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SysBioChalmers / Human-GEM

The generic genome-scale metabolic model of Homo sapiens
https://sysbiochalmers.github.io/Human-GEM-guide/
Creative Commons Attribution 4.0 International
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Incorrect metabolite formulas #58

Closed pinarkocabas closed 4 years ago

pinarkocabas commented 5 years ago

Description of the issue:

Current feature/value/output:

The following metabolites are curated accordingly:

Met ID Metabolite name Current formula MNX formula 20181029 MNX formula 20181211 MNX charge 20181211 MNX ids-20181211
m02682 PAPS C10H11N5O10P2 C10H11N5O13P2S C10H11N5O13P2S -4 MNXM49
m00737 3,5-diiodo-L-thyronine-4-O-sulfate C15H12I2NO7S C15H13I2NO7S C15H12I2NO7S -1 MNXM150744
m01195 7-Hydroxymethyl-12-methylbenz[a]anthracene sulfate C20H16O4S C20H15O4S C20H15O4S -1 MNXM15042
m01657 Dehydrodolichol diphosphate C1080H1738O70P20 C95H153O7P2 NA NA MNXM48918
m00531 1D-myo-inositol-bisdiphosphate-tetrakisphosphate C6H7O24P6 C6H7O30P8 C6H20O30P8 NA MNXM34087
m02977 tetraHCA C27H47O4 C27H45O6 C27H45O6 -1 MNXM30748
m01599 cob(II)alamin C62CoH92N13O14P C62CoH92N13O14P C62H88CoN13O14P 0 MNXM814
m01598 cob(I)alamin C62CoH88N13O14P C62CoH88N13O14P C62H88CoN13O14P -1 MNXM91519
m00676 2-S-glutathionyl acetate C12H18N3O8S C12H17N3O8S C12H17N3O8S -2 MNXM5771
m02837 retinyl palmitate C36H58O3 C36H60O2 C36H60O2 0 MNXM918
3hpvs 3'-S-hydroxy-pravastatin C23H35NaO8 C23H36O8 C23H35NaO8 0  

I hereby confirm that I have:

haowang-bioinfo commented 5 years ago

@pinarkocabas since these metabolites were curated based on the MetaNetX database, please also add the MNX ids and the charge values.

pinarkocabas commented 5 years ago

@Hao-Chalmers Dear Hao, OK! MNX IDs and MNX charges of the corresponding metabolites were added, besides formulas of four metabolites were re-curated based on METANETX and BIGG databases :)

haowang-bioinfo commented 5 years ago

A one-by-one implementing approach has been reached in dealing these curation results after group discussion. This should also helps in figuring out causes and solutions for individual cases that may vary from one to another.

JonathanRob commented 4 years ago

This issue was addressed in the recent PR #131.