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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 ChEBI #627

Closed JHL-452b closed 1 year ago

JHL-452b commented 1 year ago

Current behavior:

Suspected duplicated metabolites from ChEBI:

reference ID met ID affected rxns Action for mets Action for rxns Comments
CHEBI:9068 MAM02890c MAM02895c No replace MAM02895c to MAM02890c No Not same according to SMILES check, keep it for now
CHEBI:16285 MAM02746c MAM03884c MAM02746e MAM03884e MAM02746x MAM03884x (MAR00440 MAR01617) (MAR03480 MAR00740) (MAR09037 MAR00659) (MAR03482 MAR05323) remove MAM03884c and MAM03884e; replace MAM03884x to MAM02746x remove MAR01617, MAR00740, MAR00659 and MAR05323 same as BiGG: phyt
CHEBI:15538 MAM02747c MAM03362c MAM02747x MAM03362x No replace MAM03362c to MAM02747c; replace MAM03362x to MAM02747x No chiral metabolites, keep it for now
CHEBI:27404 MAM01739c MAM03162c (MAR12012 MAR09733) (MAR12024 MAR09734) remove MAM03162c remove MAR09733 and MAR09734 same as KEGG: C05578
CHEBI:63548 MAM00131c MAM03354c MAM00131r MAM03354r (MAR02401 MAR03441) remove MAM03354c; replace MAM03354r to MAM00131r remove MAR03441 same as EHMN: CE4837
CHEBI:81563 MAM00028c MAM00029c No replace MAM00029c to MAM00028c No same as EHMN: CE7090
CHEBI:1438 MAM00684c MAM03325c No replace MAM03325c to MAM00684c No same as HMDB: HMDB0001527
CHEBI:15481 MAM00785m MAM03226m (MAR03755 MAR00042) remove MAM03226m remove MAR00042 same as Bigg: 3hibutcoa
CHEBI:27379 MAM00748m MAM03368m MAM00748x MAM03368x No replace MAM03368m to MAM00748m; replace MAM03368x to MAM00748x No same as EHMN: CE5169
CHEBI:63543 MAM00134r MAM03353r NO replace MAM03353r to MAM00134r NO chiral metabolites, keep it for now
CHEBI:53486 MAM01696c MAM03332c MAM01696e MAM03332e (MAR00407 MAR10164) (MAR00576 MAR10433) remove MAM03332c and MAM03332e remove MAR10164 and MAR10433 same as EHMN: CE2516
CHEBI:17002 MAM01451l MAM10004l MAM01451r MAM10004r (MAR10037 MAR03537) (MAR10038 MAR03622) remove MAM10004l and MAM10004r remove MAR03537 and MAR03622 same as BiGG: xolest2_hs
CHEBI:52022 MAM03996c MAM10026c MAM03996e MAM10026e (MAR12294 MAR10101) (MAR12230 MAR10083) replace MAM10026c to MAM03996c; replace MAM10026e to MAM03996e remove MAR10101 and MAR10083 Not same according to SMILES check, keep it for now
CHEBI:34306 MAM00270c MAM00591c MAM00270e MAM00591e (MAR00934 MAR00941) (MAR02396 MAR06142) (MAR02398) MAR06143) (MAR02400 MAR06144) (MAR02402 MAR06220) (MAR02404 MAR06252) (MAR10348 MAR10025) remove MAM00591c and MAM00591e remove MAR00941, MAR06142, MAR06143, MAR06144, MAR06220, MAR06252 and MAR10025 same as KEGG: C14748
CHEBI:57277 MAM03232c MAM03231c No replace MAM03231c to MAM03232c No
CHEBI:16755 MAM01435c MAM03318c MAM01435e MAM03318e MAM01435r MAM03318r No replace MAM03318c to MAM01435c; replace MAM03318e to MAM01435e; replace MAM03318r to MAM01435r No same as HMDB: HMDB0000518
CHEBI:15958 MAM02686c MAM03316m MAM03316r R group in the formula
CHEBI:17855 MAM02956e MAM02957e MAM02958c MAM02958l MAM02958r MAM02959e MAM02959c MAM02956c MAM02956l MAM02959r R group in the formula
CHEBI:17408 MAM00503c MAM00503e MAM00504c MAM00505c MAM00506c MAM00507c MAM00508c MAM00509c MAM00510c MAM00510e R group in the formula
CHEBI:17815 MAM00233c MAM00234e MAM00235c MAM00236c MAM00236r MAM00237c MAM00238c MAM00239c MAM00240c MAM00240g MAM00240n MAM00241e MAM00240r MAM00240e MAM00235g MAM00235n MAM00235e MAM00237n R group in the formula
CHEBI:18216 MAM02008c MAM03635c MAM02008g MAM03635g MAM02008l MAM03635l MAM02008e MAM03635e MAM03635n R group in the formula
CHEBI:16975 MAM00473c MAM00485c MAM00486c MAM00487c MAM00488c MAM00489c MAM00490c MAM10006e MAM10006m MAM10006c R group in the formula
CHEBI:16337 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
CHEBI:35366 MAM01808c MAM01808r MAM01809c MAM01810c MAM01811c MAM01812c MAM01813c MAM01814c MAM01815c MAM01819e MAM01820e MAM10005e MAM10005c MAM10005l MAM10005r MAM10005x MAM01820c R group in the formula
CHEBI:15835 MAM01278c MAM01278x MAM03319c R group in the formula
CHEBI:138378 MAM10035c MAM10036c MAM10037c No duplicates
CHEBI:15525 MAM02678c MAM02678m MAM02678x MAM02678r MAM02679e change CHEBI ID annotation for MAM02679e to CHEBI:16753 No duplicates
CHEBI:17029 MAM01436c MAM01437c No duplicates
CHEBI:48940 MAM00750c MAM00750m MAM00751m MAM00751c MAM00751r No duplicates
CHEBI:16134 MAM02578c MAM02578m MAM02578n MAM02578x MAM02578r MAM02578e MAM02579c MAM02579m MAM02579e MAM02579r MAM02579n MAM02579x change CHEBI ID annotation for MAM02579 to CHEBI:28938 No duplicates
CHEBI:16094 MAM02043c MAM02991c change CHEBI ID annotation for MAM02043c to CHEBI:5587 No duplicates
CHEBI:64039 MAM03887x MAM00078x change CHEBI ID annotation for MAM03887x to CHEBI:77250 No duplicates
CHEBI:15967 MAM02487c MAM02990c MAM02487m MAM02990m No duplicates
CHEBI:18191 MAM02486m MAM02666m No duplicates
CHEBI:17278 MAM01090c MAM01090m MAM01092c MAM01092m No duplicates
CHEBI:63795 MAM00993c MAM01006c MAM00993r No duplicates
CHEBI:76628 MAM20028r MAM20029i No links
CHEBI:57402 MAM20015g MAM20017n No links
CHEBI:17935 MAM20013c MAM20053r No links
CHEBI:58210 MAM20020r MAM20023i No links
CHEBI:132031 MAM20031i MAM20030r No links
CHEBI:57400 MAM20014g MAM20016n No links
CHEBI:16509 MAM20007n MAM20009c No links
CHEBI:76298 MAM20043r MAM20044c No links
CHEBI:17925 MAM20034n MAM20035c No links
CHEBI:27667 MAM20032n MAM20033c No links
CHEBI:72745 MAM20041r MAM20042r No links
CHEBI:132025 MAM20026r MAM20027i No links
CHEBI:132024 MAM20018r MAM20021i No links
CHEBI:83276 MAM20056r MAM20057c No links
CHEBI:84067 MAM20051r MAM20052c No links
CHEBI:17034 MAM20045r MAM20046c No links
CHEBI:27836 MAM20047r MAM20048c No links
CHEBI:31457 MAM20049r MAM20050c No links
CHEBI:76636 MAM20024r MAM20025i No links
CHEBI:57618 MAM20019r MAM20022i No links
CHEBI:17594 MAM20008n MAM20010c No links
CHEBI:34787 MAM20054r MAM20055c No links
CHEBI:76647 MAM20004n MAM20006c No links
CHEBI:76645 MAM20003n MAM20005c No links
old ID new ID
MAM03231c MAM03232c
feiranl commented 1 year ago

Good to go!

haowang-bioinfo commented 1 year ago

fixed in #667