diff --git a/data/deprecatedIdentifiers/deprecatedReactions.tsv b/data/deprecatedIdentifiers/deprecatedReactions.tsv index a5532b09..60cccea9 100644 --- a/data/deprecatedIdentifiers/deprecatedReactions.tsv +++ b/data/deprecatedIdentifiers/deprecatedReactions.tsv @@ -158,6 +158,7 @@ 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" "" "" +"MAR05310" "" "GLNtN1" "" "" "" "GLNtN1" "MNXR100263" "HMR_5310" "RCR41006" "" 0 "" "" "HMR_5310" "MAR00032" "" "" "" "" "" "HMR_0032" "" "HMR_0032" "RCR14836" "" 0 "" "" "HMR_0032" "MAR02276" "" "r0993" "" "" "" "r0993" "MNXR105414" "" "" "" 0 "" "" "r0993" "MAR02277" "" "r0994" "" "" "" "r0994" "MNXR105415" "" "" "" 0 "" "" "r0994" @@ -188,3 +189,4 @@ rxns rxnKEGGID rxnBiGGID rxnEHMNID rxnHepatoNET1ID rxnREACTOMEID rxnRecon3DID rx "MAR03441" "" "RE3150C" "" "" "" "RE3150C" "MNXR103806" "" "" "" 0 "" "" "RE3150C" "MAR10164" "" "" "" "" "" "CE2516t" "" "" "" "" 0 "" "" "CE2516t" "MAR10433" "" "" "" "" "" "EX_CE2516[e]" "" "" "" "" 0 "" "" "EX_CE2516[e]" +"MAR09887" "" "GLNB0AT3tc" "" "" "" "GLNB0AT3tc" "" "" "" "" 0 "" "" "GLNB0AT3tc" diff --git a/model/Human-GEM.yml b/model/Human-GEM.yml index dcb02a0c..ae635604 100644 --- a/model/Human-GEM.yml +++ b/model/Human-GEM.yml @@ -172213,26 +172213,6 @@ - subsystem: - "Transport reactions" - confidence_score: 0 - - !!omap - - id: "MAR05310" - - name: "" - - metabolites: !!omap - - MAM01975c: 1 - - MAM01975e: -1 - - MAM02039c: -1 - - MAM02039e: 1 - - MAM02519c: 2 - - MAM02519e: -2 - - lower_bound: 0 - - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000017483 or ENSG00000188338" - - rxnNotes: "" - - rxnFrom: "HMRdatabase" - - eccodes: "" - - references: "" - - subsystem: - - "Transport reactions" - - confidence_score: 0 - !!omap - id: "MAR05311" - name: "" @@ -188970,9 +188950,9 @@ - MAM02039e: 1 - MAM02519c: 1 - MAM02519e: -1 - - lower_bound: 0 + - lower_bound: -1000 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000017483 or ENSG00000111371 or ENSG00000134294 or ENSG00000139209" + - gene_reaction_rule: "ENSG00000017483 or ENSG00000188338" - rxnNotes: "" - rxnFrom: "HMRdatabase" - eccodes: "" @@ -248845,26 +248825,6 @@ - subsystem: - "Transport reactions" - confidence_score: 0 - - !!omap - - id: "MAR09887" - - name: "Glutamine Transport by B0At3" - - metabolites: !!omap - - MAM01442c: 1 - - MAM01442e: -1 - - MAM01975c: 1 - - MAM01975e: -1 - - MAM02519c: 1 - - MAM02519e: -1 - - lower_bound: 0 - - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000147003 and ENSG00000164363" - - rxnNotes: "" - - rxnFrom: "Recon3D" - - eccodes: "" - - references: "" - - subsystem: - - "Transport reactions" - - confidence_score: 0 - !!omap - id: "MAR09888" - name: "Glutamate Transport by B0At3" diff --git a/model/reactions.tsv b/model/reactions.tsv index 572cbaed..6e3cf648 100644 --- a/model/reactions.tsv +++ b/model/reactions.tsv @@ -5397,7 +5397,6 @@ rxns rxnKEGGID rxnBiGGID rxnEHMNID rxnHepatoNET1ID rxnREACTOMEID rxnRecon3DID rx "MAR05305" "" "ALAt4" "" "r1118" "" "ALAt4" "MNXR95692" "HMR_5305" "RCR41003" "2.A.18.6.7" 0 "" "" "HMR_5305" "MAR05307" "" "ALAtN1" "" "" "" "ALAtN1" "MNXR95705" "HMR_5307" "RCR41004" "" 0 "" "" "HMR_5307" "MAR05308" "" "GLNt4" "" "r1119" "" "GLNt4" "MNXR100261" "HMR_5308" "RCR41005" "2.A.18.6.5" 0 "" "" "HMR_5308" -"MAR05310" "" "GLNtN1" "" "" "" "GLNtN1" "MNXR100263" "HMR_5310" "RCR41006" "" 0 "" "" "HMR_5310" "MAR05311" "" "ASNt4" "" "r1120" "" "ASNt4" "MNXR96057" "HMR_5311" "RCR41007" "2.A.18.6.7" 0 "" "" "HMR_5311" "MAR05313" "" "ASNtN1" "" "" "" "ASNtN1" "MNXR96068" "HMR_5313" "RCR41008" "" 0 "" "" "HMR_5313" "MAR05314" "" "VALt4" "" "r1121" "" "VALt4" "MNXR105189" "HMR_5314" "RCR41009" "2.A.1.44.1" 0 "" "" "HMR_5314" @@ -6275,7 +6274,7 @@ rxns rxnKEGGID rxnBiGGID rxnEHMNID rxnHepatoNET1ID rxnREACTOMEID rxnRecon3DID rx "MAR06375" "" "SERt4" "" "r2474" "" "SERt4" "MNXR104346" "HMR_6375" "RCR41525" "2.A.18.6.5" 0 "" "" "HMR_6375" "MAR06377" "" "CYSt4" "" "r2475" "" "CYSt4" "MNXR97028" "HMR_6377" "RCR41526" "2.A.18.6.5" 0 "" "" "HMR_6377" "MAR06379" "" "HOMt4" "" "r2476" "" "HOMt4" "MNXR100677" "HMR_6379" "RCR41527" "2.A.18.6.5" 0 "" "" "HMR_6379" -"MAR06380" "" "GLNt4" "" "r2477" "" "" "MNXR100261" "HMR_6380" "RCR41528" "2.A.18.6.2" 0 "" "" "HMR_6380" +"MAR06380" "" "GLNt4;GLNtN1" "" "r2477" "" "GLNtN1" "MNXR100261;MNXR100263" "HMR_6380;HMR_5310" "RCR41528;RCR41006" "2.A.18.6.2" 0 "" "" "HMR_6380;HMR_5310;MAR05310" "MAR06381" "" "SERt4" "" "r2478" "" "" "MNXR104346" "HMR_6381" "RCR41529" "2.A.18.6.8" 0 "" "" "HMR_6381" "MAR06382" "" "ASNt4" "" "r2479" "" "" "MNXR96057" "HMR_6382" "RCR41530" "2.A.18.6.8" 0 "" "" "HMR_6382" "MAR06383" "" "HOMt4" "" "r2480" "" "" "MNXR100677" "HMR_6383" "RCR41531" "2.A.18.6.8" 0 "" "" "HMR_6383" @@ -9504,7 +9503,7 @@ rxns rxnKEGGID rxnBiGGID rxnEHMNID rxnHepatoNET1ID rxnREACTOMEID rxnRecon3DID rx "MAR06891" "" "CYSTALArBATtc" "" "" "" "CYSTALArBATtc" "MNXR97011" "" "" "" 0 "" "" "CYSTALArBATtc" "MAR06892" "" "CYSTLEUrBATtc" "" "" "" "CYSTLEUrBATtc" "MNXR97016" "" "" "" 0 "" "" "CYSTLEUrBATtc" "MAR06893" "" "FOLt" "" "" "" "FOLTle" "MNXR99612" "" "" "" 0 "" "" "FOLTle" -"MAR06896" "" "GLNATB0tc" "" "" "" "GLNATB0tc" "MNXR100248" "" "" "" 0 "" "" "GLNATB0tc" +"MAR06896" "" "GLNATB0tc;GLNB0AT3tc" "" "" "" "GLNATB0tc;GLNB0AT3tc" "MNXR100248" "" "" "" 0 "" "" "GLNATB0tc;GLNB0AT3tc;MAR09887" "MAR06897" "" "GLNyLATthc" "" "" "" "GLNyLATthc" "MNXR100264" "" "" "" 0 "" "" "GLNyLATthc" "MAR06898" "" "GLYGLYCNc" "" "" "" "GLYGLYCNc" "MNXR100345" "" "" "" 0 "" "" "GLYGLYCNc" "MAR06899" "" "GLYGLYPEPT1tc" "" "" "" "GLYGLYPEPT1tc" "MNXR100346" "" "" "" 0 "" "" "GLYGLYPEPT1tc" @@ -9740,7 +9739,6 @@ rxns rxnKEGGID rxnBiGGID rxnEHMNID rxnHepatoNET1ID rxnREACTOMEID rxnRecon3DID rx "MAR09884" "" "FOLOAT2tc" "" "" "" "FOLOAT2tc" "" "" "" "" 0 "" "" "FOLOAT2tc" "MAR09885" "" "FOLOATPtc" "" "" "" "FOLOATPtc" "" "" "" "" 0 "" "" "FOLOATPtc" "MAR09886" "" "GABABGTtc" "" "" "" "GABABGTtc" "" "" "" "" 0 "" "" "GABABGTtc" -"MAR09887" "" "GLNB0AT3tc" "" "" "" "GLNB0AT3tc" "" "" "" "" 0 "" "" "GLNB0AT3tc" "MAR09888" "" "GLUB0AT3tc" "" "" "" "GLUB0AT3tc" "" "" "" "" 0 "" "" "GLUB0AT3tc" "MAR09889" "" "GSNt2" "" "" "" "GSNt2r" "MNXR100434" "" "" "" 0 "RHEA:29586" "RHEA:29583" "GSNt2r" "MAR09890" "" "H2OGLYAQPt" "" "" "" "H2OGLYAQPt" "" "" "" "" 0 "" "" "H2OGLYAQPt"