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Published
20 hours ago •
SBRG
SBRG
Different reaction IDs for identical reactions
Description of the issue
Identical reactions (according to the annotation) that might differ regarding the proton stoichiometry (which implies that one of the reactions is also unbalanced; e.g. FMNAT and AFAT).
A second case is where the metabolite IDs differ although it is the same compound (see issue #274, e.g. UNK3 and ARAT)
A few more candidates; I only checked whether i) the IDs are "an_ID" and "an_ID_1" ii) their Metanetx ID is identical iii) they occur in the same compartment
Did not check all of them manually afterwards:
[('3SPYRSPm_1', '3SPYRSPm'),
('4HOXPACMOF_1', '4HOXPACMOF'),
('4HOXPACt2pp_1', '4HOXPACt2pp'),
('ABTt_1', 'ABTt'),
('ACODA_1', 'ACODA'),
('ACPS1_1', 'ACPS1'),
('AKP1_1', 'AKP1'),
('ALDD31_1', 'ALDD31'),
('ARD_1', 'ARD'),
('ARGN_1', 'ARGN'),
('ARGSS_1', 'ARGSS'),
('ASNTRS_1', 'ASNTRS'),
('ASPCT_1', 'ASPCT'),
('ASPO3_1', 'ASPO3'),
('ASPO4_1', 'ASPO4'),
('ASPO5_1', 'ASPO5'),
('ASPO6_1', 'ASPO6'),
('ASPOcm_1', 'ASPOcm'),
('DHBSH_1', 'DHBSH'),
('DHCINDO_1', 'DHCINDO'),
('DHFS_1', 'DHFS'),
('DHNPA_1', 'DHNPA'),
('DHPS2_1', 'DHPS2'),
('DNTPPA_1', 'DNTPPA'),
('ECOAH1_1', 'ECOAH1'),
('ECOAH5_1', 'ECOAH5'),
('ENTCS_1', 'ENTCS'),
('FGLU_1', 'FGLU'),
('FLVR_1', 'FLVR'),
('FMETTRS_1', 'FMETTRS'),
('FOLD3_1', 'FOLD3'),
('FOLR2_1', 'FOLR2'),
('FTHFI_1', 'FTHFI'),
('G6PDA_1', 'G6PDA'),
('GALCTD_1', 'GALCTD'),
('GF6PTA_1', 'GF6PTA'),
('GLCRAL_1', 'GLCRAL'),
('GLCRD_1', 'GLCRD'),
('GMPtn_1', 'GMPtn'),
('GTPCI_1', 'GTPCI'),
('GTPDPK_1', 'GTPDPK'),
('GUAD_1', 'GUAD'),
('HACD1_1', 'HACD1'),
('HEMEAS_1', 'HEMEAS'),
('HEMEOS_1', 'HEMEOS'),
('HEMEOSm_1', 'HEMEOSm'),
('HKNDDH_1', 'HKNDDH'),
('HKNTDH_1', 'HKNTDH'),
('HP5CD_1', 'HP5CD'),
('HPPK_1', 'HPPK'),
('HPPPNDO_1', 'HPPPNDO'),
('IG3PS_1', 'IG3PS'),
('IGPDH_1', 'IGPDH'),
('IZPN_1', 'IZPN'),
('METS_1', 'METS'),
('MTHFC_1', 'MTHFC'),
('MTHFCm_1', 'MTHFCm'),
('MTHFD_1', 'MTHFD'),
('MTHFDm_1', 'MTHFDm'),
('MTHFR2_1', 'MTHFR2'),
('MTHFR3_1', 'MTHFR3'),
('NOS2_1', 'NOS2'),
('OCBT_1', 'OCBT'),
('ORNTAC_1', 'ORNTAC'),
('ORNTA_1', 'ORNTA'),
('PFK26_1', 'PFK26'),
('PRAIS_1', 'PRAIS'),
('PRAMPC_1', 'PRAMPC'),
('PRFGS_1', 'PRFGS'),
('PYDXDH_1', 'PYDXDH'),
('QULNS_1', 'QULNS'),
('SEAHCYSHYD_1', 'SEAHCYSHYD'),
('SELCYSLY2_1', 'SELCYSLY2'),
('SHCHD2_1', 'SHCHD2'),
('SULR_1', 'SULR'),
('THFGLUS_1', 'THFGLUS'),
('URCN_1', 'URCN')]
Page
http://bigg.ucsd.edu/universal/reactions/FMNAT http://bigg.ucsd.edu/universal/reactions/AFAT
http://bigg.ucsd.edu/universal/reactions/UNK3 http://bigg.ucsd.edu/universal/reactions/ARAT
http://bigg.ucsd.edu/universal/reactions/APPAT http://bigg.ucsd.edu/universal/reactions/PTPATi
http://bigg.ucsd.edu/universal/reactions/SULR http://bigg.ucsd.edu/universal/reactions/SULR_1
http://bigg.ucsd.edu/universal/reactions/IMACTD http://bigg.ucsd.edu/universal/reactions/ALDD20x_1
http://bigg.ucsd.edu/universal/reactions/OCBT http://bigg.ucsd.edu/universal/reactions/OCBT_1 http://bigg.ucsd.edu/universal/reactions/OCT
http://bigg.ucsd.edu/universal/reactions/PFK26 http://bigg.ucsd.edu/universal/reactions/PFK26_1
A more complete overview:
Table of all reactions for which another BiGG reaction exists that has i) the same Metanetx ID ii) occurs in the same compartment (based on IDs of the metabolites)
| metanetx_id | bigg_id |
|---|---|
| MNXR100010 | GALS4 |
| MNXR100010 | STACHGALACT |
| MNXR100054 | GBEZ |
| MNXR100054 | GBEZY |
| MNXR100067 | GCCam |
| MNXR100067 | GLYDHD |
| MNXR100068 | GCCbim |
| MNXR100068 | MTAM_nh4 |
| MNXR100078 | GCPN |
| MNXR100078 | PDE4 |
| MNXR100085 | GDH1 |
| MNXR100085 | GLUDxi |
| MNXR100099 | GDTP |
| MNXR100099 | GTPDPDP |
| MNXR100107 | GF6PTA |
| MNXR100107 | GF6PTA_1 |
| MNXR100155 | GLBRAN2 |
| MNXR100155 | GLDBRAN2 |
| MNXR100209 | GLCNt2ir |
| MNXR100209 | GLCNt2r |
| MNXR100219 | GLCRAL |
| MNXR100219 | GLCRAL_1 |
| MNXR100220 | GLCRD |
| MNXR100220 | GLCRD_1 |
| MNXR100283 | GLUK |
| MNXR100283 | GLUK_syn |
| MNXR100301 | GLUt5m |
| MNXR100301 | GLUt7m |
| MNXR100303 | GLXCBL |
| MNXR100303 | GLXCL |
| MNXR100330 | GLYCL |
| MNXR100330 | GLYCL_2 |
| MNXR100355 | GLYOX_1 |
| MNXR100355 | LGTHL |
| MNXR100381 | GMP5N |
| MNXR100381 | NTD9 |
| MNXR100386 | GMPtn |
| MNXR100386 | GMPtn_1 |
| MNXR100390 | GNK |
| MNXR100390 | GNKr |
| MNXR100409 | GPAR |
| MNXR100409 | GUAPRT |
| MNXR100453 | GTPCI |
| MNXR100453 | GTPCI_1 |
| MNXR100453 | GTPCI_2 |
| MNXR100457 | GTPDPK |
| MNXR100457 | GTPDPK_1 |
| MNXR100463 | GUAC |
| MNXR100463 | GUACYC |
| MNXR100464 | GUAD |
| MNXR100464 | GUAD_1 |
| MNXR100482 | H2CO3D |
| MNXR100482 | HCO3E |
| MNXR100482 | H2CO3Dm |
| MNXR100482 | HCO3Em |
| MNXR100541 | HACD1 |
| MNXR100541 | HACD1_1 |
| MNXR100541 | HACD1i |
| MNXR100543 | HACD2 |
| MNXR100543 | HACD2i |
| MNXR100544 | HACD3 |
| MNXR100544 | HACD3i |
| MNXR100545 | HACD4 |
| MNXR100545 | HACD4i |
| MNXR100546 | HACD5 |
| MNXR100546 | HACD5i |
| MNXR100547 | HACD6 |
| MNXR100547 | HACD6i |
| MNXR100548 | HACD7 |
| MNXR100548 | HACD7i |
| MNXR100549 | HACD8 |
| MNXR100549 | HACD8i |
| MNXR100581 | HDC |
| MNXR100581 | HISDC |
| MNXR100587 | HDH |
| MNXR100587 | HISTD |
| MNXR100591 | HEMEAS |
| MNXR100591 | HEMEAS_1 |
| MNXR100596 | HEMEOS |
| MNXR100596 | HEMEOS_1 |
| MNXR100596 | HEMEOSm |
| MNXR100596 | HEMEOSm_1 |
| MNXR100642 | HISTP |
| MNXR100642 | HP |
| MNXR100654 | HKNDDH |
| MNXR100654 | HKNDDH_1 |
| MNXR100655 | HKNTDH |
| MNXR100655 | HKNTDH_1 |
| MNXR100657 | HKt |
| MNXR100657 | Kabc |
| MNXR100657 | HKtpp |
| MNXR100657 | Kabcpp |
| MNXR100660 | HMGCOAS |
| MNXR100660 | MHGS |
| MNXR100662 | HMGL_1 |
| MNXR100662 | HMGLm |
| MNXR100682 | HOXPRx |
| MNXR100682 | TRSARr |
| MNXR100683 | HP5CD |
| MNXR100683 | HP5CD_1 |
| MNXR100692 | HPI |
| MNXR100692 | HPYRI |
| MNXR100693 | HPPK |
| MNXR100693 | HPPK_1 |
| MNXR100695 | HPPPNDO |
| MNXR100695 | HPPPNDO_1 |
| MNXR100698 | HPROa |
| MNXR100698 | HPROx |
| MNXR100764 | HYPTROX |
| MNXR100764 | HYPTROX_cho |
| MNXR100808 | IDPm |
| MNXR100808 | PPAm |
| MNXR100811 | IG3PS |
| MNXR100811 | IG3PS_1 |
| MNXR100813 | IGPDH |
| MNXR100813 | IGPDH_1 |
| MNXR100835 | INDOLEt2pp |
| MNXR100835 | INDOLEt2rpp |
| MNXR100877 | IPKK |
| MNXR100877 | MI13456PK |
| MNXR100877 | PMI1346PS |
| MNXR100887 | ITK1K |
| MNXR100887 | MI3456PK |
| MNXR100896 | IZPN |
| MNXR100896 | IZPN_1 |
| MNXR101007 | LALDD |
| MNXR101007 | LALDO2 |
| MNXR101032 | LCYSTCBOXL |
| MNXR101032 | SALADC2 |
| MNXR101081 | LIPATPT |
| MNXR101081 | RE1944C |
| MNXR101095 | LLDH_ferr_m |
| MNXR101095 | L_LACDm |
| MNXR101105 | LNLCCPT1 |
| MNXR101105 | LNLCCPT2rbc |
| MNXR101345 | MALMDA |
| MNXR101345 | PYRZAM |
| MNXR101382 | MAN6PI |
| MNXR101382 | MPAKI |
| MNXR101411 | MCCCrm |
| MNXR101411 | MCTC |
| MNXR101412 | MCD |
| MNXR101412 | MCDC |
| MNXR101439 | MDH |
| MNXR101439 | MDHi2 |
| MNXR101479 | METOX1s |
| MNXR101479 | METOX2s |
| MNXR101479 | METSR_S2 |
| MNXR101481 | METS |
| MNXR101481 | METS_1 |
| MNXR101482 | METSOX1abcpp |
| MNXR101482 | METSOX2abcpp |
| MNXR101483 | METSOX1tex |
| MNXR101483 | METSOX2tex |
| MNXR101484 | METSOXR1 |
| MNXR101484 | METSOXR2 |
| MNXR101484 | METSR_S1 |
| MNXR101556 | MI123456PP |
| MNXR101556 | PHYT3 |
| MNXR101556 | PMI1346PH |
| MNXR101585 | MINOHPtn |
| MNXR101585 | PPMI1346Ptn |
| MNXR101748 | MTHFC |
| MNXR101748 | MTHFC_1 |
| MNXR101748 | MTHFCm |
| MNXR101748 | MTHFCm_1 |
| MNXR101749 | MTHFD |
| MNXR101749 | MTHFD_1 |
| MNXR101749 | MTHFDm |
| MNXR101749 | MTHFDm_1 |
| MNXR101750 | MTHFD2 |
| MNXR101750 | MTHFD2i |
| MNXR101751 | MTHFR2 |
| MNXR101751 | MTHFR2_1 |
| MNXR101752 | MTHFR3 |
| MNXR101752 | MTHFR3_1 |
| MNXR101861 | NADDP |
| MNXR101861 | NPH |
| MNXR101881 | NADHtpu |
| MNXR101881 | NADtpu |
| MNXR101911 | NAPT |
| MNXR101911 | NMNS |
| MNXR101950 | NH4t |
| MNXR101950 | NH4ti |
| MNXR102007 | NOS2 |
| MNXR102007 | NOS2_1 |
| MNXR102108 | OALT |
| MNXR102108 | UDCPAT |
| MNXR102110 | OAO4t3pp |
| MNXR102110 | udcdpgalrmnmanabetpp |
| MNXR102137 | OCBT |
| MNXR102137 | OCBT_1 |
| MNXR102137 | OCT |
| MNXR102137 | OCBTm |
| MNXR102137 | OCTm |
| MNXR102158 | OGLT |
| MNXR102158 | UDCPGT |
| MNXR102186 | OMLT |
| MNXR102186 | UDCPMT |
| MNXR102216 | ORLT |
| MNXR102216 | UDCPRT |
| MNXR102220 | ORNTA |
| MNXR102220 | ORNTA_1 |
| MNXR102221 | ORNTAC |
| MNXR102221 | ORNTAC_1 |
| MNXR102224 | ORNt2 |
| MNXR102224 | ORNt2r |
| MNXR102302 | P5CR |
| MNXR102302 | PRO1y |
| MNXR102303 | P5CRx |
| MNXR102303 | PRO1x |
| MNXR102303 | P5CRxm |
| MNXR102303 | PRO1xm |
| MNXR102345 | PANTS |
| MNXR102345 | PBAL |
| MNXR102430 | PDHe2r |
| MNXR102430 | r0555 |
| MNXR102508 | PFK26 |
| MNXR102508 | PFK26_1 |
| MNXR102871 | PIcm |
| MNXR102871 | PIt5m |
| MNXR103047 | PNCDC |
| MNXR103047 | r0580 |
| MNXR103139 | PPRGL |
| MNXR103139 | PRAGSr |
| MNXR103154 | PRAMPC |
| MNXR103154 | PRAMPC_1 |
| MNXR103157 | PRAIS |
| MNXR103157 | PRAIS_1 |
| MNXR103157 | PRFGCL |
| MNXR103165 | PRFGS |
| MNXR103165 | PRFGS_1 |
| MNXR103310 | PSUDS |
| MNXR103310 | YUMPS |
| MNXR103360 | PYDXDH |
| MNXR103360 | PYDXDH_1 |
| MNXR103400 | QULNS |
| MNXR103400 | QULNS_1 |
| MNXR103639 | RE2248C |
| MNXR103639 | RE2249C |
| MNXR103746 | RE2870C |
| MNXR103746 | RE2871C |
| MNXR104302 | SEAHCYSHYD |
| MNXR104302 | SEAHCYSHYD_1 |
| MNXR104312 | SELCYSLY2 |
| MNXR104312 | SELCYSLY2_1 |
| MNXR104322 | SELNPS |
| MNXR104322 | SELNPS_cho |
| MNXR104339 | SERD_L |
| MNXR104339 | SER_AL |
| MNXR104367 | SGPL13 |
| MNXR104367 | r0786 |
| MNXR104373 | SHCHD2 |
| MNXR104373 | SHCHD2_1 |
| MNXR104375 | SHCHF |
| MNXR104375 | SHCHF_2 |
| MNXR104382 | SHSL2 |
| MNXR104382 | SHSL2r |
| MNXR104442 | SLDx |
| MNXR104442 | SLDxi2 |
| MNXR104503 | SPS |
| MNXR104503 | UFAGT |
| MNXR104635 | SUCLm |
| MNXR104635 | SUCOASm |
| MNXR104649 | SULOm |
| MNXR104649 | r0142 |
| MNXR104650 | SULR |
| MNXR104650 | SULR_1 |
| MNXR104808 | THFGLUS |
| MNXR104808 | THFGLUS_1 |
| MNXR104822 | THMMPt4 |
| MNXR104822 | THMMPtrbc |
| MNXR104822 | THMMPtm |
| MNXR104822 | THMMPtm_cho |
| MNXR104824 | THMPPt2m |
| MNXR104824 | THMPPtm |
| MNXR104824 | THMPPtm_cho |
| MNXR105000 | TYRTA |
| MNXR105000 | TYRTAi |
| MNXR105049 | UDPDOLPT |
| MNXR105049 | UDPDOLPT_cho |
| MNXR105128 | UNK2 |
| MNXR105128 | UNK2_cho |
| MNXR105137 | UPP3MT |
| MNXR105137 | UPP3MT_2 |
| MNXR105149 | URCB |
| MNXR105149 | UREASE |
| MNXR105150 | URCN |
| MNXR105150 | URCN_1 |
| MNXR105156 | UREAt |
| MNXR105156 | UREAt5 |
| MNXR105203 | VITD3t |
| MNXR105203 | VITD3t2 |
| MNXR105203 | VITD3tm |
| MNXR105203 | VITD3tm3 |
| MNXR105237 | XOLEST2te_cho |
| MNXR105237 | XOLESTte_cho |
| MNXR105262 | XYLTD_D |
| MNXR105262 | r0784 |
| MNXR94731 | 23DK5MPPISO |
| MNXR94731 | ACRS |
| MNXR94731 | DM1PE |
| MNXR94737 | 25HVITD2t |
| MNXR94737 | 25HVITD2tin |
| MNXR94737 | 25HVITD2tin_m |
| MNXR94737 | 25HVITD2tm |
| MNXR94739 | 25HVITD3t |
| MNXR94739 | 25HVITD3tin |
| MNXR94739 | 25HVITD3tin_m |
| MNXR94739 | 25HVITD3tm |
| MNXR94796 | 2HBO |
| MNXR94796 | LDH2 |
| MNXR94799 | 2HH24DDH |
| MNXR94799 | 2HH24DDH1 |
| MNXR94815 | 2OH3K5MPPISO |
| MNXR94815 | ENOPH |
| MNXR94835 | 34DHPACDO |
| MNXR94835 | DHPDO |
| MNXR94978 | 3SALACBOXL |
| MNXR94978 | 3SALACBOXL_cho |
| MNXR94980 | 3SALATAim |
| MNXR94980 | AATGm |
| MNXR94981 | 3SPYRSPm |
| MNXR94981 | 3SPYRSPm_1 |
| MNXR94990 | 44MZYMMO |
| MNXR94990 | C4STMO1 |
| MNXR94999 | 4CMLCL_kt |
| MNXR94999 | CMLDC |
| MNXR95000 | 4H2KPILY |
| MNXR95000 | DHEDAA |
| MNXR95018 | 4HOXPACMOF |
| MNXR95018 | 4HOXPACMOF_1 |
| MNXR95019 | 4HOXPACMON |
| MNXR95019 | HPA3MO |
| MNXR95020 | 4HOXPACt2pp |
| MNXR95020 | 4HOXPACt2pp_1 |
| MNXR95054 | 4hoxpactex |
| MNXR95054 | HPAtex |
| MNXR95063 | OPETDC |
| MNXR95063 | OPTCCL |
| MNXR95104 | 6PHBG |
| MNXR95104 | S6PG |
| MNXR95114 | A1E |
| MNXR95114 | GalMr |
| MNXR95133 | AABHH |
| MNXR95133 | r0466 |
| MNXR95163 | AATHB |
| MNXR95163 | TREH |
| MNXR95190 | ABTt |
| MNXR95190 | ABTt_1 |
| MNXR95194 | ACACT1r |
| MNXR95194 | KAT1 |
| MNXR95222 | ACCOALm |
| MNXR95222 | PPACOALm |
| MNXR95227 | ACDO |
| MNXR95227 | ARD |
| MNXR95227 | ARD_1 |
| MNXR95377 | ACODA |
| MNXR95377 | ACODA_1 |
| MNXR95403 | ACPS1 |
| MNXR95403 | ACPS1_1 |
| MNXR95403 | r0368 |
| MNXR95411 | ACPpds |
| MNXR95411 | r0366 |
| MNXR95415 | ACSERSULL |
| MNXR95415 | SLCYSS |
| MNXR95429 | ACt2ipp |
| MNXR95429 | ACt2rpp |
| MNXR95501 | AFAT |
| MNXR95501 | FMNAT |
| MNXR95646 | AIRCr |
| MNXR95646 | PRAIC |
| MNXR95656 | AKGDHe2r |
| MNXR95656 | AKGDbm |
| MNXR95656 | r0556 |
| MNXR95657 | AKGDam |
| MNXR95657 | r0384 |
| MNXR95665 | AKP1 |
| MNXR95665 | AKP1_1 |
| MNXR95713 | ALCD21_D |
| MNXR95713 | LCARR |
| MNXR95725 | ALCD2ir |
| MNXR95725 | ALCD2x |
| MNXR95728 | ALCD4 |
| MNXR95728 | BTS |
| MNXR95729 | ALCD4y |
| MNXR95729 | BTS_nadph |
| MNXR95745 | ALDD20x_1 |
| MNXR95745 | IMACTD |
| MNXR95752 | ALDD31 |
| MNXR95752 | ALDD31_1 |
| MNXR95815 | AMID4 |
| MNXR95815 | AMID_1 |
| MNXR95817 | AMITKPn |
| MNXR95817 | MI1456PKn |
| MNXR95841 | ANNAT |
| MNXR95841 | NMNAT |
| MNXR95841 | ANNATn |
| MNXR95841 | NMNATn |
| MNXR95850 | AO |
| MNXR95850 | HISTASE |
| MNXR95852 | HSTPT |
| MNXR95852 | HSTPTr |
| MNXR95864 | APATi |
| MNXR95864 | THPAT |
| MNXR95866 | APCPT |
| MNXR95866 | r0679 |
| MNXR95892 | APPAT |
| MNXR95892 | PTPATi |
| MNXR95911 | ARABR |
| MNXR95911 | ARABRr |
| MNXR95923 | ARAT |
| MNXR95923 | UNK3 |
| MNXR95941 | ARGDI |
| MNXR95941 | ARGDr |
| MNXR95945 | ARGN |
| MNXR95945 | ARGN_1 |
| MNXR95949 | ARGSS |
| MNXR95949 | ARGSS_1 |
| MNXR95966 | ARTCOAL1 |
| MNXR95966 | ARTCOAL1_cho |
| MNXR95967 | ARTCOAL2 |
| MNXR95967 | ARTCOAL2_cho |
| MNXR95968 | ARTCOAL3 |
| MNXR95968 | ARTCOAL3_cho |
| MNXR96064 | ASNTRS |
| MNXR96064 | ASNTRS_1 |
| MNXR96080 | ASPCT |
| MNXR96080 | ASPCT_1 |
| MNXR96091 | ASPO3 |
| MNXR96091 | ASPO3_1 |
| MNXR96092 | ASPO4 |
| MNXR96092 | ASPO4_1 |
| MNXR96093 | ASPO5 |
| MNXR96093 | ASPO5_1 |
| MNXR96094 | ASPO6 |
| MNXR96094 | ASPO6_1 |
| MNXR96095 | ASPOcm |
| MNXR96095 | ASPOcm_1 |
| MNXR96118 | ATDGDm |
| MNXR96118 | NDPK5m |
| MNXR96119 | ATGDm |
| MNXR96119 | NDPK1m |
| MNXR96131 | ATPM |
| MNXR96131 | NTP1 |
| MNXR96229 | LEUTA |
| MNXR96229 | LEUTAi |
| MNXR96241 | BGLA |
| MNXR96241 | CLBH |
| MNXR96342 | BTS3r |
| MNXR96342 | BTS_1 |
| MNXR96347 | BUPN |
| MNXR96347 | UPPN |
| MNXR96384 | C160CPT1 |
| MNXR96384 | C160CPT2rbc |
| MNXR96396 | C181CPT1 |
| MNXR96396 | C181CPT2rbc |
| MNXR96634 | CERASE124er |
| MNXR96634 | CERS124er |
| MNXR96635 | CERASE126er |
| MNXR96635 | CERS126er |
| MNXR96636 | CERASE224er |
| MNXR96636 | CERS224er |
| MNXR96637 | CERASE226er |
| MNXR96637 | CERS226er |
| MNXR96671 | CHITPH |
| MNXR96671 | DC6PH |
| MNXR96720 | CHYA1 |
| MNXR96720 | CHYA2 |
| MNXR96757 | CKc |
| MNXR96757 | CKc_cho |
| MNXR96757 | CK |
| MNXR96757 | CK_cho |
| MNXR96840 | CODSCL8XI |
| MNXR96840 | CPC8MM |
| MNXR96916 | CRTNsyn |
| MNXR96916 | CRTNsyn_cho |
| MNXR96926 | CSNATirm |
| MNXR96926 | CSNATm |
| MNXR96955 | CXHY |
| MNXR96955 | ZHY |
| MNXR96988 | CYSAMO |
| MNXR96988 | CYSAMO_cho |
| MNXR96990 | CYSATm |
| MNXR96990 | CYSTAm |
| MNXR96994 | CYSDS |
| MNXR96994 | TRPAS1 |
| MNXR97007 | CYSS |
| MNXR97007 | CYSS_2 |
| MNXR97151 | DASCBH |
| MNXR97151 | DASCBH_cho |
| MNXR97317 | DGGH |
| MNXR97317 | GALS3 |
| MNXR97327 | DGTPtm |
| MNXR97327 | DNDPt62m |
| MNXR97369 | DHBS |
| MNXR97369 | DHBSr |
| MNXR97370 | DHBSH |
| MNXR97370 | DHBSH_1 |
| MNXR97379 | DHCINDO |
| MNXR97379 | DHCINDO_1 |
| MNXR97399 | DHFOR |
| MNXR97399 | r0512 |
| MNXR97400 | FOLR2 |
| MNXR97400 | FOLR2_1 |
| MNXR97403 | DHFS |
| MNXR97403 | DHFS_1 |
| MNXR97414 | DHNPA |
| MNXR97414 | DHNPA_1 |
| MNXR97432 | DHPD |
| MNXR97432 | DHPM1 |
| MNXR97439 | DHPS2 |
| MNXR97439 | DHPS2_1 |
| MNXR97439 | FOLD3 |
| MNXR97439 | FOLD3_1 |
| MNXR97450 | DHRT_2mbcoa |
| MNXR97450 | r0604 |
| MNXR97452 | DHRT_ivcoa |
| MNXR97452 | r0656 |
| MNXR97628 | DNDPt10m |
| MNXR97628 | DNDPt29m |
| MNXR97629 | DNDPt11m |
| MNXR97629 | DNDPt35m |
| MNXR97632 | DNDPt14m |
| MNXR97632 | DNDPt22m |
| MNXR97633 | DNDPt15m |
| MNXR97633 | DNDPt33m |
| MNXR97634 | DNDPt16m |
| MNXR97634 | DNDPt8m |
| MNXR97635 | DNDPt17m |
| MNXR97635 | DNDPt26m |
| MNXR97641 | DNDPt23m |
| MNXR97641 | DNDPt34m |
| MNXR97642 | DNDPt24m |
| MNXR97642 | DNDPt9m |
| MNXR97643 | DNDPt25m |
| MNXR97643 | DNDPt27m |
| MNXR97644 | DNDPt28m |
| MNXR97644 | DNDPt36m |
| MNXR97680 | DNTPPA |
| MNXR97680 | DNTPPA_1 |
| MNXR97767 | DPHAPC100 |
| MNXR97767 | PHAPC100 |
| MNXR97768 | DPHAPC120 |
| MNXR97768 | PHAPC120 |
| MNXR97769 | DPHAPC121 |
| MNXR97769 | PHAPC121 |
| MNXR97770 | DPHAPC140 |
| MNXR97770 | PHAPC140 |
| MNXR97771 | DPHAPC141 |
| MNXR97771 | PHAPC141 |
| MNXR97772 | DPHAPC60 |
| MNXR97772 | PHAPC60 |
| MNXR97773 | DPHAPC80 |
| MNXR97773 | PHAPC80 |
| MNXR97796 | DSCLCOCH |
| MNXR97796 | SHCHCC |
| MNXR97836 | D_LACDHm |
| MNXR97836 | D_LACDm |
| MNXR97883 | ECOAH1 |
| MNXR97883 | ECOAH1_1 |
| MNXR97890 | ECOAH5 |
| MNXR97890 | ECOAH5_1 |
| MNXR97933 | ENTCS |
| MNXR97933 | ENTCS_1 |
| MNXR98064 | EX_4hoxpac_e |
| MNXR98064 | EX_4hphac_e |
| MNXR98131 | EX_CE5868_e |
| MNXR98131 | EX_asp__L_e |
| MNXR98137 | EX_HC00822_e |
| MNXR98137 | EX_chitob_e |
| MNXR98152 | EX_HC02172_e |
| MNXR98152 | EX_zn2_e |
| MNXR98195 | EX_abt__L_e |
| MNXR98195 | EX_abt_e |
| MNXR98307 | EX_buts_e |
| MNXR98307 | EX_butso3_e |
| MNXR98460 | EX_eths_e |
| MNXR98460 | EX_ethso3_e |
| MNXR98539 | EX_galct__D_e |
| MNXR98539 | EX_galctr__D_e |
| MNXR98574 | EX_glcn__D_e |
| MNXR98574 | EX_glcn_e |
| MNXR98639 | EX_h2co3_e |
| MNXR98639 | EX_hco3_e |
| MNXR98641 | EX_h2o_e |
| MNXR98641 | EX_oh1_e |
| MNXR98684 | EX_isetac_e |
| MNXR98684 | EX_istnt_e |
| MNXR98715 | EX_lipoate_e |
| MNXR98715 | EX_lipt_e |
| MNXR98755 | EX_metox_e |
| MNXR98755 | EX_metsox_R__L_e |
| MNXR98755 | EX_metsox_S__L_e |
| MNXR98813 | EX_orn__L_e |
| MNXR98813 | EX_orn_e |
| MNXR98950 | EX_sula_e |
| MNXR98950 | EX_sulfac_e |
| MNXR99043 | EX_xolest2_cho_e |
| MNXR99043 | EX_xolest_cho_e |
| MNXR99275 | FAOXC121_3Em |
| MNXR99275 | FAOXC121_3Zm |
| MNXR99284 | FAOXC141_5Em |
| MNXR99284 | FAOXC141_5Zm |
| MNXR99284 | FAOXC141_7Em |
| MNXR99303 | FAOXC161_7Em |
| MNXR99303 | FAOXC161_7Zm |
| MNXR99303 | FAOXC161_9Em |
| MNXR99466 | FBP26 |
| MNXR99466 | FBPPH |
| MNXR99468 | FCI |
| MNXR99468 | r0598 |
| MNXR99471 | FCLT |
| MNXR99471 | FCLT_2 |
| MNXR99473 | FCOAH |
| MNXR99473 | FCOAH2 |
| MNXR99505 | FE2utm |
| MNXR99505 | FEtm |
| MNXR99593 | FGLU |
| MNXR99593 | FGLU_1 |
| MNXR99601 | FLVR |
| MNXR99601 | FLVR_1 |
| MNXR99604 | FMETTRS |
| MNXR99604 | FMETTRS_1 |
| MNXR99614 | FOMETRi |
| MNXR99614 | THFAT |
| MNXR99614 | MTAM |
| MNXR99614 | THFATm |
| MNXR99615 | FORA |
| MNXR99615 | FORAMD |
| MNXR99636 | FRD |
| MNXR99636 | SUCD1 |
| MNXR99636 | FRDm |
| MNXR99636 | SUCD1m |
| MNXR99641 | FRD7 |
| MNXR99641 | SUCDi |
| MNXR99667 | FTAL |
| MNXR99667 | FTCD |
| MNXR99668 | FTCL |
| MNXR99668 | FTHFCLm |
| MNXR99671 | FTHFI |
| MNXR99671 | FTHFI_1 |
| MNXR99905 | G6PDA |
| MNXR99905 | G6PDA_1 |
| MNXR99910 | G6PI2 |
| MNXR99910 | G6PI3 |
| MNXR99955 | GALCTD |
| MNXR99955 | GALCTD_1 |
| MNXR99962 | GALCTRt2 |
| MNXR99962 | GALCTt2r |
Thanks for collecting these here! We will definitely go through them for the next release.
@ChristianLieven, @Midnighter, the code that generated this list would also make a really nice unit test for memote
@zakandrewking: Thanks for looking into this. I guess the same should be done for the metabolites (see #274).
If you decide to merge entries, how will this be documented?
- Will the IDs be stored in "old_bigg_ids"?
- If you update models then accordingly, would it be possible to start a versioning of the models so that changes can easily be tracked?
When we merge things, we do store previous ids in old_bigg_ids
We are now building a web application from the ground up for model reconstruction, so it will solve many of the open challenges with bigg (collaboration, versioning, identifiers, etc.)
BTW, @willigott, thanks for all of the issues you opened. We do plan to make all of these fixes, either in BiGG Models itself, or in its successor.
@willigott would you mind sharing the code you used to generate this list with us over at https://github.com/opencobra/memote. We'd like to implement this as a test in our tool. Of course you're also more than welcome to implement it yourself and open a PR!
https://github.com/opencobra/memote/issues/240
@ChristianLieven: Sure, no problem. As this was just a very quick check, the code is not generic enough i.e. not of sufficient quality for a PR and I would also not know where and how exactly this should be incorporated, so I just leave it here; feel free to use/adapt whatever you consider as useful (I never gave it a try but maybe one could use DD-DeCaF's id-mapper to do this). I guess something similar should be done for metabolites, too (see #274) . Please also keep in mind that this only works for annotated entries; for example for http://bigg.ucsd.edu/universal/metabolites/C02712 and http://bigg.ucsd.edu/universal/metabolites/acmet one could not do it as the latter does not have any annotation; not sure what the best way is to filter those (same could apply to reactions).
import pandas as pd
import re
"""
This file determines potential duplicate reactions in bigg. Reactions are considered as duplicates if:
i) they have the same MetanetX ID
ii) they show the same compartment information (which is retrieved from the metabolite IDs)
"""
def retrieve_compartment_info(rea_string):
"""
given a reaction string, it will return compartment information based on the metabolite IDs' suffix
:param rea_string: reaction string
:return: compartment string
Example:
retrieve_compartment_info('atp_c + coa_c + ppa_c <-> adp_c + pi_c + ppcoa_c') returns 'c'
retrieve_compartment_info('acgam_e <-> acgam_p') returns 'ep'
"""
# extract all compounds from the reaction string
all_compounds = re.findall(r'\w+', rea_string)
# get sorted set of compartments
all_compartments = sorted(list(set(mi[-1] for mi in all_compounds if len(mi.split('_')) > 1)))
return ''.join(all_compartments)
# reaction information from bigg; downloaded from http://bigg.ucsd.edu/data_access
rea_bigg = pd.read_csv('bigg_models_reactions.txt', sep='\t')
# get the metanetx ID for a given bigg reaction
metnetx_pat = 'MetaNetX \(MNX\) Equation\: http\:\/\/identifiers\.org\/metanetx\.reaction\/(MNXR\d+)'
rea_bigg['metanetx_id'] = rea_bigg.loc[:, 'database_links'].str.extract(metnetx_pat, expand=False)
# for now, we are only interested in reactions with a metanetx ID
rea_bigg = rea_bigg.dropna(subset=['metanetx_id'])
# get the compartment info for a given bigg reaction
rea_bigg['comp_info_bigg'] = rea_bigg['reaction_string'].apply(lambda x: retrieve_compartment_info(x))
# for now we only check whether metanetx id and compartment are identical
rea_bigg = rea_bigg[['metanetx_id', 'comp_info_bigg', 'bigg_id']]
# group by metanetx id and compartment and identify groups with more than one member
dupls = rea_bigg.groupby(['metanetx_id', 'comp_info_bigg'])['metanetx_id'].transform('size') > 1
# select all potential duplicate reactions
rea_bigg_identical = rea_bigg[dupls].sort_values(['metanetx_id', 'comp_info_bigg', 'bigg_id']).reset_index(drop=True)
rea_bigg_identical.drop('comp_info_bigg', axis=1).to_csv('potential_identical_reactions_bigg.csv', index=False)
Thanks @willigott! You can follow the progress here: https://github.com/opencobra/memote/issues/240