite(s)' in this page of MAM02679c, that at the end make conflicting reports in MetaNetX for M_MAM02678 and M_MAM02679: trying to solve a conflict between 'palmitoyl-coA' and 'pantetheine' for metatlas_HumanGEM, see here (not sure I can access directly this link, but if you import the model and go to page 'Import' you will see this page)

https://beta.metanetx.org/cgi-bin/mnxweb/result?analysis=Import&model=metatlas_HumanGEM

Thank you in advance for your help in solving this issue

haowang-bioinfo commented 3 years ago

@ANiknejad nice spot!

This error is due to the wrong annotation of ChEBI association to MAM02679c. Please continue the investigation and do let us know if there are more such cases.

haowang-bioinfo commented 2 years ago

Planned corrections to MAM02679 annotation:

Database Current Planned action
BiGG ptth remove keep
ChEBI 15525 change to 16753
HMDB HMDB01338 change to HMDB0003426
HMR 2.0 m02679c keep
HepatoNET1 HC00554 keep
KEGG C00154 change to C00831
MetaNetX MNXM1154 change to MNXM727034
PubChem 15667 change to 439322
Recon3D ptth remove

@ANiknejad @JonathanRob what do you think?

ANiknejad commented 2 years ago

hi Hao,

sounds good to me, thank you

mihai-sysbio commented 2 years ago

As far as I can see #325 has completely resolved this issue, which is why I am closing it.