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Suspected duplicated metabolites from Recon3D #618
Description
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 |
Activity
feiranl commentedon Jun 12, 2023
@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 commentedon Aug 13, 2023
yes, they (MAM03970c and MAM03971e) do appear to be duplicate to each other and should be merged at some point
chore: annotation overhaul plan and structure/formula/charge audit
chore: annotation overhaul plan and structure/formula/charge audit
feat: structure-verified annotation overhaul (metabolite + reaction c…
edkerk commentedon Sep 27, 2026
Small follow-up to #1090 in #1105: the biomass pair from this issue was merged in #1090 by renaming MAM03971e to MAM03970e, but the new id did not record the old one. MAM03970e's
metRetirednow lists MAM03971e (temp001s;MAM03971e), as for the other renamed ids; MAM03971e stays indeprecatedMetabolites.tsv. The same bookkeeping was added for the 13 MAM200xx renames from #626 (see the comment there).edkerk commentedon Oct 5, 2026
Fixed in Human 2.1.0.