diff --git a/data/deprecatedIdentifiers/deprecatedMetabolites.tsv b/data/deprecatedIdentifiers/deprecatedMetabolites.tsv index 193acd1e..56337256 100644 --- a/data/deprecatedIdentifiers/deprecatedMetabolites.tsv +++ b/data/deprecatedIdentifiers/deprecatedMetabolites.tsv @@ -2247,3 +2247,4 @@ mets metsNoComp metBiGGID metKEGGID metHMDBID metChEBIID metPubChemID metLipidMa "MAM02757l" "MAM02757" "" "" "" "" "" "" "" "" "M02757" "" "m02757l" "m02757l" "MAM02757n" "MAM02757" "" "" "" "" "" "" "" "" "M02757" "" "m02757n" "m02757n" "MAM01816n" "MAM01816" "" "" "" "" "" "PROTEIN" "" "" "M01816" "" "m01816n" "m01816n" +"MAM00926c" "MAM00926" "4aphdob" "C01252" "HMDB0000978" "CHEBI:17442" "472" "" "" "" "4aphdob" "MNXM163204" "m00926c" "m00926c" diff --git a/data/deprecatedIdentifiers/deprecatedReactions.tsv b/data/deprecatedIdentifiers/deprecatedReactions.tsv index 5524225a..f4b34adf 100644 --- a/data/deprecatedIdentifiers/deprecatedReactions.tsv +++ b/data/deprecatedIdentifiers/deprecatedReactions.tsv @@ -238,4 +238,6 @@ rxns rxnKEGGID rxnBiGGID rxnEHMNID rxnHepatoNET1ID rxnREACTOMEID rxnRecon3DID rx "MAR07771" "" "NADtpu" "" "" "" "NADtx" "MNXR101881" "HMR_7771" "RCR20023" "" 0 "" "" "HMR_7771" "MAR07782" "" "ADPtx" "" "" "" "ADPtx" "MNXR95484" "HMR_7782" "RCR20201" "" 0 "" "" "HMR_7782" "MAR07783" "" "AMPtp" "" "" "" "AMPtp" "MNXR95830" "HMR_7783" "RCR20046" "" 0 "" "" "HMR_7783" -"MAR07790" "" "FADtx" "" "" "" "FADtx" "MNXR99217" "HMR_7790" "RCR20203" "" 0 "" "" "HMR_7790" \ No newline at end of file +"MAR07790" "" "FADtx" "" "" "" "FADtx" "MNXR99217" "HMR_7790" "RCR20203" "" 0 "" "" "HMR_7790" +"MAR08564" "" "KYNAKGAT" "" "" "" "KYNAKGAT" "MNXR100948" "HMR_8564" "RCR11356" "" 0 "" "" "HMR_8564" +"MAR08565" "R03445" "KYNATESYN" "" "" "" "KYNATESYN" "MNXR100949" "HMR_8565" "RCR11357" "" 0 "" "RHEA:42452" "HMR_8565" diff --git a/model/Human-GEM.yml b/model/Human-GEM.yml index c6a46e87..1472f093 100644 --- a/model/Human-GEM.yml +++ b/model/Human-GEM.yml @@ -11729,14 +11729,6 @@ - charge: -1 - inchis: "" - metFrom: "HMRdatabase" - - !!omap - - id: "MAM00926c" - - name: "4-(2-aminophenyl)-2,4-dioxobutanoate" - - compartment: "c" - - formula: "C10H8NO4" - - charge: -1 - - inchis: "" - - metFrom: "HMRdatabase" - !!omap - id: "MAM00927c" - name: "4-(methylnitrosamino)-1-(1-oxido-3-pyridinyl)-1-butanone" @@ -81699,41 +81691,6 @@ - subsystem: - "Tryptophan metabolism" - confidence_score: 0 - - !!omap - - id: "MAR08564" - - name: "" - - metabolites: !!omap - - MAM00926c: 1 - - MAM01306c: -1 - - MAM01974c: 1 - - MAM02319c: -1 - - lower_bound: 0 - - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000109576 or ENSG00000137944 or ENSG00000171097" - - rxnNotes: "" - - rxnFrom: "HMRdatabase" - - eccodes: "2.6.1.7" - - references: "" - - subsystem: - - "Tryptophan metabolism" - - confidence_score: 0 - - !!omap - - id: "MAR08565" - - name: "" - - metabolites: !!omap - - MAM00926c: -1 - - MAM00990c: 1 - - MAM02040c: 1 - - lower_bound: 0 - - upper_bound: 1000 - - gene_reaction_rule: "" - - rxnNotes: "" - - rxnFrom: "HMRdatabase" - - eccodes: "" - - references: "" - - subsystem: - - "Tryptophan metabolism" - - confidence_score: 0 - !!omap - id: "MAR08566" - name: "" @@ -82834,14 +82791,14 @@ - id: "MAR04222" - name: "" - metabolites: !!omap - - MAM00990c: -1 - - MAM01306c: 1 - - MAM01974c: -1 - - MAM02040c: -1 - - MAM02319c: 1 - - lower_bound: -1000 + - MAM00990c: 1 + - MAM01306c: -1 + - MAM01974c: 1 + - MAM02040c: 1 + - MAM02319c: -1 + - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000109576 or ENSG00000137944 or ENSG00000171097" + - gene_reaction_rule: "ENSG00000137944 or ENSG00000171097" - rxnNotes: "" - rxnFrom: "HMRdatabase" - eccodes: "2.6.1.7" @@ -218228,7 +218185,7 @@ - MAM02553m: 1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000111275 or ENSG00000137124 or ENSG00000159423" + - gene_reaction_rule: "ENSG00000111275 or ENSG00000137124" - rxnNotes: "" - rxnFrom: "Recon3D" - eccodes: "1.5.1.12" @@ -230344,7 +230301,7 @@ - MAM01974m: 1 - MAM02040m: 1 - MAM02319m: -1 - - lower_bound: -1000 + - lower_bound: 0 - upper_bound: 1000 - gene_reaction_rule: "ENSG00000109576 or ENSG00000137944" - rxnNotes: "" diff --git a/model/metabolites.tsv b/model/metabolites.tsv index 63fa75cc..076825d0 100644 --- a/model/metabolites.tsv +++ b/model/metabolites.tsv @@ -1464,7 +1464,6 @@ mets metsNoComp metBiGGID metKEGGID metHMDBID metChEBIID metPubChemID metLipidMa "MAM00923c" "MAM00923" "cala" "C02642" "HMDB0000026" "CHEBI:18261" "111" "" "" "HC00975" "cala" "MNXM802" "m00923c" "m00923c" "MAM00924c" "MAM00924" "42A3HP24DB" "C05645" "" "" "440741" "" "" "HC01547" "42A3HP24DB" "MNXM163203;MNXM4997" "m00924c" "m00924c" "MAM00925c" "MAM00925" "" "" "" "" "10948689" "" "CE3086" "" "CE3086" "MNXM166294" "m00925c" "m00925c" -"MAM00926c" "MAM00926" "4aphdob" "C01252" "HMDB0000978" "CHEBI:17442" "472" "" "" "" "4aphdob" "MNXM163204" "m00926c" "m00926c" "MAM00927c" "MAM00927" "" "C19602" "" "" "" "" "" "" "M00927" "MNXM14691" "m00927c" "m00927c" "MAM00928c" "MAM00928" "" "C19605" "" "" "" "" "" "" "M00928" "MNXM14692" "m00928c" "m00928c" "MAM00929c" "MAM00929" "" "C19574" "" "" "" "" "" "" "M00929" "MNXM4356" "m00929c" "m00929c" diff --git a/model/reactions.tsv b/model/reactions.tsv index 34c5374f..7ec1a1fb 100644 --- a/model/reactions.tsv +++ b/model/reactions.tsv @@ -748,8 +748,6 @@ rxns rxnKEGGID rxnBiGGID rxnEHMNID rxnHepatoNET1ID rxnREACTOMEID rxnRecon3DID rx "MAR08091" "" "3HXKYNDCL" "" "" "" "3HXKYNDCL" "MNXR94906" "HMR_8091" "RCR11354" "" 0 "" "" "HMR_8091" "MAR08092" "R04907" "3HXKYNOXDA" "" "" "" "3HXKYNOXDA" "MNXR94907" "HMR_8092" "RCR11355" "" 0 "" "" "HMR_8092" "MAR08563" "R02678" "ALDD20xm" "" "" "" "ALDD20xm" "MNXR95744" "HMR_8563" "RCR10320" "" 0 "" "RHEA:30867" "HMR_8563" -"MAR08564" "" "KYNAKGAT" "" "" "" "KYNAKGAT" "MNXR100948" "HMR_8564" "RCR11356" "" 0 "" "" "HMR_8564" -"MAR08565" "R03445" "KYNATESYN" "" "" "" "KYNATESYN" "MNXR100949" "HMR_8565" "RCR11357" "" 0 "" "RHEA:42452" "HMR_8565" "MAR08566" "" "MELATNOX" "" "" "" "MELATNOX" "MNXR101458" "HMR_8566" "RCR11358" "" 0 "" "" "HMR_8566" "MAR03935" "R06982" "r1377" "" "r1377" "" "r1377" "MNXR105462;MNXR99239" "HMR_3935" "RCR11359" "" 0 "" "RHEA:22488" "HMR_3935" "MAR04681" "R00699" "" "" "" "" "PHYCBOXL" "MNXR102650" "HMR_4681" "RCR10321" "" 0 "" "RHEA:19717" "HMR_4681" @@ -808,7 +806,7 @@ rxns rxnKEGGID rxnBiGGID rxnEHMNID rxnHepatoNET1ID rxnREACTOMEID rxnRecon3DID rx "MAR04218" "R03936" "LFORKYNHYD" "R03936C" "r0646" "" "LFORKYNHYD" "MNXR101060;MNXR108539" "HMR_4218" "RCR11391" "" 0 "" "" "HMR_4218" "MAR04219" "R00988" "" "R00988C" "r0239" "" "r0239" "MNXR105316;MNXR106774" "HMR_4219" "RCR11392" "" 0 "" "" "HMR_4219" "MAR04220" "R01960" "KYN3OX" "R01960C" "r0455" "" "KYN3OX" "MNXR100947" "HMR_4220" "RCR11393" "" 0 "RHEA:20548" "RHEA:20545" "HMR_4220" -"MAR04222" "" "" "RE1233C" "" "" "RE1233C" "" "HMR_4222" "RCR11394" "" 0 "" "" "HMR_4222" +"MAR04222" "" "" "RE1233C" "" "" "RE1233C" "" "HMR_4222" "RCR11394" "" 0 "RHEA:65561" "RHEA:65560" "HMR_4222;MAR08564+MAR08565" "MAR04224" "R00987" "KYN" "R00987C" "r0238" "" "KYN" "MNXR100946" "HMR_4224" "RCR11395" "" 0 "" "RHEA:16813" "HMR_4224" "MAR04225" "R02668" "HKYNH" "R02668C" "r0563" "" "HKYNH" "MNXR100656" "HMR_4225" "RCR10534" "" 0 "" "RHEA:25143" "HMR_4225" "MAR04227" "R02670" "" "" "" "" "HMR_4227" "MNXR107655" "HMR_4227" "RCR14355" "" 0 "" "" "HMR_4227" @@ -8726,7 +8724,7 @@ rxns rxnKEGGID rxnBiGGID rxnEHMNID rxnHepatoNET1ID rxnREACTOMEID rxnRecon3DID rx "MAR02751" "" "RE1134M" "" "" "" "RE1134M" "MNXR102255" "" "" "" 0 "" "" "RE1134M" "MAR02756" "" "" "" "" "" "RE1135G" "" "" "" "" 0 "" "" "RE1135G" "MAR02763" "" "" "" "" "" "RE1135L" "" "" "" "" 0 "" "" "RE1135L" -"MAR02765" "" "" "" "" "" "RE1233M" "" "" "" "" 0 "" "" "RE1233M" +"MAR02765" "" "" "" "" "" "RE1233M" "" "" "" "" 0 "RHEA:65561" "RHEA:65560" "RE1233M" "MAR02767" "" "RE1309M" "" "" "" "RE1309M" "MNXR103507" "" "" "" 0 "" "" "RE1309M" "MAR02779" "" "RE1342C" "" "" "" "RE1342C" "MNXR103511" "" "" "" 0 "" "" "RE1342C" "MAR02781" "" "RE1447M" "" "" "" "RE1447M" "MNXR102717" "" "" "" 0 "" "" "RE1447M"