nel3
commented
7 years ago Thanks for pointing that out. These come from different models, but should be merged.
Sent from my Android phone.
On Oct 20, 2016 1:14 PM, "Jeremy Zucker" notifications@github.com wrote:
Description of the issue
duplicate compounds are pervasive. For example, tagD and tagatD are the same compound and map to the same MetaNetX ID.
MetaNetX has identified many other duplicates: XREF Evidence Description MNX_ID MNXM1037 bigg:oxoargL inferred 2-Oxoarginine MNXM1037 bigg:5g2oxpt inferred 5-Guanidino-2-oxopentanoate MNXM1039 bigg:zcarote inferred zeta-Carotene MNXM1039 bigg:zcaro inferred zeta-Carotene MNXM1048 bigg:gcarote inferred gamma-Carotene MNXM1048 bigg:gcaro inferred gamma-Carotene MNXM105630 bigg:hso3 inferred HSO3- MNXM105630 bigg:so3 inferred Sulfite MNXM1155 bigg:phllqne inferred Phylloquinone MNXM1155 bigg:phyQ inferred Phylloquinone MNXM1157 bigg:slnt inferred selenite MNXM1157 bigg:selt inferred Selenite MNXM1163 bigg:5cmhm inferred 5-Carboxymethyl-2-hydroxymuconate MNXM1163 bigg:5cm2hmu inferred 5-Carboxymethyl-2-hydroxymuconate MNXM1176 bigg:4h2oxov inferred 4-Hydroxy-2-oxovalerate MNXM1176 bigg:4h2opntn inferred 4-Hydroxy-2-oxopentanoate MNXM12007 bigg:ksii_core4_pre1 structural keratan sulfate II biosynthesis, precursor 1 MNXM12007 bigg:ksii_core2_pre1 identity keratan sulfate II biosynthesis, precursor 1 MNXM12009 bigg:ksii_core4_pre10 structural keratan sulfate II biosynthesis, precursor 10 MNXM12009 bigg:ksii_core2_pre10 identity keratan sulfate II biosynthesis, precursor 10 MNXM12012 bigg:ksii_core2_pre3 identity keratan sulfate II biosynthesis, precursor 3 MNXM12012 bigg:ksii_core4_pre3 structural keratan sulfate II biosynthesis, precursor 3 MNXM12014 bigg:ksii_core2_pre4 identity keratan sulfate II biosynthesis, precursor 4 MNXM12014 bigg:ksii_core4_pre4 structural keratan sulfate II biosynthesis, precursor 4 MNXM12016 bigg:ksii_core4_pre5 structural keratan sulfate II biosynthesis, precursor 5 MNXM12016 bigg:ksii_core2_pre5 identity keratan sulfate II biosynthesis, precursor 5 MNXM12019 bigg:ksii_core2_pre6 identity keratan sulfate II biosynthesis, precursor 6 MNXM12019 bigg:ksii_core4_pre6 structural keratan sulfate II biosynthesis, precursor 6 MNXM12021 bigg:ksii_core4_pre7 structural keratan sulfate II biosynthesis, precursor 7 MNXM12021 bigg:ksii_core2_pre7 identity keratan sulfate II biosynthesis, precursor 7 MNXM12023 bigg:ksii_core4_pre8 structural keratan sulfate II biosynthesis, precursor 8 MNXM12023 bigg:ksii_core2_pre8 identity keratan sulfate II biosynthesis, precursor 8 MNXM12025 bigg:ksii_core2_pre9 identity keratan sulfate II biosynthesis, precursor 9 MNXM12025 bigg:ksii_core4_pre9 structural keratan sulfate II biosynthesis, precursor 9 MNXM1206 bigg:kdolipid4_HP inferred KDO-lipid IV(A) MNXM1206 bigg:kdolipid4 inferred KDO-lipid IV(A) MNXM1231 bigg:foam inferred Formamide MNXM1231 bigg:frmd inferred Formamide MNXM1243 bigg:Ncbmpts inferred N-Carbamoylputrescine MNXM1243 bigg:cbmp inferred N-carbamoylputrescine MNXM1272 bigg:chla inferred Chlorophyll a MNXM1272 bigg:cholphya inferred Chlorophyll a MNXM1352 bigg:omppp9me inferred 13(1)-Oxo-magnesium-protoporphyrin IX 13-monom... MNXM1352 bigg:omppp9 inferred 13(1)-Oxo-magnesium-protoporphyrin IX 13-monom... MNXM141 bigg:cmp_nate inferred CMP-N-acetylneuraminate MNXM141 bigg:cmpacna inferred CMP-N-acetylneuraminate MNXM145541 bigg:fdxo_42 identity ferredoxin (oxidized form 4:2) MNXM145541 bigg:fdxo_4_2 inferred ferredoxin (oxidized form 4:2) MNXM145542 bigg:fdxr_42 identity ferredoxin (reduced form 4:2) MNXM145542 bigg:fdxr_4_2 inferred ferredoxin (reduced form 4:2) MNXM145572 bigg:udcpo4 structural Undecaprenyl diphosphate galactose-rhamnose-ma... MNXM145572 bigg:udcdpgalrmnmanabe identity Undecaprenyl-diphosphate- galactose-rhamnose-ma... MNXM145629 bigg:2ohed inferred 2-Oxohept-3-ene-1,7-dioate MNXM145629 bigg:2oh3d inferred 2-Oxohept-3-ene-1,7-dioate MNXM145921 bigg:pcrd inferred Plastocyanin(Cu+) MNXM145921 bigg:pccu1p identity Plastocyanin(Cu+) MNXM145922 bigg:pccu2p identity Plastocyanin(Cu2+) MNXM145922 bigg:pcox inferred Plastocyanin(Cu2+) MNXM147330 bigg:udcpg inferred Undecaprenyl diphosphate galactose MNXM147330 bigg:udcdpgal identity Undecaprenyl-diphosphate-galactose MNXM147331 bigg:udcpgr structural Undecaprenyl diphosphate galactose-rhamnose MNXM147331 bigg:udcdpgalrmn identity Undecaprenyl-diphosphate- galactose-rhamnose MNXM147332 bigg:udcdpgalrmnman identity Undecaprenyl-diphosphate- galactose-rhamnose-ma... MNXM147332 bigg:udcpgrm structural Undecaprenyl diphosphate galactose-rhamnose-ma... MNXM147493 bigg:kokdolipid4 identity KO-KDO-LIPID A MNXM147493 bigg:kokdolipidA inferred KO-KDO-LIPID A MNXM1503 bigg:stc inferred stachyose MNXM1503 bigg:stys inferred stachyose MNXM1521 bigg:2c25dho inferred 2-Carboxy-2,5-dihydro-5-oxofuran-2-acetate MNXM1521 bigg:4cml inferred 4-Carboxymuconolactone MNXM1541 bigg:bcrptxan inferred beta-Cryptoxanthin MNXM1541 bigg:bcryptox inferred beta-Cryptoxanthin MNXM1623 bigg:4h2kpi inferred 4-Hydroxy-2-ketopimelate MNXM1623 bigg:24dhhed inferred 2,4-Dihydroxyhept-2-enedioate MNXM1628 bigg:2h5cmmusa inferred 2-Hydroxy-5-carboxymethylmuconate- Semialdehyde MNXM1628 bigg:5cmhmsa inferred 2-Hydroxy-5-carboxymethylmuconate- Semialdehyde MNXM1641 bigg:pcdme inferred 2-Phospho-4-(cytidine 5'-diphospho)-2-C-methyl... MNXM1641 bigg:2p4c2me inferred 2-phospho-4-(cytidine 5'-diphospho)-2-C-methyl... MNXM169 bigg:fdxrd inferred Reduced ferredoxin MNXM169 bigg:fdxr_2_2 inferred Reduced ferredoxin MNXM1692 bigg:AEP inferred 2-Aminoethylphosphonate MNXM1692 bigg:2ameph inferred (2-Aminoethyl)phosphonate MNXM1697 bigg:appp inferred D-1-Aminopropan-2-ol-O-phosphate MNXM1697 bigg:applp inferred D-1-Aminopropan-2-ol O-phosphate MNXM1927 bigg:gulnL inferred L-gulonate MNXM1927 bigg:guln inferred L-Gulonate MNXM2 bigg:h2o inferred H2O MNXM2 bigg:oh1 inferred hydroxide ion MNXM2361 bigg:codscl4 inferred Cobalt-precorrin-4 MNXM2361 bigg:copre4 inferred cobalt-precorrin 4 MNXM2379 bigg:gdchola inferred glycochenodeoxycholate MNXM2379 bigg:dgchol inferred Chenodeoxyglycocholate MNXM2428 bigg:scysL inferred S-Sulfo-L-cysteine MNXM2428 bigg:slcys inferred S-Sulfo-L-cysteine MNXM2522 bigg:yvite inferred gamma-Tocopherol MNXM2522 bigg:gtocophe inferred gamma-Tocopherol MNXM2563 bigg:hpglu inferred Tetrahydropteroyltri L glutamate MNXM2563 bigg:thglu inferred Tetrahydropteroyltri-L-glutamate MNXM2623 bigg:5mthglu inferred 5-Methyltetrahydropteroyltri-L-glutamate MNXM2623 bigg:mhpglu inferred 5 Methyltetrahydropteroyltri L glutamate MNXM264 bigg:coucoa inferred p coumaroyl CoA MNXM264 bigg:4cmcoa inferred 4-Coumaroyl-CoA MNXM2653 bigg:codscl6b inferred Cobalt-precorrin-6b MNXM2653 bigg:codhpre6 inferred cobalt-dihydro-precorrin 6 MNXM2741 bigg:atocophe inferred alpha-Tocopherol MNXM2741 bigg:avite1 inferred alpha-Tocopherol MNXM2782 bigg:mtpp inferred 3-methylthiopropionate MNXM2782 bigg:3mtpa inferred 3-(Methylthio)propionic acid MNXM3059 bigg:4pcys inferred N-((R)-pantothenoyl)-L-cysteine MNXM3059 bigg:ptcys inferred N-Pantothenoylcysteine MNXM312 bigg:op4en inferred 2-Oxopent-4-enoate MNXM312 bigg:chpd inferred 2-Hydroxy-2,4-pentadienoate MNXM3160 bigg:mpq inferred 2-Methyl-6-phytylquinol MNXM3160 bigg:2m6phol inferred 2-Methyl-6-phytylquinol MNXM3194 bigg:6ctd inferred 6-carboxy-5,6,7,8-tetrahydropterin MNXM3194 bigg:cph4 inferred 6-carboxy-5,6,7,8-tetrahydropterin MNXM320 bigg:phenol inferred Phenol MNXM320 bigg:phen inferred Phenol MNXM3356 bigg:salcn6p inferred Salicin 6 phosphate MNXM3356 bigg:salc6p inferred Salicin 6-phosphate MNXM3505 bigg:5cohe inferred 5-Carboxy-2-oxohept-3-enedioate MNXM3505 bigg:5c2o3ed inferred 5-Carboxy-2-oxohept-3-enedioate MNXM3591 bigg:echn inferred Echinenone MNXM3591 bigg:echin inferred Echinenone MNXM3863 bigg:4hphac inferred 4-Hydroxyphenylacetate MNXM3863 bigg:4hoxpac inferred 4 Hydroxyphenylacetic acid MNXM3903 bigg:zxan inferred Zeinoxanthin MNXM3903 bigg:crpxan inferred alpha-Cryptoxanthin MNXM403 bigg:zaxan inferred Zeaxanthin MNXM403 bigg:zeax inferred Zeaxanthin MNXM409 bigg:2h3kmtp inferred 2-Hydroxy-3-keto-5- methylthiopentenyl-1-phosphate MNXM409 bigg:hkmpp inferred 2-Hydroxy-3-keto-5- methylthiopentenyl-1-phosphate MNXM41 bigg:glcD inferred D-Glucose MNXM41 bigg:glc_B inferred D-Glucose MNXM41358 bigg:fucfucgalacglcgalacglcgal14acglcgalglusid... structural (Gal)4 (Glc)1 (GlcNAc)3 (LFuc)2 (Cer)1 MNXM41358 bigg:fucfucgalacglc13galacglcgal14acglcgalglus... inferred (Gal)4 (Glc)1 (GlcNAc)3 (LFuc)2 (Cer)1 MNXM4266 bigg:23dmphol inferred 2,3-Dimethyl-5-phytylquinol MNXM4266 bigg:dmpq inferred 2,3-Dimethyl-5-phytylquinol MNXM445 bigg:lyc inferred Lycopene MNXM445 bigg:lycop inferred Lycopene MNXM4488 bigg:bvite inferred beta-tocopherol MNXM4488 bigg:btocophe inferred beta-Tocopherol MNXM4610 bigg:hemeA inferred Heme A MNXM4610 bigg:hemeA_1 inferred Heme A MNXM4615 bigg:dplpt inferred Diploptene MNXM4615 bigg:dptne inferred Diploptene MNXM474 bigg:quin_kt inferred Quinate MNXM474 bigg:quin inferred Quinate MNXM47441 bigg:copre6 inferred cobalt-precorrin 6 MNXM47441 bigg:codscl6a inferred Cobalt-precorrin-6a MNXM47447 bigg:copre2 inferred cobalt-precorrin 2 MNXM47447 bigg:codscl2 inferred Cobalt-precorrin-2 MNXM47647 bigg:colipaA inferred core oligosaccharide lipid A MNXM47647 bigg:colipa inferred core oligosaccharide lipid A MNXM4851 bigg:tamlgnc inferred tri-methyl lignoceric acid MNXM4851 bigg:tmlgnc structural tri-methyl lignoceric acid MNXM491 bigg:ppmi1346p inferred Diphosphoinositol tetrakisphosphate MNXM491 bigg:minohp inferred myo-Inositol hexakisphosphate MNXM494 bigg:dhmtp inferred 1,2-Dihydroxy-5-(methylthio)pent-1-en-3-one MNXM494 bigg:12dmpo inferred 1,2-Dihydroxy-5-(methylthio)pent-1-en-3-one MNXM5121 bigg:dtocophe inferred delta-Tocopherol MNXM5121 bigg:dvite inferred delta-Tocopherol MNXM513 bigg:3ohodcoa inferred 3 Oxooctadecanoyl CoA MNXM513 bigg:3oodcoa inferred 3-Oxooctadecanoyl-CoA MNXM535 bigg:ckdo inferred CMP-3-deoxy-D-manno-octulosonate MNXM535 bigg:cmpkdo inferred CMP-3-deoxy-D-manno-octulosonate MNXM56168 bigg:hphhlipaA inferred heptosyl phospho heptosyl heptosyl kdo2 lipidA MNXM56168 bigg:hphhlipa inferred heptosyl-phospho-heptosyl- heptosyl-kdo2-lipidA MNXM563 bigg:formcoa inferred Formyl-CoA MNXM563 bigg:forcoa inferred Formyl-CoA MNXM5750 bigg:focytc inferred Ferrocytochrome MNXM5750 bigg:focytb inferred Ferrocytochrome MNXM60922 bigg:hmppp9me inferred 13(1)-Hydroxy-magnesium-protoporphyrin IX 13-m... MNXM60922 bigg:hmppp9 inferred 13(1)-Hydroxy-magnesium-protoporphyrin IX 13-m... MNXM614 bigg:caro inferred beta-Carotene MNXM614 bigg:bcarote inferred beta-Carotene MNXM626 bigg:4tmeabutn inferred 4-Trimethylammoniobutanoate MNXM626 bigg:gbbtn inferred gamma-butyrobetaine MNXM631 bigg:chlld inferred Chlorophyllide a MNXM631 bigg:chlda inferred Chlorophyllide a MNXM643 bigg:dhocholoylcoa inferred 3alpha,7alpha,12alpha,26- Tetrahydroxy-5beta-ch... MNXM643 bigg:xoltetrol inferred 3alpha,7alpha,12alpha,26- Tetrahydroxy-5beta-ch... MNXM6536 bigg:m5masnB1 identity (alpha-D-mannosyl)5-beta-D- mannosyl-diacetylch... MNXM6536 bigg:m5masnB2 inferred (alpha-D-mannosyl)5-beta-D- mannosyl-diacetylch... MNXM6536 bigg:m5masnC structural (alpha-D-mannosyl)5-beta-D- mannosyl-diacetylch... MNXM672 bigg:pre2 inferred dihydrosirohydrochlorin MNXM672 bigg:dscl inferred dihydrosirohydrochlorin MNXM685 bigg:rblL inferred L-Ribulose MNXM685 bigg:xyluD inferred D-Xylulose MNXM700 bigg:urocan inferred Urocanate MNXM700 bigg:urcan inferred Urocanate MNXM710 bigg:lum3 inferred Lumisterol 3 MNXM710 bigg:7dhchsterol inferred 7-Dehydrocholesterol MNXM75042 bigg:phphtna inferred Pheophytin a MNXM75042 bigg:chlaemr inferred Chlorophyll a' MNXM7865 bigg:uGgla inferred UDP-N-acetylmuramoyl-L-alanyl- gamma-D-glutamyl... MNXM7865 bigg:uAgla inferred UDP-N-acetylmuramoyl-L-alanyl- D-glutamyl-L-lys... MNXM8637 bigg:gd1a_hs identity GD1a (homo sapiens) MNXM8637 bigg:gd1alpha_hs inferred GD1a (homo sapiens) MNXM903 bigg:phdp inferred Phytyl diphosphate MNXM903 bigg:pdp inferred Phytyl diphosphate MNXM90394 bigg:4iz5pp inferred 4-Imidazolone-5-propanoate MNXM90394 bigg:4izp inferred 4-Imidazolone-5-propanoate MNXM9139 bigg:tetpent3crn identity tetracosapentaenoyl carnitine MNXM9139 bigg:tetpent6crn structural tetracosapentaenoyl carnitine MNXM920 bigg:hacon_T inferred trans-homoaconitate MNXM920 bigg:hacon_C inferred cis-homoaconitate MNXM92204 bigg:copre3 inferred cobalt-precorrin 3 MNXM92204 bigg:codscl3 inferred Cobalt-precorrin-3 MNXM92210 bigg:cobn inferred Cobyrinate MNXM92210 bigg:cobya inferred Cobyrinate MNXM92401 bigg:tagatD inferred D-Tagatose MNXM92401 bigg:tagD inferred D-Tagatose MNXM927 bigg:Lcystin inferred L Cystine MNXM927 bigg:cysi__L inferred L-Cystine MNXM933 bigg:mmtsa inferred (S)-Methylmalonate semialdehyde MNXM933 bigg:mmsa inferred (S)-Methylmalonate semialdehyde MNXM9451 bigg:m6masnB2 inferred (alpha-D-mannosyl)6-beta-D- mannosyl-diacetylch... MNXM9451 bigg:m6masnC inferred (alpha-D-mannosyl)6-beta-D- mannosyl-diacetylch... MNXM9451 bigg:m6masnA identity (alpha-D-mannosyl)6-beta-D- mannosyl-diacetylch... MNXM9451 bigg:m6masnB1 structural (alpha-D-mannosyl)6-beta-D- mannosyl-diacetylch... MNXM949 bigg:neuspn inferred Neurosporene MNXM949 bigg:norsp inferred Neurosporene MNXM99 bigg:glc_A inferred alpha-D-glucose MNXM99 bigg:Glc_aD inferred alpha D-glucose Page
http://bigg.ucsd.edu/universal/metabolites/tag__D Browser
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zakandrewking
Description of the issue
duplicate compounds are pervasive. For example, tagD and tagatD are the same compound and map to the same MetaNetX ID.
MetaNetX has identified many other duplicates:
Page
http://bigg.ucsd.edu/universal/metabolites/tag__D
Browser
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