From 543c1ba6808035620ef4658182be771e6c076132 Mon Sep 17 00:00:00 2001 From: Jiahao Luo <67491919+JHL-452b@users.noreply.github.com> Date: Mon, 19 Jun 2023 08:51:26 +0800 Subject: [PATCH 1/3] fix-remove mets and rxns --- .../deprecatedMetabolites.tsv | 3 +- .../deprecatedReactions.tsv | 3 + model/Human-GEM.yml | 66 ++----------------- model/metabolites.tsv | 3 +- model/reactions.tsv | 9 +-- 5 files changed, 13 insertions(+), 71 deletions(-) diff --git a/data/deprecatedIdentifiers/deprecatedMetabolites.tsv b/data/deprecatedIdentifiers/deprecatedMetabolites.tsv index b1cf6528..c1f8c166 100644 --- a/data/deprecatedIdentifiers/deprecatedMetabolites.tsv +++ b/data/deprecatedIdentifiers/deprecatedMetabolites.tsv @@ -2203,4 +2203,5 @@ mets metsNoComp metBiGGID metKEGGID metHMDBID metChEBIID metPubChemID metLipidMa "MAM03573m" "MAM03573" "etfox" "" "" "" "" "" "" "" "etfox" "MNXM11479" "" "etfox_m" "MAM03574m" "MAM03574" "etfrd" "" "" "" "" "" "" "" "etfrd" "MNXM11480" "" "etfrd_m" "MAM03494c" "MAM03494" "c3dc" "" "" "" "22833583" "" "" "" "c3dc" "" "" "c3dc_c" -"MAM03494e" "MAM03494" "c3dc" "" "" "" "22833583" "" "" "" "c3dc" "" "" "c3dc_s" \ No newline at end of file +"MAM03494e" "MAM03494" "c3dc" "" "" "" "22833583" "" "" "" "c3dc" "" "" "c3dc_s" +"MAM03684e" "MAM03684" "hxa" "" "" "" "" "" "" "" "hxa" "MNXM1653" "" "hxa_s" diff --git a/data/deprecatedIdentifiers/deprecatedReactions.tsv b/data/deprecatedIdentifiers/deprecatedReactions.tsv index 96e470b5..5474d1cc 100644 --- a/data/deprecatedIdentifiers/deprecatedReactions.tsv +++ b/data/deprecatedIdentifiers/deprecatedReactions.tsv @@ -111,3 +111,6 @@ rxns rxnKEGGID rxnBiGGID rxnEHMNID rxnHepatoNET1ID rxnREACTOMEID rxnRecon3DID rx "MAR20015" "R02549" "ABUTD;ABUTDm;R_ABUTD;R_ABUTDm" "" "" "" "" "MNXR95191" "" "" "" 0 "RHEA:19105" "" "" "MAR20014" "R03283" "R_TMABADH;TMABADH" "" "" "" "" "MNXR104876" "" "" "" 0 "RHEA:17985" "" "" "MAR20052" "" "ALDD21;RE3076X;R_ALDD21;R_RE3076X" "" "" "" "" "MNXR95747" "" "" "" 0 "RHEA:44016" "" "" +"MAR09949" "" "FACOAE60" "" "" "" "HXCOAc" "MNXR99139" "" "" "" 0 "" "" "HXCOAc" +"MAR11292" "" "HXAt3" "" "" "" "HXAt3" "" "" "" "" 0 "" "" "HXAt3" +"MAR11293" "" "EX_hxa_e" "" "" "" "EX_hxa[e]" "MNXR98664" "" "" "" 0 "" "" "EX_hxa[e]" diff --git a/model/Human-GEM.yml b/model/Human-GEM.yml index b2c7fa08..57f17de5 100644 --- a/model/Human-GEM.yml +++ b/model/Human-GEM.yml @@ -4,7 +4,7 @@ short_name: "Human-GEM" full_name: "Generic genome-scale metabolic model of Homo sapiens" version: "" - date: "2023-06-07" + date: "2023-06-19" taxonomy: "9606" github: "https://github.com/SysBioChalmers/Human-GEM" description: "Genome-scale metabolic models are valuable tools to study metabolism and provide a scaffold for the integrative analysis of omics data. This is the latest version of Human-GEM, which is a genome-scale metabolic model of a generic human cell. The objective of Human-GEM is to serve as a community model for enabling integrative and mechanistic studies of human metabolism." @@ -58993,14 +58993,6 @@ - charge: 0 - inchis: "" - metFrom: "Recon3D" - - !!omap - - id: "MAM03684e" - - name: "Hexanoate (N-C6:0)" - - compartment: "e" - - formula: "C6H11O2" - - charge: -1 - - inchis: "" - - metFrom: "Recon3D" - !!omap - id: "MAM01954c" - name: "glcnac-alpha-1,4-core 1" @@ -167720,7 +167712,7 @@ - upper_bound: 1000 - gene_reaction_rule: "ENSG00000113396 or ENSG00000121769 or ENSG00000130304 or ENSG00000135218 or ENSG00000143554 or ENSG00000145384 or ENSG00000163586 or ENSG00000164434 or ENSG00000164687 or ENSG00000167114 or ENSG00000170231 or ENSG00000170323 or ENSG00000197416 or ENSG00000205186" - rxnNotes: "" - - rxnFrom: "HMRdatabase" + - rxnFrom: "HMRdatabase;Recon3D" - eccodes: "" - references: "" - subsystem: @@ -212293,7 +212285,7 @@ - upper_bound: 1000 - gene_reaction_rule: "" - rxnNotes: "" - - rxnFrom: "HMRdatabase" + - rxnFrom: "HMRdatabase;Recon3D" - eccodes: "" - references: "" - subsystem: @@ -251030,25 +251022,6 @@ - subsystem: - "Fatty acid oxidation" - confidence_score: 0 - - !!omap - - id: "MAR09949" - - name: "Acylcoa Hydrolase, Cytosolic" - - metabolites: !!omap - - MAM01597c: 1 - - MAM02039c: 1 - - MAM02040c: -1 - - MAM02122c: -1 - - MAM03684c: 1 - - lower_bound: -1000 - - upper_bound: 1000 - - gene_reaction_rule: "" - - rxnNotes: "" - - rxnFrom: "Recon3D" - - eccodes: "3.1.2.2" - - references: "" - - subsystem: - - "Fatty acid oxidation" - - confidence_score: 0 - !!omap - id: "MAR09950" - name: "Hydrolysis of Tetradecadienoyl Coenzyme A to Cis-5, 8-Tetradecadienoic Acid" @@ -271801,37 +271774,6 @@ - subsystem: - "Transport reactions" - confidence_score: 0 - - !!omap - - id: "MAR11292" - - name: "Transport of Hexanoate (N-C6:0), Extracellular" - - metabolites: !!omap - - MAM03684c: -1 - - MAM03684e: 1 - - lower_bound: -1000 - - upper_bound: 1000 - - gene_reaction_rule: "" - - rxnNotes: "" - - rxnFrom: "Recon3D" - - eccodes: "" - - references: "" - - subsystem: - - "Transport reactions" - - confidence_score: 0 - - !!omap - - id: "MAR11293" - - name: "Exchange of Hexanoate (N-C6:0)" - - metabolites: !!omap - - MAM03684e: -1 - - lower_bound: -1000 - - upper_bound: 1000 - - gene_reaction_rule: "" - - rxnNotes: "" - - rxnFrom: "Recon3D" - - eccodes: "" - - references: "" - - subsystem: - - "Exchange/demand reactions" - - confidence_score: 0 - !!omap - id: "MAR11294" - name: "Hydrolysis of Fatty Acyl Coenzyme A (14:1)" @@ -275993,7 +275935,7 @@ - gene_reaction_rule: "" - rxnNotes: "https://www.springer.com/gp/book/9789400957800" - rxnFrom: "Recon3D" - - eccodes: "" + - eccodes: "3.1.2.2" - references: "PMID:8371066" - subsystem: - "Fatty acid oxidation" diff --git a/model/metabolites.tsv b/model/metabolites.tsv index a4d6f762..0e79611c 100644 --- a/model/metabolites.tsv +++ b/model/metabolites.tsv @@ -3671,7 +3671,7 @@ mets metsNoComp metBiGGID metKEGGID metHMDBID metChEBIID metPubChemID metLipidMa "MAM02119m" "MAM02119" "6thf" "" "" "" "169691" "" "" "" "6thf" "MNXM3616" "m02119m" "m02119m" "MAM02119e" "MAM02119" "6thf" "" "" "" "169691" "" "" "" "6thf" "MNXM3616" "m02119s" "m02119s" "MAM02120c" "MAM02120" "" "C01585" "HMDB0000535" "CHEBI:17120;CHEBI:30776" "" "LMFA01010006" "" "" "caproic" "MNXM1653" "m02120c" "m02120c" -"MAM02120e" "MAM02120" "" "C01585" "HMDB0000535" "CHEBI:17120;CHEBI:30776" "" "LMFA01010006" "" "" "caproic" "MNXM1653" "m02120s" "m02120s" +"MAM02120e" "MAM02120" "hxa" "C01585" "HMDB0000535" "CHEBI:17120;CHEBI:30776" "" "LMFA01010006" "" "" "caproic;hxa" "MNXM1653" "m02120s" "hxa_s;m02120s" "MAM02121c" "MAM02121" "" "C05749" "" "" "" "" "" "HC01592" "HC01592" "MNXM23683" "m02121c" "m02121c" "MAM02122c" "MAM02122" "" "C05270" "HMDB0002845" "CHEBI:27540" "440611" "LMFA07050001" "" "HC01409" "hxcoa" "MNXM162502;MNXM553" "m02122c" "m02122c" "MAM02122m" "MAM02122" "" "C05270" "HMDB0002845" "CHEBI:27540" "440611" "LMFA07050001" "" "HC01409" "hxcoa" "MNXM162502;MNXM553" "m02122m" "m02122m" @@ -7372,7 +7372,6 @@ mets metsNoComp metBiGGID metKEGGID metHMDBID metChEBIID metPubChemID metLipidMa "MAM04078c" "MAM04078" "" "" "" "" "" "" "" "" "xolest204_hs" "" "" "xolest204_hs_c" "MAM04080c" "MAM04080" "xolest226_hs" "" "" "" "" "" "" "" "xolest226_hs" "" "" "xolest226_hs_c" "MAM02908e" "MAM02908" "sphmyln_hs" "C00550" "" "CHEBI:17636" "" "LMSP03010000" "" "HC02007" "sphmyln_hs" "MNXM5930" "" "m02908s" -"MAM03684e" "MAM03684" "hxa" "" "" "" "" "" "" "" "hxa" "MNXM1653" "" "hxa_s" "MAM01954c" "MAM01954" "gncore1" "" "" "" "" "" "" "" "gncore1" "MNXM18091" "" "m01954c" "MAM01954e" "MAM01954" "gncore1" "" "" "" "" "" "" "" "gncore1" "MNXM18091" "" "m01954s" "MAM03394c" "MAM03394" "Lhcystin" "" "" "" "" "" "" "" "Lhcystin" "" "" "Lhcystin_c" diff --git a/model/reactions.tsv b/model/reactions.tsv index dc2c1b61..f524dbba 100644 --- a/model/reactions.tsv +++ b/model/reactions.tsv @@ -5132,7 +5132,7 @@ rxns rxnKEGGID rxnBiGGID rxnEHMNID rxnHepatoNET1ID rxnREACTOMEID rxnRecon3DID rx "MAR00019" "" "" "" "" "" "HMR_0019" "" "HMR_0019" "RCR40176" "" 0 "" "" "HMR_0019" "MAR00155" "" "" "" "" "" "HMR_0155" "" "HMR_0155" "RCR40028" "4.C.1.1.5;4.C.1.1.8" 0 "" "" "HMR_0155" "MAR00164" "" "" "" "" "" "HMR_0164" "" "HMR_0164" "RCR40177" "4.C.1.1.5;4.C.1.1.8" 0 "" "" "HMR_0164" -"MAR00167" "" "" "" "" "" "HMR_0167" "" "HMR_0167" "RCR40350" "4.C.1.1.5;4.C.1.1.8" 0 "" "" "HMR_0167" +"MAR00167" "" "HXAt3" "" "" "" "HMR_0167;HXAt3" "" "HMR_0167" "RCR40350" "4.C.1.1.5;4.C.1.1.8" 0 "" "" "HMR_0167;HXAt3" "MAR00170" "" "" "" "" "" "HMR_0170" "" "HMR_0170" "RCR40351" "4.C.1.1.5;4.C.1.1.8" 0 "" "" "HMR_0170" "MAR00173" "" "" "" "" "" "OCTAt;OCTAte" "" "HMR_0173" "RCR40178" "4.C.1.1.5;4.C.1.1.8" 0 "" "" "HMR_0173" "MAR00176" "" "" "" "" "" "HMR_0176" "" "HMR_0176" "RCR40352" "4.C.1.1.5;4.C.1.1.8" 0 "" "" "HMR_0176" @@ -7655,7 +7655,7 @@ rxns rxnKEGGID rxnBiGGID rxnEHMNID rxnHepatoNET1ID rxnREACTOMEID rxnRecon3DID rx "MAR09808" "" "" "" "" "" "EX_ppa[e]" "" "HMR_9808" "RCR30309" "" 0 "" "" "HMR_9808" "MAR09809" "" "" "" "" "" "EX_but[e]" "" "HMR_9809" "RCR30041" "" 0 "" "" "HMR_9809" "MAR09810" "" "" "" "" "" "EX_M03134[e]" "" "HMR_9810" "RCR30012" "" 0 "" "" "HMR_9810" -"MAR09811" "" "" "" "" "" "EX_caproic[e]" "" "HMR_9811" "RCR30310" "" 0 "" "" "HMR_9811" +"MAR09811" "" "EX_hxa_e" "" "" "" "EX_caproic[e];EX_hxa[e]" "MNXR98664" "HMR_9811" "RCR30310" "" 0 "" "" "EX_hxa[e];HMR_9811" "MAR09812" "" "" "" "" "" "EX_M02108[e]" "" "HMR_9812" "RCR30311" "" 0 "" "" "HMR_9812" "MAR09813" "" "" "" "" "" "EX_octa[e]" "" "HMR_9813" "RCR30142" "" 0 "" "" "HMR_9813" "MAR09814" "" "" "" "" "" "EX_C01601[e]" "" "HMR_9814" "RCR30312" "" 0 "" "" "HMR_9814" @@ -9846,7 +9846,6 @@ rxns rxnKEGGID rxnBiGGID rxnEHMNID rxnHepatoNET1ID rxnREACTOMEID rxnRecon3DID rx "MAR09946" "" "" "" "" "" "XOLEST204CEH" "" "" "" "" 0 "" "" "XOLEST204CEH" "MAR09947" "" "XOLEST226CEH" "" "" "" "XOLEST226CEH" "" "" "" "" 0 "" "" "XOLEST226CEH" "MAR09948" "" "CE4843HYDc" "" "" "" "CE4843HYDc" "" "" "" "" 0 "" "" "CE4843HYDc" -"MAR09949" "" "FACOAE60" "" "" "" "HXCOAc" "MNXR99139" "" "" "" 0 "" "" "HXCOAc" "MAR09950" "" "TETDECA511ACc" "" "" "" "TETDECA511ACc" "" "" "" "" 0 "" "" "TETDECA511ACc" "MAR09951" "" "GPDDACHOL" "" "" "" "GPDDACHOL" "" "" "" "" 0 "" "" "GPDDACHOL" "MAR09952" "" "ACLYSHYc" "" "" "" "ACLYSHYc" "" "" "" "" 0 "" "" "ACLYSHYc" @@ -11076,8 +11075,6 @@ rxns rxnKEGGID rxnBiGGID rxnEHMNID rxnHepatoNET1ID rxnREACTOMEID rxnRecon3DID rx "MAR11289" "" "PHEACGLYtm" "" "" "" "PHEACGLYtm" "MNXR157011" "" "" "" 0 "" "" "PHEACGLYtm" "MAR11290" "" "HXAt1" "" "" "" "HXAt1" "" "" "" "" 0 "" "" "HXAt1" "MAR11291" "" "HXAt2" "" "" "" "HXAt2" "" "" "" "" 0 "" "" "HXAt2" -"MAR11292" "" "HXAt3" "" "" "" "HXAt3" "" "" "" "" 0 "" "" "HXAt3" -"MAR11293" "" "EX_hxa_e" "" "" "" "EX_hxa[e]" "MNXR98664" "" "" "" 0 "" "" "EX_hxa[e]" "MAR11294" "" "TTDCEAc" "" "" "" "TTDCEAc" "" "" "" "" 0 "" "" "TTDCEAc" "MAR11295" "" "PACCOALm" "" "" "" "PACCOALm" "" "" "" "" 0 "" "" "PACCOALm" "MAR11296" "" "PACALDtm" "" "" "" "PACALDtm" "MNXR102312" "" "" "" 0 "" "" "PACALDtm" @@ -11326,7 +11323,7 @@ rxns rxnKEGGID rxnBiGGID rxnEHMNID rxnHepatoNET1ID rxnREACTOMEID rxnRecon3DID rx "MAR11541" "" "3OHSUBACtxc" "" "" "" "3OHSUBACtxc" "" "" "" "" 0 "" "" "3OHSUBACtxc" "MAR11542" "" "3OHSUBACte" "" "" "" "3OHSUBACte" "" "" "" "" 0 "" "" "3OHSUBACte" "MAR11543" "" "EX_3ohsubac_e" "" "" "" "EX_3ohsubac[e]" "" "" "" "" 0 "" "" "EX_3ohsubac[e]" -"MAR11544" "" "CAPROICc" "" "" "" "CAPROICc" "" "" "" "" 0 "" "" "CAPROICc" +"MAR11544" "" "CAPROICc;FACOAE60" "" "" "" "CAPROICc;HXCOAc" "MNXR99139" "" "" "" 0 "" "" "CAPROICc;HXCOAc" "MAR11545" "" "5OHHEXAc" "" "" "" "5OHHEXAc" "" "" "" "" 0 "" "" "5OHHEXAc" "MAR11546" "" "5OHHEXAte" "" "" "" "5OHHEXAte" "" "" "" "" 0 "" "" "5OHHEXAte" "MAR11547" "" "EX_5ohhexa_e" "" "" "" "EX_5ohhexa[e]" "" "" "" "" 0 "" "" "EX_5ohhexa[e]" From 5fbc4d47010b38c47ec2005c37fe205fa18409e9 Mon Sep 17 00:00:00 2001 From: Jiahao Luo <67491919+JHL-452b@users.noreply.github.com> Date: Mon, 19 Jun 2023 09:35:58 +0800 Subject: [PATCH 2/3] fix-change MetaNetX ID annotations --- model/metabolites.tsv | 62 +++++++++++++++++++++---------------------- 1 file changed, 31 insertions(+), 31 deletions(-) diff --git a/model/metabolites.tsv b/model/metabolites.tsv index 0e79611c..d1bd1e61 100644 --- a/model/metabolites.tsv +++ b/model/metabolites.tsv @@ -516,7 +516,7 @@ mets metsNoComp metBiGGID metKEGGID metHMDBID metChEBIID metPubChemID metLipidMa "MAM00270c" "MAM00270" "wharachd" "C14748" "" "CHEBI:34306" "5283157" "" "" "" "wharachd" "MNXM22451" "m00270c" "m00270c" "MAM00270r" "MAM00270" "wharachd" "C14748" "" "CHEBI:34306" "5283157" "" "" "" "wharachd" "MNXM22451" "m00270r" "m00270r" "MAM00271c" "MAM00271" "" "" "" "" "" "" "CE6447" "" "CE6447" "MNXM163636" "m00271c" "m00271c" -"MAM00272c" "MAM00272" "" "" "" "" "" "" "CE6459" "" "CE6459" "MNXM164048" "m00272c" "m00272c" +"MAM00272c" "MAM00272" "" "" "" "" "" "" "CE6459" "" "CE6459" "MNXM727334" "m00272c" "m00272c" "MAM00273c" "MAM00273" "" "" "" "" "" "" "CE6458" "" "CE6458" "MNXM164048" "m00273c" "m00273c" "MAM00274c" "MAM00274" "" "" "" "" "" "" "CE2304" "" "CE2304" "MNXM150158" "m00274c" "m00274c" "MAM00274r" "MAM00274" "" "" "" "" "" "" "CE2304" "" "CE2304" "MNXM150158" "m00274r" "m00274r" @@ -697,7 +697,7 @@ mets metsNoComp metBiGGID metKEGGID metHMDBID metChEBIID metPubChemID metLipidMa "MAM00380x" "MAM00380" "15HPET" "C05966" "HMDB0004244" "CHEBI:15628" "5280893" "LMFA03060014" "" "" "15HPET" "MNXM162620;MNXM2314" "m00380p" "m00380p" "MAM00380r" "MAM00380" "15HPET" "C05966" "HMDB0004244" "CHEBI:15628" "5280893" "LMFA03060014" "" "" "15HPET" "MNXM162620;MNXM2314" "m00380r" "m00380r" "MAM00381c" "MAM00381" "" "" "" "" "" "LMFA03010206" "" "" "M00381" "MNXM4253" "m00381c" "m00381c" -"MAM00382c" "MAM00382" "" "" "" "" "" "LMFA03010051" "" "" "M00382" "MNXM33412" "m00382c" "m00382c" +"MAM00382c" "MAM00382" "" "" "" "" "" "LMFA03010051" "" "" "M00382" "MNXM734306" "m00382c" "m00382c" "MAM00383c" "MAM00383" "" "" "" "" "" "LMFA03010021" "" "" "M00383" "MNXM33413" "m00383c" "m00383c" "MAM00384c" "MAM00384" "" "" "" "" "5283052" "" "CE5304" "" "CE5304" "MNXM33412" "m00384c" "m00384c" "MAM00385c" "MAM00385" "" "" "" "" "404025" "" "CE4877" "" "CE4877" "MNXM164061" "m00385c" "m00385c" @@ -1177,8 +1177,8 @@ mets metsNoComp metBiGGID metKEGGID metHMDBID metChEBIID metPubChemID metLipidMa "MAM00716c" "MAM00716" "" "" "" "" "" "" "CE4849" "" "CE4849" "MNXM150760" "m00716c" "m00716c" "MAM00717x" "MAM00717" "" "" "" "" "" "" "CE4832" "" "CE4832" "MNXM481924" "m00717p" "m00717p" "MAM00718c" "MAM00718" "" "" "" "" "" "" "CE4818" "" "CE4818" "MNXM164189" "m00718c" "m00718c" -"MAM00719c" "MAM00719" "" "" "" "" "" "" "CE2878" "" "CE2878" "MNXM140" "m00719c" "m00719c" -"MAM00719r" "MAM00719" "" "" "" "" "" "" "CE2878" "" "CE2878" "MNXM140" "m00719r" "m00719r" +"MAM00719c" "MAM00719" "" "" "" "" "" "" "CE2878" "" "CE2878" "MNXM1106760" "m00719c" "m00719c" +"MAM00719r" "MAM00719" "" "" "" "" "" "" "CE2878" "" "CE2878" "MNXM1106760" "m00719r" "m00719r" "MAM00720c" "MAM00720" "" "" "" "" "107564" "" "CE2866" "" "CE2866" "MNXM1986" "m00720c" "m00720c" "MAM00720r" "MAM00720" "" "" "" "" "107564" "" "CE2866" "" "CE2866" "MNXM1986" "m00720r" "m00720r" "MAM00721c" "MAM00721" "" "" "" "" "" "" "CE2870" "" "CE2870" "MNXM164192" "m00721c" "m00721c" @@ -1668,7 +1668,7 @@ mets metsNoComp metBiGGID metKEGGID metHMDBID metChEBIID metPubChemID metLipidMa "MAM01058x" "MAM01058" "" "" "" "" "" "LMFA03060075" "CE2567" "" "CE2567" "MNXM162458;MNXM6912" "m01058p" "m01058p" "MAM01058r" "MAM01058" "" "" "" "" "" "LMFA03060075" "CE2567" "" "CE2567" "MNXM162458;MNXM6912" "m01058r" "m01058r" "MAM01059c" "MAM01059" "" "C17938" "" "" "" "" "CE1562" "" "CE1562" "MNXM6292" "m01059c" "m01059c" -"MAM01060c" "MAM01060" "" "" "" "" "92945" "" "CE2964" "" "CE2964" "MNXM164331" "m01060c" "m01060c" +"MAM01060c" "MAM01060" "" "" "" "" "92945" "" "CE2964" "" "CE2964" "MNXM726413" "m01060c" "m01060c" "MAM01061c" "MAM01061" "" "" "" "" "" "" "CE5828" "" "CE5828" "MNXM130498" "m01061c" "m01061c" "MAM01062c" "MAM01062" "" "" "" "" "" "" "CE5931" "" "CE5931" "" "m01062c" "m01062c" "MAM01063c" "MAM01063" "" "" "" "" "" "" "CE5930" "" "CE5930" "" "m01063c" "m01063c" @@ -2097,8 +2097,8 @@ mets metsNoComp metBiGGID metKEGGID metHMDBID metChEBIID metPubChemID metLipidMa "MAM01318c" "MAM01318" "" "C19592" "" "" "" "" "" "" "M01318" "MNXM10642" "m01318c" "m01318c" "MAM01319c" "MAM01319" "" "C19581" "" "" "" "" "" "" "M01319" "MNXM10644" "m01319c" "m01319c" "MAM01320c" "MAM01320" "" "C19580" "" "" "" "" "" "" "M01320" "MNXM10645" "m01320c" "m01320c" -"MAM01321c" "MAM01321" "" "" "" "" "" "" "CE5853" "" "CE5853" "MNXM15963" "m01321c" "m01321c" -"MAM01322c" "MAM01322" "gal1p" "C03384" "" "CHEBI:17973" "123912" "" "" "" "gal1p" "MNXM336" "m01322c" "m01322c" +"MAM01321c" "MAM01321" "" "" "" "" "" "" "CE5853" "" "CE5853" "MNXM739689" "m01321c" "m01321c" +"MAM01322c" "MAM01322" "gal1p" "C03384" "" "CHEBI:17973" "123912" "" "" "" "gal1p" "MNXM1106067" "m01322c" "m01322c" "MAM01323c" "MAM01323" "m1mpdol__L" "C05861" "" "CHEBI:28067" "" "" "" "" "m1mpdol_L" "MNXM148043" "m01323c" "m01323c" "MAM01324c" "MAM01324" "acgagbside_hs" "" "" "" "" "" "" "" "acgagbside_hs" "MNXM7051" "m01324c" "m01324c" "MAM01324g" "MAM01324" "acgagbside_hs" "" "" "" "" "" "" "" "acgagbside_hs" "MNXM7051" "m01324g" "m01324g" @@ -2712,7 +2712,7 @@ mets metsNoComp metBiGGID metKEGGID metHMDBID metChEBIID metPubChemID metLipidMa "MAM01630m" "MAM01630" "cytd" "C00475" "HMDB0000089" "CHEBI:17562" "6175" "" "" "HC00381" "cytd" "MNXM338" "m01630m" "m01630m" "MAM01630n" "MAM01630" "cytd" "C00475" "HMDB0000089" "CHEBI:17562" "6175" "" "" "HC00381" "cytd" "MNXM338" "m01630n" "m01630n" "MAM01630e" "MAM01630" "cytd" "C00475" "HMDB0000089" "CHEBI:17562" "6175" "" "" "HC00381" "cytd" "MNXM338" "m01630s" "m01630s" -"MAM01631m" "MAM01631" "" "C00524" "" "CHEBI:83739" "" "" "" "" "M01631" "MNXM5749" "m01631m" "m01631m" +"MAM01631m" "MAM01631" "" "C00524" "" "CHEBI:83739" "" "" "" "" "M01631" "MNXM11246" "m01631m" "m01631m" "MAM01632c" "MAM01632" "csn" "C00380" "HMDB0000630" "CHEBI:16040" "597" "" "" "" "csn" "MNXM761" "m01632c" "m01632c" "MAM01632e" "MAM01632" "csn" "C00380" "HMDB0000630" "CHEBI:16040" "597" "" "" "" "csn" "MNXM761" "m01632s" "m01632s" "MAM01633c" "MAM01633" "3aib__D" "C01205" "" "CHEBI:16320" "5459822" "" "" "HC00715" "3aib_D" "MNXM162802;MNXM786" "m01633c" "m01633c" @@ -2812,7 +2812,7 @@ mets metsNoComp metBiGGID metKEGGID metHMDBID metChEBIID metPubChemID metLipidMa "MAM01674m" "MAM01674" "dpcoa" "C00882" "" "CHEBI:15468" "444485" "" "" "HC00575" "dpcoa" "MNXM481" "m01674m" "m01674m" "MAM01675c" "MAM01675" "dsmsterol" "C01802" "HMDB0002719" "CHEBI:17737" "439577" "LMST01010016" "" "HC00847" "dsmsterol" "MNXM162959;MNXM695" "m01675c" "m01675c" "MAM01676c" "MAM01676" "" "C05234" "" "" "" "" "" "" "M01676" "MNXM17230" "m01676c" "m01676c" -"MAM01677c" "MAM01677" "" "C00721" "" "" "" "" "" "" "M01677" "MNXM1003" "m01677c" "m01677c" +"MAM01677c" "MAM01677" "" "C00721" "" "" "" "" "" "" "M01677" "MNXM1103451" "m01677c" "m01677c" "MAM01678c" "MAM01678" "" "C00721" "" "" "" "" "" "" "M01678" "MNXM1003" "m01678c" "m01678c" "MAM01679c" "MAM01679" "galside_hs" "C02686" "" "CHEBI:12947" "" "" "" "" "galside_hs" "MNXM5165" "m01679c" "m01679c" "MAM01679g" "MAM01679" "galside_hs" "C02686" "" "CHEBI:12947" "" "" "" "" "galside_hs" "MNXM5165" "m01679g" "m01679g" @@ -2992,7 +2992,7 @@ mets metsNoComp metBiGGID metKEGGID metHMDBID metChEBIID metPubChemID metLipidMa "MAM01758c" "MAM01758" "xyl__D" "C00181" "" "CHEBI:15936" "644160" "" "" "" "xyl_D" "MNXM348" "m01758c" "m01758c" "MAM01758l" "MAM01758" "xyl__D" "C00181" "" "CHEBI:15936" "644160" "" "" "" "xyl_D" "MNXM348" "m01758l" "m01758l" "MAM01758e" "MAM01758" "xyl__D" "C00181" "" "CHEBI:15936" "644160" "" "" "" "xyl_D" "MNXM348" "m01758s" "m01758s" -"MAM01759c" "MAM01759" "xylu__D" "C00310" "HMDB0001644" "CHEBI:17140" "5289590" "" "" "" "xylu_D" "MNXM597" "m01759c" "m01759c" +"MAM01759c" "MAM01759" "xylu__D" "C00310" "HMDB0001644" "CHEBI:17140" "5289590" "" "" "" "xylu_D" "MNXM731281" "m01759c" "m01759c" "MAM01760c" "MAM01760" "xu1p__D" "" "HMDB0006534" "" "14844436" "" "" "" "xu1p_D" "MNXM164720" "m01760c" "m01760c" "MAM01761c" "MAM01761" "xu5p__D" "C00231" "" "CHEBI:16332" "439190" "" "" "HC00209" "xu5p_D" "MNXM186" "m01761c" "m01761c" "MAM01762c" "MAM01762" "" "" "" "" "" "" "CE2751" "" "CE2751" "MNXM164752" "m01762c" "m01762c" @@ -3127,8 +3127,8 @@ mets metsNoComp metBiGGID metKEGGID metHMDBID metChEBIID metPubChemID metLipidMa "MAM01822c" "MAM01822" "fe3" "C14819" "" "CHEBI:29034" "29936" "" "" "HC01847" "fe3" "MNXM196" "m01822c" "m01822c" "MAM01822e" "MAM01822" "fe3" "C14819" "" "CHEBI:29034" "29936" "" "" "HC01847" "fe3" "MNXM196" "m01822s" "m01822s" "MAM01823c" "MAM01823" "" "C00996" "" "CHEBI:18097" "" "" "" "HC00617" "HC00617" "MNXM1083" "m01823c" "m01823c" -"MAM01824c" "MAM01824" "ficytC" "C00125" "" "CHEBI:15991" "" "" "CE5919" "HC00123" "ficytC" "MNXM5749" "m01824c" "m01824c" -"MAM01824m" "MAM01824" "ficytC" "C00125" "" "CHEBI:15991" "" "" "CE5919" "HC00123" "ficytC" "MNXM5749" "m01824m" "m01824m" +"MAM01824c" "MAM01824" "ficytC" "C00125" "" "CHEBI:15991" "" "" "CE5919" "HC00123" "ficytC" "MNXM731952" "m01824c" "m01824c" +"MAM01824m" "MAM01824" "ficytC" "C00125" "" "CHEBI:15991" "" "" "CE5919" "HC00123" "ficytC" "MNXM731952" "m01824m" "m01824m" "MAM01825c" "MAM01825" "" "C00999" "" "" "" "" "" "HC00619" "HC00619" "MNXM1084" "m01825c" "m01825c" "MAM01826c" "MAM01826" "focytC" "C00126" "" "CHEBI:16928" "" "" "CE5918" "HC00124" "focytC" "MNXM5749" "m01826c" "m01826c" "MAM01826m" "MAM01826" "focytC" "C00126" "" "CHEBI:16928" "" "" "CE5918" "HC00124" "focytC" "MNXM5749" "m01826m" "m01826m" @@ -3413,7 +3413,7 @@ mets metsNoComp metBiGGID metKEGGID metHMDBID metChEBIID metPubChemID metLipidMa "MAM01993c" "MAM01993" "glygn3" "" "" "" "" "" "" "HC02137" "glygn3" "MNXM11715" "m01993c" "m01993c" "MAM01994c" "MAM01994" "" "" "" "" "" "" "" "HC02136" "HC02136" "MNXM164816" "m01994c" "m01994c" "MAM01995c" "MAM01995" "" "" "" "" "" "" "" "HC02132" "M01995" "MNXM12747" "m01995c" "m01995c" -"MAM01996c" "MAM01996" "ggn" "C01702" "" "" "" "" "" "HC02131" "ggn" "MNXM12747" "m01996c" "m01996c" +"MAM01996c" "MAM01996" "ggn" "C01702" "" "" "" "" "" "HC02131" "ggn" "MNXM93437" "m01996c" "m01996c" "MAM01997c" "MAM01997" "gcald" "C00266" "HMDB0003344" "CHEBI:17071" "756" "" "" "" "gcald" "MNXM349" "m01997c" "m01997c" "MAM01997m" "MAM01997" "gcald" "C00266" "HMDB0003344" "CHEBI:17071" "756" "" "" "" "gcald" "MNXM349" "m01997m" "m01997m" "MAM01998c" "MAM01998" "glyclt" "C00160" "HMDB0000115" "CHEBI:17497" "757" "" "" "" "glyclt" "MNXM222" "m01998c" "m01998c" @@ -3523,14 +3523,14 @@ mets metsNoComp metBiGGID metKEGGID metHMDBID metChEBIID metPubChemID metLipidMa "MAM02039x" "MAM02039" "h" "C00080" "" "CHEBI:24636" "1038" "" "" "HC00083" "h" "MNXM1" "m02039p" "m02039p" "MAM02039r" "MAM02039" "h" "C00080" "" "CHEBI:24636" "1038" "" "" "HC00083" "h" "MNXM1" "m02039r" "m02039r" "MAM02039e" "MAM02039" "h" "C00080" "" "CHEBI:24636" "1038" "" "" "HC00083" "h" "MNXM1" "m02039s" "m02039s" -"MAM02040c" "MAM02040" "h2o" "C00001" "HMDB0002111" "CHEBI:15377" "962" "LMST01040128" "" "HC00011" "h2o" "MNXM2" "m02040c" "m02040c" -"MAM02040g" "MAM02040" "h2o" "C00001" "HMDB0002111" "CHEBI:15377" "962" "LMST01040128" "" "HC00011" "h2o" "MNXM2" "m02040g" "m02040g" -"MAM02040l" "MAM02040" "h2o" "C00001" "HMDB0002111" "CHEBI:15377" "962" "LMST01040128" "" "HC00011" "h2o" "MNXM2" "m02040l" "m02040l" -"MAM02040m" "MAM02040" "h2o" "C00001" "HMDB0002111" "CHEBI:15377" "962" "LMST01040128" "" "HC00011" "h2o" "MNXM2" "m02040m" "m02040m" -"MAM02040n" "MAM02040" "h2o" "C00001" "HMDB0002111" "CHEBI:15377" "962" "LMST01040128" "" "HC00011" "h2o" "MNXM2" "m02040n" "m02040n" -"MAM02040x" "MAM02040" "h2o" "C00001" "HMDB0002111" "CHEBI:15377" "962" "LMST01040128" "" "HC00011" "h2o" "MNXM2" "m02040p" "m02040p" -"MAM02040r" "MAM02040" "h2o" "C00001" "HMDB0002111" "CHEBI:15377" "962" "LMST01040128" "" "HC00011" "h2o" "MNXM2" "m02040r" "m02040r" -"MAM02040e" "MAM02040" "h2o" "C00001" "HMDB0002111" "CHEBI:15377" "962" "LMST01040128" "" "HC00011" "h2o" "MNXM2" "m02040s" "m02040s" +"MAM02040c" "MAM02040" "h2o" "C00001" "HMDB0002111" "CHEBI:15377" "962" "LMST01040128" "" "HC00011" "h2o" "WATER" "m02040c" "m02040c" +"MAM02040g" "MAM02040" "h2o" "C00001" "HMDB0002111" "CHEBI:15377" "962" "LMST01040128" "" "HC00011" "h2o" "WATER" "m02040g" "m02040g" +"MAM02040l" "MAM02040" "h2o" "C00001" "HMDB0002111" "CHEBI:15377" "962" "LMST01040128" "" "HC00011" "h2o" "WATER" "m02040l" "m02040l" +"MAM02040m" "MAM02040" "h2o" "C00001" "HMDB0002111" "CHEBI:15377" "962" "LMST01040128" "" "HC00011" "h2o" "WATER" "m02040m" "m02040m" +"MAM02040n" "MAM02040" "h2o" "C00001" "HMDB0002111" "CHEBI:15377" "962" "LMST01040128" "" "HC00011" "h2o" "WATER" "m02040n" "m02040n" +"MAM02040x" "MAM02040" "h2o" "C00001" "HMDB0002111" "CHEBI:15377" "962" "LMST01040128" "" "HC00011" "h2o" "WATER" "m02040p" "m02040p" +"MAM02040r" "MAM02040" "h2o" "C00001" "HMDB0002111" "CHEBI:15377" "962" "LMST01040128" "" "HC00011" "h2o" "WATER" "m02040r" "m02040r" +"MAM02040e" "MAM02040" "h2o" "C00001" "HMDB0002111" "CHEBI:15377" "962" "LMST01040128" "" "HC00011" "h2o" "WATER" "m02040s" "m02040s" "MAM02041c" "MAM02041" "h2o2" "C00027" "HMDB0003125" "CHEBI:16240" "784" "" "" "HC00036" "h2o2" "MNXM22" "m02041c" "m02041c" "MAM02041l" "MAM02041" "h2o2" "C00027" "HMDB0003125" "CHEBI:16240" "784" "" "" "HC00036" "h2o2" "MNXM22" "m02041l" "m02041l" "MAM02041m" "MAM02041" "h2o2" "C00027" "HMDB0003125" "CHEBI:16240" "784" "" "" "HC00036" "h2o2" "MNXM22" "m02041m" "m02041m" @@ -3708,7 +3708,7 @@ mets metsNoComp metBiGGID metKEGGID metHMDBID metChEBIID metPubChemID metLipidMa "MAM02141e" "MAM02141" "ha" "C00518" "" "CHEBI:16336" "24759" "" "" "" "ha" "MNXM18575" "m02141s" "m02141s" "MAM02142m" "MAM02142" "3hpp" "C01013" "HMDB0000700" "CHEBI:33404" "68152" "" "" "HC00625" "3hpp" "MNXM872" "m02142m" "m02142m" "MAM02143c" "MAM02143" "" "C13645" "" "CHEBI:47266" "" "" "" "" "M02143" "MNXM833" "m02143c" "m02143c" -"MAM02144c" "MAM02144" "" "C01327" "" "" "" "" "" "" "M02144" "MNXM43" "m02144c" "m02144c" +"MAM02144c" "MAM02144" "" "C01327" "" "" "" "" "" "" "M02144" "MNXM56769" "m02144c" "m02144c" "MAM02145c" "MAM02145" "cyan" "C01326" "" "CHEBI:18407" "768" "" "" "" "cyan" "MNXM254" "m02145c" "m02145c" "MAM02145m" "MAM02145" "cyan" "C01326" "" "CHEBI:18407" "768" "" "" "" "cyan" "MNXM254" "m02145m" "m02145m" "MAM02145e" "MAM02145" "cyan" "C01326" "" "CHEBI:18407" "768" "" "" "" "cyan" "MNXM254" "m02145s" "m02145s" @@ -4142,7 +4142,7 @@ mets metsNoComp metBiGGID metKEGGID metHMDBID metChEBIID metPubChemID metLipidMa "MAM02422c" "MAM02422" "lum3" "" "HMDB0006505" "" "111049" "" "" "" "lum3" "MNXM19109" "m02422c" "m02422c" "MAM02423c" "MAM02423" "" "C02554" "" "CHEBI:29164" "" "" "" "" "M02423" "MNXM90110" "m02423c" "m02423c" "MAM02424c" "MAM02424" "xylnt" "C05411" "" "CHEBI:48092" "6971043" "" "" "" "xylnt" "MNXM169422;MNXM8831" "m02424c" "m02424c" -"MAM02425c" "MAM02425" "xylu__L" "C00312" "HMDB0000751" "CHEBI:17399" "22253" "" "" "HC00267" "xylu_L" "MNXM597" "m02425c" "m02425c" +"MAM02425c" "MAM02425" "xylu__L" "C00312" "HMDB0000751" "CHEBI:17399" "22253" "" "" "HC00267" "xylu_L" "MNXM727819" "m02425c" "m02425c" "MAM02426c" "MAM02426" "lys__L" "C00047" "HMDB0000182" "CHEBI:18019" "5962" "" "" "HC00053" "lys_L" "MNXM78" "m02426c" "m02426c" "MAM02426l" "MAM02426" "lys__L" "C00047" "HMDB0000182" "CHEBI:18019" "5962" "" "" "HC00053" "lys_L" "MNXM78" "m02426l" "m02426l" "MAM02426m" "MAM02426" "lys__L" "C00047" "HMDB0000182" "CHEBI:18019" "5962" "" "" "HC00053" "lys_L" "MNXM78" "m02426m" "m02426m" @@ -4355,7 +4355,7 @@ mets metsNoComp metBiGGID metKEGGID metHMDBID metChEBIID metPubChemID metLipidMa "MAM02547c" "MAM02547" "aprut" "C02714" "HMDB0002064" "CHEBI:17768" "122356" "" "" "" "aprut" "MNXM1153" "m02547c" "m02547c" "MAM02548c" "MAM02548" "" "" "" "" "" "" "CE2088" "" "CE2088" "MNXM168488" "m02548c" "m02548c" "MAM02549c" "MAM02549" "Nacsertn" "C00978" "" "CHEBI:17697" "903" "" "" "" "Nacsertn" "MNXM164995;MNXM780" "m02549c" "m02549c" -"MAM02550c" "MAM02550" "" "" "" "" "" "" "CE5868" "" "CE5868" "MNXM42" "m02550c" "m02550c" +"MAM02550c" "MAM02550" "" "" "" "" "" "" "CE5868" "" "CE5868" "MNXM725868" "m02550c" "m02550c" "MAM02551c" "MAM02551" "" "" "" "" "14181658" "" "CE5867" "" "CE5867" "MNXM163855" "m02551c" "m02551c" "MAM02552c" "MAM02552" "nad" "C00003" "HMDB0000902" "CHEBI:15846" "5893" "" "" "HC00013" "nad" "MNXM8" "m02552c" "m02552c" "MAM02552m" "MAM02552" "nad" "C00003" "HMDB0000902" "CHEBI:15846" "5893" "" "" "HC00013" "nad" "MNXM8" "m02552m" "m02552m" @@ -5523,7 +5523,7 @@ mets metsNoComp metBiGGID metKEGGID metHMDBID metChEBIID metPubChemID metLipidMa "MAM03140c" "MAM03140" "" "" "" "" "" "" "" "" "M03140" "" "m03140c" "m03140c" "MAM03143c" "MAM03143" "" "" "" "" "" "" "" "" "M03143" "" "m03143c" "m03143c" "MAM01004m" "MAM01004" "34hpl" "C03672" "HMDB0000755" "CHEBI:17385" "9378" "" "" "" "34hpl" "MNXM114141" "" "m01004m" -"MAM03226m" "MAM03226" "3hibutcoa" "C04047" "" "CHEBI:15481" "" "" "" "" "3hibutcoa" "MNXM446" "" "3hibutcoa_m" +"MAM03226m" "MAM03226" "3hibutcoa" "C04047" "" "CHEBI:15481" "" "" "" "" "3hibutcoa" "MNXM1105906" "" "3hibutcoa_m" "MAM00799c" "MAM00799" "3hpcoa" "C05668" "" "CHEBI:27762" "440753" "" "" "HC01557" "3hpcoa" "MNXM1263" "" "m00799c" "MAM02142c" "MAM02142" "3hpp" "C01013" "HMDB0000700" "CHEBI:33404" "68152" "" "" "HC00625" "3hpp" "MNXM872" "" "m02142c" "MAM00900c" "MAM00900" "msa" "C00222" "" "CHEBI:17960" "868" "" "" "HC00203" "msa" "MNXM244" "" "m00900c" @@ -5942,7 +5942,7 @@ mets metsNoComp metBiGGID metKEGGID metHMDBID metChEBIID metPubChemID metLipidMa "MAM03372c" "MAM03372" "CE5839" "" "" "" "" "" "CE5839" "" "CE5839" "MNXM166480" "" "CE5839_c" "MAM03373c" "MAM03373" "CE5840" "" "" "" "" "" "CE5840" "" "CE5840" "MNXM165601" "" "CE5840_c" "MAM00766r" "MAM00766" "" "" "" "" "9943542" "" "CE1925" "" "CE1925" "MNXM163170" "" "m00766r" -"MAM01321r" "MAM01321" "" "" "" "" "" "" "CE5853" "" "CE5853" "MNXM15963" "" "m01321r" +"MAM01321r" "MAM01321" "" "" "" "" "" "" "CE5853" "" "CE5853" "MNXM739689" "" "m01321r" "MAM01923r" "MAM01923" "" "" "" "" "133098" "" "CE1926" "" "CE1926" "MNXM163392" "" "m01923r" "MAM01924r" "MAM01924" "" "" "" "" "" "" "CE5854" "" "CE5854" "MNXM163393" "" "m01924r" "MAM01675n" "MAM01675" "dsmsterol" "C01802" "HMDB0002719" "CHEBI:17737" "439577" "LMST01010016" "" "HC00847" "dsmsterol" "MNXM162959;MNXM695" "" "m01675n" @@ -5953,7 +5953,7 @@ mets metsNoComp metBiGGID metKEGGID metHMDBID metChEBIID metPubChemID metLipidMa "MAM03374c" "MAM03374" "CE5865" "" "" "" "40489070" "" "CE5865" "" "CE5865" "MNXM127276" "" "CE5865_c" "MAM03375c" "MAM03375" "CE5866" "" "" "" "6992388" "" "CE5866" "" "CE5866" "MNXM15786" "" "CE5866_c" "MAM02551e" "MAM02551" "" "" "" "" "14181658" "" "CE5867" "" "CE5867" "MNXM163855" "" "m02551s" -"MAM02550e" "MAM02550" "" "" "" "" "" "" "CE5868" "" "CE5868" "MNXM42" "" "m02550s" +"MAM02550e" "MAM02550" "" "" "" "" "" "" "CE5868" "" "CE5868" "MNXM725868" "" "m02550s" "MAM02429e" "MAM02429" "" "" "" "" "" "" "CE5869" "" "CE5869" "MNXM19120" "" "m02429s" "MAM03356c" "MAM03356" "CE5016" "" "" "" "" "" "CE5016" "" "CE5016" "MNXM165531" "" "CE5016_c" "MAM03323c" "MAM03323" "C06948" "C06948" "" "" "3016" "" "" "" "C06948" "MNXM50391" "" "C06948_c" @@ -6123,9 +6123,9 @@ mets metsNoComp metBiGGID metKEGGID metHMDBID metChEBIID metPubChemID metLipidMa "MAM00838c" "MAM00838" "" "" "" "" "" "" "CE5337" "" "CE5337" "MNXM162903" "" "m00838c" "MAM00751r" "MAM00751" "" "C01301" "" "CHEBI:48940" "" "" "CE4872" "" "CE4872" "MNXM867" "" "m00751r" "MAM00766e" "MAM00766" "" "" "" "" "9943542" "" "CE1925" "" "CE1925" "MNXM163170" "" "m00766s" -"MAM01321e" "MAM01321" "" "" "" "" "" "" "CE5853" "" "CE5853" "MNXM15963" "" "m01321s" +"MAM01321e" "MAM01321" "" "" "" "" "" "" "CE5853" "" "CE5853" "MNXM739689" "" "m01321s" "MAM00766l" "MAM00766" "" "" "" "" "9943542" "" "CE1925" "" "CE1925" "MNXM163170" "" "m00766l" -"MAM01321l" "MAM01321" "" "" "" "" "" "" "CE5853" "" "CE5853" "MNXM15963" "" "m01321l" +"MAM01321l" "MAM01321" "" "" "" "" "" "" "CE5853" "" "CE5853" "MNXM739689" "" "m01321l" "MAM02796m" "MAM02796" "" "C05957" "HMDB0002710" "CHEBI:27485" "5280884" "LMFA03010019" "" "" "C05957" "MNXM7704" "" "m02796m" "MAM01662m" "MAM01662" "" "" "" "" "114678" "" "CE4876" "" "CE4876" "MNXM6638" "" "m01662m" "MAM00252r" "MAM00252" "" "" "" "" "" "" "CE4988" "" "CE4988" "MNXM162617" "" "m00252r" @@ -7629,8 +7629,8 @@ mets metsNoComp metBiGGID metKEGGID metHMDBID metChEBIID metPubChemID metLipidMa "MAM02756e" "MAM02756" "ppbng" "C00931" "HMDB0000245" "CHEBI:17381" "1021" "" "" "HC00588" "ppbng" "MNXM554" "" "m02756s" "MAM02771e" "MAM02771" "12ppd__R" "C00583" "HMDB0001881" "CHEBI:16997" "1030" "" "" "" "12ppd_R" "MNXM1118;MNXM1255;MNXM90191" "" "m02771s" "MAM02870e" "MAM02870" "ametam" "C01137" "HMDB0000988" "CHEBI:15625" "439415" "" "" "HC00683" "ametam" "MNXM321" "" "m02870s" -"MAM02425e" "MAM02425" "xylu__L" "C00312" "HMDB0000751" "CHEBI:17399" "22253" "" "" "HC00267" "xylu_L" "MNXM597" "" "m02425s" -"MAM01759e" "MAM01759" "xylu__D" "C00310" "HMDB0001644" "CHEBI:17140" "5289590" "" "" "" "xylu_D" "MNXM597" "" "m01759s" +"MAM02425e" "MAM02425" "xylu__L" "C00312" "HMDB0000751" "CHEBI:17399" "22253" "" "" "HC00267" "xylu_L" "MNXM727819" "" "m02425s" +"MAM01759e" "MAM01759" "xylu__D" "C00310" "HMDB0001644" "CHEBI:17140" "5289590" "" "" "" "xylu_D" "MNXM731281" "" "m01759s" "MAM02441e" "MAM02441" "" "C19440" "HMDB0006112" "CHEBI:566274" "10964" "" "CE0737" "" "CE0737" "MNXM61004" "" "m02441s" "MAM02166e" "MAM02166" "im4ac" "C02835" "HMDB0002024" "CHEBI:16974" "96215" "" "" "" "im4ac" "MNXM1330" "" "m02166s" "MAM01332e" "MAM01332" "aact" "C01888" "" "" "215" "" "" "" "aact" "MNXM1106" "" "m01332s" From 0c28ca2c0e46f5579ed8b57b4510f14116bbdde7 Mon Sep 17 00:00:00 2001 From: Jiahao Luo <67491919+JHL-452b@users.noreply.github.com> Date: Mon, 19 Jun 2023 10:08:00 +0800 Subject: [PATCH 3/3] fix-replace mets --- .../deprecatedMetabolites.tsv | 4 ++ model/Human-GEM.yml | 66 +++++++------------ model/metabolites.tsv | 4 -- 3 files changed, 29 insertions(+), 45 deletions(-) diff --git a/data/deprecatedIdentifiers/deprecatedMetabolites.tsv b/data/deprecatedIdentifiers/deprecatedMetabolites.tsv index c1f8c166..fd4daa6a 100644 --- a/data/deprecatedIdentifiers/deprecatedMetabolites.tsv +++ b/data/deprecatedIdentifiers/deprecatedMetabolites.tsv @@ -2205,3 +2205,7 @@ mets metsNoComp metBiGGID metKEGGID metHMDBID metChEBIID metPubChemID metLipidMa "MAM03494c" "MAM03494" "c3dc" "" "" "" "22833583" "" "" "" "c3dc" "" "" "c3dc_c" "MAM03494e" "MAM03494" "c3dc" "" "" "" "22833583" "" "" "" "c3dc" "" "" "c3dc_s" "MAM03684e" "MAM03684" "hxa" "" "" "" "" "" "" "" "hxa" "MNXM1653" "" "hxa_s" +"MAM03684x" "MAM03684" "hxa" "" "" "" "" "" "" "" "hxa" "MNXM1653" "" "hxa_p" +"MAM03684m" "MAM03684" "hxa" "" "" "" "" "" "" "" "hxa" "MNXM1653" "" "hxa_m" +"MAM03684c" "MAM03684" "hxa" "" "" "CHEBI:17120" "" "" "" "" "hxa" "MNXM1653" "" "hxa_c" +"MAM00759c" "MAM00759" "" "C13712" "" "" "" "LMST02030130" "" "" "M00759" "MNXM3494" "m00759c" "m00759c" diff --git a/model/Human-GEM.yml b/model/Human-GEM.yml index 57f17de5..56d904f1 100644 --- a/model/Human-GEM.yml +++ b/model/Human-GEM.yml @@ -9961,14 +9961,6 @@ - charge: -1 - inchis: "" - metFrom: "HMRdatabase" - - !!omap - - id: "MAM00759c" - - name: "3alpha-hydroxy-5alpha-pregnan-20-one" - - compartment: "c" - - formula: "C21H34O2" - - charge: 0 - - inchis: "" - - metFrom: "HMRdatabase" - !!omap - id: "MAM00760c" - name: "3-amino-propanal" @@ -53553,14 +53545,6 @@ - charge: -1 - inchis: "" - metFrom: "Recon3D" - - !!omap - - id: "MAM03684c" - - name: "Hexanoate (N-C6:0)" - - compartment: "c" - - formula: "C6H11O2" - - charge: -1 - - inchis: "" - - metFrom: "Recon3D" - !!omap - id: "MAM03976c" - name: "Cia-5,8, Tetradecadienoic Acid" @@ -54705,22 +54689,6 @@ - charge: -1 - inchis: "" - metFrom: "Recon3D" - - !!omap - - id: "MAM03684m" - - name: "Hexanoate (N-C6:0)" - - compartment: "m" - - formula: "C6H11O2" - - charge: -1 - - inchis: "" - - metFrom: "Recon3D" - - !!omap - - id: "MAM03684x" - - name: "Hexanoate (N-C6:0)" - - compartment: "x" - - formula: "C6H11O2" - - charge: -1 - - inchis: "" - - metFrom: "Recon3D" - !!omap - id: "MAM02169e" - name: "indoleacetate" @@ -67993,6 +67961,22 @@ - charge: -1 - inchis: "" - metFrom: "" + - !!omap + - id: "MAM02120x" + - name: "hexanoic acid" + - compartment: "x" + - formula: "C6H11O2" + - charge: -1 + - inchis: "" + - metFrom: "HMRdatabase" + - !!omap + - id: "MAM02120m" + - name: "hexanoic acid" + - compartment: "m" + - formula: "C6H11O2" + - charge: -1 + - inchis: "" + - metFrom: "HMRdatabase" - reactions: - !!omap - id: "MAR03905" @@ -123746,8 +123730,8 @@ - id: "MAR02003" - name: "3alpha-hydroxy-5alpha-pregnan-20-one:NADP+ 3-oxidoreductase (A-specific)" - metabolites: !!omap - - MAM00759c: -1 - MAM01072c: 1 + - MAM01314c: -1 - MAM02039c: 1 - MAM02554c: -1 - MAM02555c: 1 @@ -219324,7 +219308,6 @@ - MAM00660c: -1 - MAM00660r: -1 - MAM00747r: -1 - - MAM00759c: -1 - MAM00828r: -1 - MAM00830c: -1 - MAM00925c: -1 @@ -219343,6 +219326,7 @@ - MAM01001x: -1 - MAM01011c: -1 - MAM01012c: -1 + - MAM01314c: -1 - MAM01792r: -1 - MAM01794r: -1 - MAM02469c: -1 @@ -256142,8 +256126,8 @@ - MAM01597m: 1 - MAM02039m: 1 - MAM02040m: -1 + - MAM02120m: 1 - MAM02122m: -1 - - MAM03684m: 1 - lower_bound: 0 - upper_bound: 1000 - gene_reaction_rule: "" @@ -256193,8 +256177,8 @@ - MAM01597x: 1 - MAM02039x: 1 - MAM02040x: -1 + - MAM02120x: 1 - MAM02122x: -1 - - MAM03684x: 1 - lower_bound: -1000 - upper_bound: 1000 - gene_reaction_rule: "" @@ -271746,8 +271730,8 @@ - id: "MAR11290" - name: "Transport of Hexanoate (N-C6:0), Mitochondrial" - metabolites: !!omap - - MAM03684c: 1 - - MAM03684m: -1 + - MAM02120c: 1 + - MAM02120m: -1 - lower_bound: -1000 - upper_bound: 1000 - gene_reaction_rule: "" @@ -271762,8 +271746,8 @@ - id: "MAR11291" - name: "Transport of Hexanoate (N-C6:0), Peroxisome" - metabolites: !!omap - - MAM03684c: 1 - - MAM03684x: -1 + - MAM02120c: 1 + - MAM02120x: -1 - lower_bound: -1000 - upper_bound: 1000 - gene_reaction_rule: "" @@ -305883,9 +305867,9 @@ - metabolites: !!omap - MAM02039c: 2 - MAM02040c: -1 + - MAM02120c: 1 - MAM02554c: -1 - MAM02555c: 1 - - MAM03684c: 1 - MAM20037c: -1 - lower_bound: 0 - upper_bound: 1000 diff --git a/model/metabolites.tsv b/model/metabolites.tsv index d1bd1e61..1a268fa6 100644 --- a/model/metabolites.tsv +++ b/model/metabolites.tsv @@ -1243,7 +1243,6 @@ mets metsNoComp metBiGGID metKEGGID metHMDBID metChEBIID metPubChemID metLipidMa "MAM00758m" "MAM00758" "dhcholestanate" "C04554" "HMDB0000359" "CHEBI:48467" "53477686" "LMST04030066" "" "HC01313" "dhcholestanate" "MNXM162671;MNXM688" "m00758m" "m00758m" "MAM00758x" "MAM00758" "dhcholestanate" "C04554" "HMDB0000359" "CHEBI:48467" "53477686" "LMST04030066" "" "HC01313" "dhcholestanate" "MNXM162671;MNXM688" "m00758p" "m00758p" "MAM00758r" "MAM00758" "dhcholestanate" "C04554" "HMDB0000359" "CHEBI:48467" "53477686" "LMST04030066" "" "HC01313" "dhcholestanate" "MNXM162671;MNXM688" "m00758r" "m00758r" -"MAM00759c" "MAM00759" "" "C13712" "" "" "" "LMST02030130" "" "" "M00759" "MNXM3494" "m00759c" "m00759c" "MAM00760c" "MAM00760" "" "C05665" "" "CHEBI:58374" "75" "" "" "" "bamppald" "MNXM43758" "m00760c" "m00760c" "MAM00761m" "MAM00761" "" "" "" "" "3081084" "" "CE3038" "" "CE3038" "MNXM6853" "m00761m" "m00761m" "MAM00762g" "MAM00762" "cs_hs_linkage" "C04903" "" "G00157" "" "" "" "" "cs_hs_linkage" "MNXM147451" "m00762g" "m00762g" @@ -6692,7 +6691,6 @@ mets metsNoComp metBiGGID metKEGGID metHMDBID metChEBIID metPubChemID metLipidMa "MAM03814c" "MAM03814" "pchollinl_hs" "" "" "CHEBI:28733" "" "" "" "" "pchollinl_hs" "" "" "pchollinl_hs_c" "MAM03856c" "MAM03856" "pelinl_hs" "" "" "CHEBI:83058" "" "" "" "" "pelinl_hs" "" "" "pelinl_hs_c" "MAM03569c" "MAM03569" "eidi1114ac" "C16525" "HMDB0005060" "CHEBI:603631" "6439848" "" "" "" "eidi1114ac" "" "" "eidi1114ac_c" -"MAM03684c" "MAM03684" "hxa" "" "" "CHEBI:17120" "" "" "" "" "hxa" "MNXM1653" "" "hxa_c" "MAM03976c" "MAM03976" "tetdeca511ac" "" "" "" "" "" "" "" "tetdeca511ac" "" "" "tetdeca511ac_c" "MAM03619c" "MAM03619" "glyc2p" "" "" "CHEBI:58083" "" "" "" "" "glyc2p" "MNXM2527" "" "glyc2p_c" "MAM03401c" "MAM03401" "aclys" "" "" "" "" "" "" "" "aclys" "" "" "aclys_c" @@ -6836,8 +6834,6 @@ mets metsNoComp metBiGGID metKEGGID metHMDBID metChEBIID metPubChemID metLipidMa "MAM03619e" "MAM03619" "glyc2p" "" "" "" "" "" "" "" "glyc2p" "MNXM2527" "" "glyc2p_s" "MAM01998e" "MAM01998" "glyclt" "C00160" "HMDB0000115" "CHEBI:17497" "757" "" "" "" "glyclt" "MNXM222" "" "m01998s" "MAM03232e" "MAM03232" "3hpppn" "" "" "" "" "" "" "" "3hpppn" "MNXM1634" "" "3hpppn_s" -"MAM03684m" "MAM03684" "hxa" "" "" "" "" "" "" "" "hxa" "MNXM1653" "" "hxa_m" -"MAM03684x" "MAM03684" "hxa" "" "" "" "" "" "" "" "hxa" "MNXM1653" "" "hxa_p" "MAM02169e" "MAM02169" "ind3ac" "C00954" "HMDB0000197" "CHEBI:16411" "802" "" "" "" "ind3ac" "MNXM383" "" "m02169s" "MAM02350e" "MAM02350" "Lcyst" "C00506" "HMDB0002757" "CHEBI:21260" "25701" "" "" "" "Lcyst" "MNXM713" "" "m02350s" "MAM02413c" "MAM02413" "Lpipecol" "C00408" "HMDB0000716" "CHEBI:30913" "439227" "" "" "" "Lpipecol" "MNXM684" "" "m02413c"