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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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Suspected duplicated metabolites from Recon3D #618

Open JHL-452b opened 1 year ago

JHL-452b commented 1 year ago

Current behavior:

Suspected duplicated metabolites from Recon3D:

reference ID met ID affected rxns Action for mets Action for rxns Comments
CE4820 MAM00853x MAM00902c MAM00853r No replace MAM00902c to MAM00853c No same as EMHN: CE4820
CE7090 MAM00028c MAM00029c (MAR02586 MAR02588) replace MAM00029c to MAM00028c remove MAR02588 same as EHMN: CE7090
Temp001 MAM03970c MAM03971e Biomass
acgalfucgalacglcgal14acglcgalgluside_hs MAM01263g MAM01877c R group in the formula
fucfucgalacglcgal14acglcgalgluside_hs MAM01855g MAM01882c R group in the formula
galfucgalacglcgal14acglcgalgluside_hs MAM01884c MAM01884e MAM01915c MAM01915g MAM01915e R group in the formula
pail35p_hs MAM00555c MAM00555g MAM00555r MAM02735c MAM02735r MAM02735g MAM02735n R group in the formula
galacgalfucgalacglcgal14acglcgalgluside_hs MAM01878c MAM01908g R group in the formula
fucgalfucgalacglcgalgluside_hs MAM01859c MAM01859g MAM01859e MAM01874c MAM01874e R group in the formula
fucfucfucgalacglcgal14acglcgalgluside_hs MAM01853c MAM01853g MAM01853e MAM01883c MAM01883e R group in the formula
fucgalacgalfucgalacglcgal14acglcgalgluside_hs MAM01857g MAM01879c R group in the formula
fucgalacglc13galacglcgal14acglcgalgluside_hs MAM01858g MAM01885c R group in the formula
galacgalfuc12gal14acglcgalgluside_hs MAM01876c MAM01907g R group in the formula
ak2lgchol_hs MAM00516c MAM00516e MAM00549c MAM00549e R group in the formula
fucfucfucgalacglc13galacglcgal14acglcgalgluside_hs MAM01852c MAM01852g MAM01852e MAM01887c MAM01887e R group in the formula
acngalacglcgalgluside_hs MAM01264g MAM01873c R group in the formula
trdrd MAM02487c MAM02487m MAM02990c MAM02990m MAM02990n No duplicates
trdox MAM02486m MAM02666c MAM02666m MAM02666n No duplicates
feiranl commented 1 year ago

@haowang-bioinfo Please help to double check the MAM03970c MAM03971e. I think we should merge the ID together since they are same, but I am not sure whether there are other specific reason for having different IDs for biomass in cytosol and extracellular.

Except these two, others contain R group which makes it difficult to determine wether they are duplicates, I suggest we keep them for now.

haowang-bioinfo commented 1 year ago

@haowang-bioinfo Please help to double check the MAM03970c MAM03971e. I think we should merge the ID together since they are same, but I am not sure whether there are other specific reason for having different IDs for biomass in cytosol and extracellular.

yes, they (MAM03970c and MAM03971e) do appear to be duplicate to each other and should be merged at some point