diff --git a/data/deprecatedIdentifiers/deprecatedReactions.tsv b/data/deprecatedIdentifiers/deprecatedReactions.tsv index f423e2b1..a23bb63c 100644 --- a/data/deprecatedIdentifiers/deprecatedReactions.tsv +++ b/data/deprecatedIdentifiers/deprecatedReactions.tsv @@ -195,3 +195,8 @@ rxns rxnKEGGID rxnBiGGID rxnEHMNID rxnHepatoNET1ID rxnREACTOMEID rxnRecon3DID rx "MAR10164" "" "" "" "" "" "CE2516t" "" "" "" "" 0 "" "" "CE2516t" "MAR10433" "" "" "" "" "" "EX_CE2516[e]" "" "" "" "" 0 "" "" "EX_CE2516[e]" "MAR09887" "" "GLNB0AT3tc" "" "" "" "GLNB0AT3tc" "" "" "" "" 0 "" "" "GLNB0AT3tc" +"MAR01515" "" "MAOX" "" "" "" "MAOX" "MNXR101406" "" "" "" 0 "RHEA:59421" "RHEA:59420" "MAOX" +"MAR00039" "" "13DAMPPOX" "" "" "" "13DAMPPOX" "MNXR94687" "" "" "" 0 "" "" "13DAMPPOX" +"MAR00096" "" "BUP2" "" "" "" "BUP2" "MNXR96346" "" "" "" 0 "" "" "BUP2" +"MAR02027" "" "r0193" "" "" "" "r0193" "MNXR105313" "" "" "" 0 "" "" "r0193" +"MAR02006" "" "CPS_m" "" "" "" "r0034" "" "" "" "" 0 "" "" "r0034" diff --git a/model/Human-GEM.yml b/model/Human-GEM.yml index d7a04a32..94385efb 100644 --- a/model/Human-GEM.yml +++ b/model/Human-GEM.yml @@ -74595,9 +74595,9 @@ - upper_bound: 1000 - gene_reaction_rule: "ENSG00000100024" - rxnNotes: "" - - rxnFrom: "HMRdatabase" + - rxnFrom: "HMRdatabase;Recon3D" - eccodes: "3.5.1.6" - - references: "PMID:10542323;PMID:3678231" + - references: "PMID:10542323;PMID:3678231;PMID:11508704;PMID:5773299" - subsystem: - "Pyrimidine metabolism" - confidence_score: 0 @@ -77360,7 +77360,7 @@ - upper_bound: 1000 - gene_reaction_rule: "ENSG00000021826" - rxnNotes: "" - - rxnFrom: "HMRdatabase" + - rxnFrom: "HMRdatabase;Recon3D" - eccodes: "6.3.4.16" - references: "PMID:15897806;PMID:175068;PMID:2893372;PMID:3886433;PMID:4347313;PMID:7248316" - subsystem: @@ -82179,9 +82179,9 @@ - upper_bound: 1000 - gene_reaction_rule: "ENSG00000002726 or ENSG00000131471 or ENSG00000131480" - rxnNotes: "" - - rxnFrom: "HMRdatabase" + - rxnFrom: "HMRdatabase;Recon3D" - eccodes: "1.4.3.6;1.4.3.21;1.4.3.22" - - references: "" + - references: "PMID:11136547;PMID:14715500;PMID:9131641" - subsystem: - "Tyrosine metabolism" - confidence_score: 0 @@ -86091,7 +86091,7 @@ - upper_bound: 1000 - gene_reaction_rule: "ENSG00000116761" - rxnNotes: "" - - rxnFrom: "HMRdatabase" + - rxnFrom: "HMRdatabase;Recon3D" - eccodes: "4.4.1.1;4.4.1.8" - references: "PMID:10212249;PMID:629532" - subsystem: @@ -87151,9 +87151,9 @@ - upper_bound: 1000 - gene_reaction_rule: "ENSG00000002726 or ENSG00000131471 or ENSG00000131480" - rxnNotes: "" - - rxnFrom: "HMRdatabase" + - rxnFrom: "HMRdatabase;Recon3D" - eccodes: "1.4.3.6;1.4.3.21;1.4.3.22" - - references: "" + - references: "PMID:15035803;PMID:8920635;PMID:9653080" - subsystem: - "Beta-alanine metabolism" - confidence_score: 0 @@ -218786,26 +218786,6 @@ - subsystem: - "Transport reactions" - confidence_score: 0 - - !!omap - - id: "MAR00039" - - name: "1, 3-Diaminopropane:Oxygen Oxidoreductase (Deaminating)" - - metabolites: !!omap - - MAM00248c: -1 - - MAM00760c: 1 - - MAM02040c: -1 - - MAM02041c: 1 - - MAM02579c: 1 - - MAM02630c: -1 - - lower_bound: 0 - - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000002726 or ENSG00000131471 or ENSG00000131480" - - rxnNotes: "" - - rxnFrom: "Recon3D" - - eccodes: "1.4.3.6" - - references: "PMID:15035803;PMID:8920635;PMID:9653080" - - subsystem: - - "Beta-alanine metabolism" - - confidence_score: 0 - !!omap - id: "MAR00040" - name: "3- (4-Hydroxyphenyl-)Lactate Formation" @@ -219810,26 +219790,6 @@ - subsystem: - "Transport reactions" - confidence_score: 0 - - !!omap - - id: "MAR00096" - - name: "Beta-Ureidopropionase (D-3-Amino-Isobutanoate Forming)" - - metabolites: !!omap - - MAM00922c: -1 - - MAM01596c: 1 - - MAM01633c: 1 - - MAM02039c: -2 - - MAM02040c: -1 - - MAM02579c: 1 - - lower_bound: 0 - - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000100024" - - rxnNotes: "" - - rxnFrom: "Recon3D" - - eccodes: "3.5.1.6" - - references: "PMID:11508704;PMID:5773299" - - subsystem: - - "Pyrimidine metabolism" - - confidence_score: 0 - !!omap - id: "MAR00097" - name: "Butyrate Mitochondrial Transport via Proton Symport, Reversible" @@ -225234,26 +225194,6 @@ - subsystem: - "Transport reactions" - confidence_score: 0 - - !!omap - - id: "MAR01515" - - name: "Methylamine Oxidase" - - metabolites: !!omap - - MAM01831c: 1 - - MAM02040c: -1 - - MAM02041c: 1 - - MAM02473c: -1 - - MAM02579c: 1 - - MAM02630c: -1 - - lower_bound: 0 - - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000002726 or ENSG00000131471 or ENSG00000131480" - - rxnNotes: "" - - rxnFrom: "Recon3D" - - eccodes: "1.4.3.6" - - references: "PMID:11136547;PMID:14715500;PMID:9131641" - - subsystem: - - "Tyrosine metabolism" - - confidence_score: 0 - !!omap - id: "MAR01517" - name: "Malonyl Coenzyme A-Acp Transacylase, Mitochondrial" @@ -227945,28 +227885,6 @@ - subsystem: - "Exchange/demand reactions" - confidence_score: 0 - - !!omap - - id: "MAR02006" - - name: "Carbon-Dioxide:Ammonia Ligase (ADP-Forming, Carbamate-Phosphorylating)" - - metabolites: !!omap - - MAM01285m: 2 - - MAM01371m: -2 - - MAM01420m: 1 - - MAM01596m: -1 - - MAM02039m: 3 - - MAM02040m: -1 - - MAM02579m: -1 - - MAM02751m: 1 - - lower_bound: 0 - - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000021826" - - rxnNotes: "" - - rxnFrom: "Recon3D" - - eccodes: "6.3.4.16" - - references: "PMID:15897806;PMID:175068;PMID:2893372;PMID:3886433;PMID:4347313;PMID:7248316" - - subsystem: - - "Urea cycle" - - confidence_score: 0 - !!omap - id: "MAR02021" - name: "UDPglucose Pyrophosphohydrolase" @@ -228024,26 +227942,6 @@ - subsystem: - "Cholesterol metabolism" - confidence_score: 0 - - !!omap - - id: "MAR02027" - - name: "L-Cysteine L-Homocysteine-Lyase (Deaminating)" - - metabolites: !!omap - - MAM01628c: -1 - - MAM02039c: 1 - - MAM02040c: -1 - - MAM02042c: 1 - - MAM02579c: 1 - - MAM02819c: 1 - - lower_bound: -1000 - - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000116761" - - rxnNotes: "" - - rxnFrom: "Recon3D" - - eccodes: "4.4.1.1" - - references: "PMID:10212249;PMID:629532" - - subsystem: - - "Cysteine and methionine metabolism" - - confidence_score: 0 - !!omap - id: "MAR02028" - name: "Trans-Hexadec-2-Enoyl Coenzyme A Reductase" diff --git a/model/reactions.tsv b/model/reactions.tsv index cfff2549..99a89d3d 100644 --- a/model/reactions.tsv +++ b/model/reactions.tsv @@ -363,7 +363,7 @@ rxns rxnKEGGID rxnBiGGID rxnEHMNID rxnHepatoNET1ID rxnREACTOMEID rxnRecon3DID rx "MAR04672" "R02325" "" "" "" "" "HMR_4672" "" "HMR_4672" "RCR10128" "" 0 "" "RHEA:22680" "HMR_4672" "MAR04676" "R02372" "" "R02372E" "r0531" "" "r0531" "MNXR97821" "HMR_4676" "RCR11173" "" 0 "" "" "HMR_4676" "MAR04736" "R03055" "DHPM2" "R03055C" "r0593" "" "DHPM2" "MNXR107917;MNXR97433" "HMR_4736" "RCR11174" "" 0 "" "" "HMR_4736" -"MAR04819" "R04666" "BUP2" "R04666C" "r0710" "" "" "MNXR109033;MNXR96346" "HMR_4819" "RCR11175" "" 0 "" "" "HMR_4819" +"MAR04819" "R04666" "BUP2" "R04666C" "r0710" "" "BUP2" "MNXR109033;MNXR96346" "HMR_4819" "RCR11175" "" 0 "" "" "HMR_4819;BUP2;MAR00096" "MAR05299" "R00964" "URIK1" "R00964E" "r1115" "" "URIK1" "MNXR105162" "HMR_5299" "RCR11176" "" 0 "RHEA:16826" "RHEA:16825" "HMR_5299" "MAR05352" "R02332" "" "R02332E" "r1156" "" "r1156" "MNXR97823" "HMR_5352" "RCR11177" "" 0 "" "" "HMR_5352" "MAR05415" "R02017" "" "R02018M" "r1431" "" "" "MNXR104066" "HMR_5415" "RCR11178" "" 0 "" "RHEA:28034" "HMR_5415" @@ -513,7 +513,7 @@ rxns rxnKEGGID rxnBiGGID rxnEHMNID rxnHepatoNET1ID rxnREACTOMEID rxnRecon3DID rx "MAR03862" "R00485" "ASNNm" "" "" "" "ASNNm" "MNXR96056" "HMR_3862" "RCR10305" "" 0 "" "RHEA:21016" "HMR_3862" "MAR03865" "R02619" "3SALATAim" "" "" "" "3SALATAim" "" "HMR_3865" "RCR11245" "" 0 "" "RHEA:70295" "HMR_3865" "MAR03870" "R00115" "GTHOm" "R00115C" "r0026" "" "GTHOm" "MNXR100098" "HMR_3870" "RCR11246" "" 0 "RHEA:11742" "RHEA:11740" "HMR_3870" -"MAR03873" "R00149" "CPS" "R00149M" "r0034" "" "" "MNXR96884" "HMR_3873" "RCR10504" "" 0 "" "" "HMR_3873" +"MAR03873" "R00149" "CPS;CPS_m" "R00149M" "r0034" "" "r0034" "MNXR96884" "HMR_3873" "RCR10504" "" 0 "" "" "HMR_3873;r0034;MAR02006" "MAR08654" "" "CBPter" "" "" "" "CBPSam" "MNXR96487" "HMR_8654" "RCR10505" "" 0 "" "" "HMR_8654" "MAR03890" "R00253" "GLNS" "R00253C" "r0077" "" "GLNS" "MNXR100024" "HMR_3890" "RCR10506" "" 0 "" "RHEA:16169" "HMR_3890" "MAR03892" "R00256" "GLUNm" "R00256M" "r0078" "" "GLUNm" "MNXR100030" "HMR_3892" "RCR11247" "" 0 "RHEA:15890" "RHEA:15889" "HMR_3892" @@ -765,7 +765,7 @@ rxns rxnKEGGID rxnBiGGID rxnEHMNID rxnHepatoNET1ID rxnREACTOMEID rxnRecon3DID rx "MAR07689" "" "DOPASULT" "" "" "" "DOPASULT" "MNXR97755" "HMR_7689" "RCR14340" "" 0 "" "" "HMR_7689" "MAR07701" "R07172" "H2O2syn" "" "" "" "H2O2syn" "MNXR100492" "HMR_7701" "RCR11365" "" 0 "RHEA:11261" "RHEA:11260" "HMR_7701" "MAR08094" "" "NRPPHRSULT" "" "" "" "NRPPHRSULT" "MNXR102016" "HMR_8094" "RCR11366" "" 0 "" "" "HMR_8094" -"MAR08529" "R06154" "MAOX" "" "" "" "" "MNXR101406" "HMR_8529" "RCR14341" "" 0 "" "RHEA:59420" "HMR_8529" +"MAR08529" "R06154" "MAOX" "" "" "" "MAOX" "MNXR101406" "HMR_8529" "RCR14341" "" 0 "RHEA:59421" "RHEA:59420" "HMR_8529;MAOX;MAR01515" "MAR08530" "" "FALDtm" "" "" "" "FALDH" "MNXR99238" "HMR_8530" "RCR14342" "" 0 "" "" "HMR_8530" "MAR08533" "" "DOPAQNISO1" "" "" "" "DOPACHRMISO" "MNXR97753" "HMR_8533" "RCR10532" "" 0 "" "" "HMR_8533" "MAR08534" "" "TRIODTHYSULT" "" "" "" "TRIODTHYSULT" "MNXR104937" "HMR_8534" "RCR10322" "" 0 "" "" "HMR_8534" @@ -974,7 +974,7 @@ rxns rxnKEGGID rxnBiGGID rxnEHMNID rxnHepatoNET1ID rxnREACTOMEID rxnRecon3DID rx "MAR03996" "R00892" "HMR_3996" "" "" "" "HMR_3996" "MNXR106737" "HMR_3996" "RCR10546" "" 0 "" "RHEA:20597" "HMR_3996" "MAR04072" "R00380" "" "" "" "" "HMR_4072" "MNXR97627" "HMR_4072" "RCR10547" "" 0 "" "RHEA:13681" "HMR_4072" "MAR04189" "R00533" "" "R00533C" "r0142" "" "r0142" "MNXR104649" "HMR_4189" "RCR11488" "" 0 "RHEA:24601" "RHEA:24600" "HMR_4189" -"MAR04302" "R00782" "" "R00782C" "r0193" "" "" "MNXR105313;MNXR96994" "HMR_4302" "RCR11489" "" 0 "" "RHEA:24931" "HMR_4302" +"MAR04302" "R00782" "r0193" "R00782C" "r0193" "" "r0193" "MNXR105313;MNXR96994" "HMR_4302" "RCR11489" "" 0 "" "RHEA:24931" "HMR_4302;r0193;MAR02027" "MAR04323" "R00891" "" "R00891C" "r0210" "" "r0210" "MNXR105314;MNXR96986" "HMR_4323" "RCR11490" "" 0 "" "" "HMR_4323" "MAR05381" "R02021" "" "RE3009C" "" "" "RE3009C" "MNXR102376" "HMR_5381" "RCR10548" "" 0 "" "RHEA:11724" "HMR_5381" "MAR05385" "R04420" "" "" "" "" "MTRI" "MNXR101759" "HMR_5385" "RCR14401" "" 0 "RHEA:19990" "RHEA:19989" "HMR_5385" @@ -1030,7 +1030,7 @@ rxns rxnKEGGID rxnBiGGID rxnEHMNID rxnHepatoNET1ID rxnREACTOMEID rxnRecon3DID rx "MAR04689" "R02549" "ABUTD;ABUTDm;R_ABUTD;R_ABUTDm" "" "" "" "ABUTD" "MNXR95191" "HMR_4689" "RCR10338" "" 0 "" "RHEA:19105" "HMR_4689" "MAR04735" "R03045" "PRPNCOAHYDm" "R03045M" "r0592" "" "PRPNCOAHYDm" "MNXR100691" "HMR_4735" "RCR10555" "" 0 "" "RHEA:26518" "HMR_4735" "MAR07991" "R01914" "SPMDOX" "" "" "" "SPMDOX" "MNXR104481" "HMR_7991" "RCR10339" "" 0 "" "RHEA:25820" "HMR_7991" -"MAR07992" "" "13DAMPPOX" "" "" "" "" "MNXR94687" "HMR_7992" "RCR10340" "" 0 "" "" "HMR_7992" +"MAR07992" "" "13DAMPPOX" "" "" "" "13DAMPPOX" "MNXR94687" "HMR_7992" "RCR10340" "" 0 "" "" "HMR_7992;13DAMPPOX;MAR00039" "MAR07993" "" "BAMPPALDOX" "" "" "" "BAMPPALDOX" "MNXR95891" "HMR_7993" "RCR10341" "" 0 "" "" "HMR_7993" "MAR07128" "R04929" "SELADT" "" "" "" "SELADT" "MNXR104310;MNXR109227" "HMR_7128" "RCR11509" "" 0 "" "" "HMR_7128" "MAR07129" "R04928" "ADSELK" "" "" "" "ADSELK" "MNXR109226;MNXR95491" "HMR_7129" "RCR11510" "" 0 "" "" "HMR_7129" @@ -8083,7 +8083,6 @@ rxns rxnKEGGID rxnBiGGID rxnEHMNID rxnHepatoNET1ID rxnREACTOMEID rxnRecon3DID rx "MAR00036" "" "" "" "" "" "arachidonates" "" "" "RCR21134" "" 0 "" "" "arachidonates" "MAR00037" "" "" "" "" "" "steroids" "" "" "RCR21042" "" 0 "" "" "steroids" "MAR00038" "" "10FTHFtm" "" "" "" "10FTHFtm" "MNXR94672" "" "" "" 0 "" "" "10FTHFtm" -"MAR00039" "" "13DAMPPOX" "" "" "" "13DAMPPOX" "MNXR94687" "" "" "" 0 "" "" "13DAMPPOX" "MAR00040" "" "34HPLFM" "" "" "" "34HPLFM" "MNXR94842" "" "" "" 0 "" "" "34HPLFM" "MAR00041" "" "3DPHBH1" "" "" "" "3DPHBH1" "MNXR94864" "" "" "" 0 "" "" "3DPHBH1" "MAR00043" "" "3HPCOAHYD" "" "" "" "3HPCOAHYD" "MNXR94900" "" "" "" 0 "" "" "3HPCOAHYD" @@ -8139,7 +8138,6 @@ rxns rxnKEGGID rxnBiGGID rxnEHMNID rxnHepatoNET1ID rxnREACTOMEID rxnRecon3DID rx "MAR00093" "" "BTNt2m" "" "" "" "BTNt2m" "MNXR96334" "" "" "" 0 "" "" "BTNt2m" "MAR00094" "" "BTNt3i" "" "" "" "BTNt3i" "MNXR96336" "" "" "" 0 "" "" "BTNt3i" "MAR00095" "" "BTNt4i" "" "" "" "BTNt4i" "MNXR96337" "" "" "" 0 "" "" "BTNt4i" -"MAR00096" "" "BUP2" "" "" "" "BUP2" "MNXR96346" "" "" "" 0 "" "" "BUP2" "MAR00097" "" "BUTt2m" "" "" "" "BUTt2m" "MNXR96353" "" "" "" 0 "" "" "BUTt2m" "MAR00098" "" "BVITEt" "" "" "" "BVITEt" "MNXR96355" "" "" "" 0 "" "" "BVITEt" "MAR00099" "" "BZt" "" "" "" "BZt" "MNXR96370" "" "" "" 0 "RHEA:32814" "RHEA:32811" "BZt" @@ -8433,7 +8431,6 @@ rxns rxnKEGGID rxnBiGGID rxnEHMNID rxnHepatoNET1ID rxnREACTOMEID rxnRecon3DID rx "MAR01511" "" "M4ATAer" "" "" "" "M4ATAer" "MNXR101312" "" "" "" 0 "" "" "M4ATAer" "MAR01513" "" "M4BET2er" "" "" "" "M4BET2er" "MNXR101314" "" "" "" 0 "" "" "M4BET2er" "MAR01514" "" "MAGt" "" "" "" "MAGt" "MNXR101333" "" "" "" 0 "" "" "MAGt" -"MAR01515" "" "MAOX" "" "" "" "MAOX" "MNXR101406" "" "" "" 0 "RHEA:59421" "RHEA:59420" "MAOX" "MAR01517" "" "MCOATAm" "" "" "" "MCOATAm" "MNXR101421" "" "" "" 0 "" "" "MCOATAm" "MAR01518" "" "MEPIVESSte" "" "" "" "MEPIVESSte" "MNXR101465" "" "" "" 0 "" "" "MEPIVESSte" "MAR01520" "" "MEVK1x" "" "" "" "MEVK1x" "MNXR101495" "" "" "" 0 "RHEA:17066" "RHEA:17065" "MEVK1x" @@ -8590,11 +8587,9 @@ rxns rxnKEGGID rxnBiGGID rxnEHMNID rxnHepatoNET1ID rxnREACTOMEID rxnRecon3DID rx "MAR01975" "" "EX_HC02161_e" "" "" "" "EX_HC02161[e]" "MNXR98151" "" "" "" 0 "" "" "EX_HC02161[e]" "MAR01984" "" "EX_prpp_e" "" "" "" "EX_prpp[e]" "MNXR98875" "" "" "" 0 "" "" "EX_prpp[e]" "MAR01986" "" "EX_udpg_e" "" "" "" "EX_udpg[e]" "MNXR99017" "" "" "" 0 "" "" "EX_udpg[e]" -"MAR02006" "" "CPS_m" "" "" "" "r0034" "" "" "" "" 0 "" "" "r0034" "MAR02021" "" "r0093" "" "" "" "r0093" "MNXR105070" "" "" "" 0 "" "" "r0093" "MAR02023" "" "r0145" "" "" "" "r0145" "" "" "" "" 0 "" "" "r0145" "MAR02026" "" "r0170" "" "" "" "r0170" "" "" "" "" 0 "" "" "r0170" -"MAR02027" "" "r0193" "" "" "" "r0193" "MNXR105313" "" "" "" 0 "" "" "r0193" "MAR02028" "" "ACOAR7m" "" "" "" "r0309" "MNXR95375" "" "" "" 0 "" "" "r0309" "MAR02119" "" "r0403" "" "" "" "r0403" "" "" "" "" 0 "" "" "r0403" "MAR02120" "" "r0410" "" "" "" "r0410" "MNXR102049" "" "" "" 0 "RHEA:28365" "RHEA:28362" "r0410"