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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 MetaNetX #626

Open JHL-452b opened 1 year ago

JHL-452b commented 1 year ago

Current behavior:

Suspected duplicated metabolites from MetaNetX:

reference ID met ID affected rxns Action for mets Action for rxns Comments
MNXM1653 MAM02120c MAM03684c MAM02120e MAM03684e MAM03684x MAM03684m (MAR11544 MAR09949) (MAR00167 MAR11292) (MAR09811 MAR11293 remove MAM03684e; replace MAM03684c to MAM02120c; replace MAM03684x to MAM02120x; replace MAM03684m to MAM02120m remove MAR09949, MAR11292 and MAR11293
MNXM2782 MAM00684c MAM03325c MAM03248c MAM03248e No replace MAM03325c to MAM00684c; replace MAM03248c to MAM00684c; replace MAM03248e to MAM00684e No MAM03325c and MAM00684c same as HMDB: HMDB0001527; MAM03248e and MAM03248c are not duplicates
MNXM33782 MAM00028c MAM00029c No replace MAM00029c to MAM00028c No same as EHMN: CE7090
MNXM750 MAM02641c MAM02642c MAM02642e MAM02642r No replace MAM02641c to MAM02642c No Not same according to SMILES check, keep it for now
MNXM1183 MAM01435c MAM03318c MAM01435e MAM03318e MAM01435r MAM03318r No replace MAM03318c to MAM01435c; replace MAM03318e to MAM01435e; replace MAM03318r to MAM01435r No same as HMDB: HMDB0000518
MNXM3494 MAM00759c MAM01314c No replace MAM00759c to MAM01314c No suspect chiral metabolites, keep it for now
MNXM153 MAM00643c MAM01005c MAM01005m MAM01005e No replace MAM00643c to MAM01005c No Not same according to SMILES check, keep it for now
MNXM446 MAM00173m MAM00173x MAM03226m change MetaNetX ID annotation for MAM03226m to MNXM1105906 No duplicates
MNXM42 MAM00520c MAM01370c MAM01370l MAM01370m MAM01370e MAM02550c MAM02550e change MetaNetX ID annotation for MAM02550c and MAM02550e to MNXM725868 No duplicates
MNXM164259 MAM00853x MAM00902c MAM00853r No duplicates
MNXM60 MAM01421c MAM01421m MAM01421e MAM02046c MAM02046m MAM02046e change MetaNetX ID annotation for MAM01421 to MNXM45583 No duplicates
MNXM96993 MAM02487c MAM02990c MAM02487m MAM02990m No duplicates
MNXM468808 MAM00578m MAM00934m No duplicates
MNXM140 MAM00719c MAM00719r MAM02360c MAM02360l MAM02360m MAM02360e change MetaNetX ID annotation for MAM00719 to MNXM1106760 No duplicates
MNXM165154 MAM01979c MAM03034x MAM01979m MAM03034m No duplicates
MNXM597 MAM01759c MAM02425c MAM02425e MAM01759e change MetaNetX ID annotation for MAM01759 to MNXM731281; change MetaNetX ID annotation for MAM02425 to MNXM727819 No duplicates
MNXM1003 MAM01677c MAM01678c change MetaNetX ID annotation for MAM01677c to MNXM1103451 No duplicates
MNXM162897 MAM00281c MAM00691m MAM00691x MAM00691c No duplicates
MNXM148 MAM02486m MAM02666m No duplicates
MNXM164048 MAM00272c MAM00273c MAM00275c change MetaNetX ID annotation for MAM00272c to MNXM727334 No duplicates
MNXM15963 MAM01317c MAM01321c MAM01321r MAM01321e MAM01321l change MetaNetX ID annotation for MAM01321 to MNXM739689 No duplicates
MNXM164331 MAM00702c MAM00702m MAM00702x MAM01057c MAM01057r MAM01060c change MetaNetX ID annotation for MAM01060c to MNXM726413 No duplicates
MNXM336 MAM01322c MAM01911c change MetaNetX ID annotation for MAM01322c to MNXM1106067 No duplicates
MNXM5749 MAM01631m MAM01824c MAM01824m MAM01826c MAM01826m change MetaNetX ID annotation for MAM01631m to MNXM11246; change MetaNetX ID annotation for MAM01824 to MNXM731952 No duplicates
MNXM12747 MAM01995c MAM01996c change MetaNetX ID annotation for MAM01996c to MNXM93437 No duplicates
MNXM33412 MAM00382c MAM00384c MAM00384e change MetaNetX ID annotation for MAM00382c to MNXM734306 No duplicates
MNXM2 MAM02040c MAM02040g MAM02040l MAM02040m MAM02040n MAM02040x MAM02040r MAM02040e MAM02147c MAM02147m MAM02147e change MetaNetX ID annotation for MAM02040 to WATER No duplicates
MNXM43 MAM01442c MAM01442e MAM02144c MAM01442l MAM01442n MAM01442m change MetaNetX ID annotation for MAM02144c to MNXM56769 No duplicates
MNXM41010 MAM01264g MAM01873c R group in the formula
MNXM248 MAM02956e MAM02957e MAM02958c MAM02958l MAM02958r MAM02956c MAM02956l R group in the formula
MNXM9478 MAM01858g MAM01885c R group in the formula
MNXM5281 MAM02381c MAM02767c MAM02381e R group in the formula
MNXM15750 MAM00136c MAM00137c R group in the formula
MNXM9476 MAM01878c MAM01908g R group in the formula
MNXM72 MAM01808c MAM01808r MAM01809c MAM01810c MAM01811c MAM01812c MAM01813c MAM01814c MAM01815c MAM01819e MAM01820e MAM10005e MAM10005c MAM10005l MAM10005r MAM10005x MAM01820c R group in the formula
MNXM9474 MAM01855g MAM01882c R group in the formula
MNXM7940 MAM01853c MAM01853g MAM01853e MAM01883c MAM01883e R group in the formula
MNXM7942 MAM01852c MAM01852g MAM01852e MAM01887c MAM01887e R group in the formula
MNXM96054 MAM02726c MAM02727m MAM02728c MAM02728g MAM02728r MAM02729c MAM02730c MAM02731c MAM02732c MAM02733c MAM02733r MAM02733m MAM02733n MAM02733g MAM02733e MAM02728m MAM02730m MAM02730r MAM02730g MAM02731r MAM02731g R group in the formula
MNXM8835 MAM01999c MAM01999g MAM01999e MAM03578e MAM03578c MAM03578g R group in the formula
MNXM44 MAM01272c MAM10007c MAM10007m MAM10007g MAM10007x R group in the formula
MNXM7941 MAM01884c MAM01884e MAM01915c MAM01915g MAM01915e R group in the formula
MNXM1256 MAM00516c MAM00516e MAM00549c MAM00549e R group in the formula
MNXM2963 MAM00503c MAM00503e MAM00504c MAM00505c MAM00506c MAM00507c MAM00508c MAM00509c MAM00510c MAM00510e R group in the formula
MNXM7939 MAM01859c MAM01859g MAM01859e MAM01874c MAM01874e R group in the formula
MNXM59 MAM00233c MAM00234e MAM00235c MAM00236c MAM00236r MAM00237c MAM00238c MAM00239c MAM00240c MAM00240g MAM00240n MAM00241e MAM00240r MAM00240e MAM00235g MAM00235n MAM00235e MAM00237n R group in the formula
MNXM9477 MAM01857g MAM01879c R group in the formula
MNXM149166 MAM00204c MAM00204n MAM00204e MAM02768c R group in the formula
MNXM91270 MAM02686c MAM03316m MAM03316r R group in the formula
MNXM145527 MAM00473c MAM00485c MAM00486c MAM00487c MAM00488c MAM00489c MAM00490c MAM10006e MAM10006m MAM10006c R group in the formula
MNXM9471 MAM01876c MAM01907g R group in the formula
MNXM75100 MAM02758c MAM03321m MAM03321r R group in the formula
MNXM9472 MAM01263g MAM01877c R group in the formula
MNXM91381 MAM00627c MAM00704c MAM00846m MAM00846x MAM00847m MAM00848m MAM00850m MAM00851m MAM00862c MAM00846c R group in the formula
BIOMASS MAM03970c MAM03971e Biomass
MNXM740100 MAM20007n MAM20009c No links
MNXM2269 MAM20045r MAM20046c No links
MNXM1107623 MAM20019r MAM20022i No links
MNXM1105928 MAM20020r MAM20023i No links
MNXM145653 MAM20003n MAM20005c No links
MNXM146872 MAM20024r MAM20025i No links
MNXM23130 MAM20004n MAM20006c No links
MNXM31465 MAM20041r MAM20042r No links
MNXM22530 MAM20028r MAM20029i No links
MNXM376 MAM20008n MAM20010c No links
MNXM11432 MAM20047r MAM20048c No links
MNXM2705 MAM20013c MAM20053r No links
MNXM1619 MAM20014g MAM20016n No links
MNXM163120 MAM20031i MAM20030r No links
MNXM112 MAM20032n MAM20033c No links
MNXM6762 MAM20043r MAM20044c No links
MNXM7260 MAM20049r MAM20050c No links
MNXM1105027 MAM20034n MAM20035c No links
MNXM735429 MAM20056r MAM20057c No links
MNXM733372 MAM20015g MAM20017n No links
MNXM13002 MAM20051r MAM20052c No links
MNXM163133 MAM20018r MAM20021i No links
MNXM35542 MAM20026r MAM20027i No links
MNXM8711 MAM20054r MAM20055c No links
old ID new ID
MAM03684x MAM02120x
MAM03684m MAM02120m
MAM03684c MAM02120c
feiranl commented 1 year ago

@haowang-bioinfo Is that possible that we can turn to MNX group for help on globally updating MNX IDs?

haowang-bioinfo commented 1 year ago

@haowang-bioinfo Is that possible that we can turn to MNX group for help on globally updating MNX IDs?

@feiranl good idea - @smoretti, @ANiknejad if you have any code for consistency check?