From b05a1a2936078e3e37d5610cb0b868fb07141185 Mon Sep 17 00:00:00 2001 From: Devlin-Moyer Date: Tue, 20 Jun 2023 17:23:31 -0400 Subject: [PATCH 1/5] fix: removes MAR05310 for being duplicate of MAR06380 with wrong stoich & merges annotations for MAR05310 into annotations for MAR06380 --- .../deprecatedReactions.tsv | 1 + model/Human-GEM.yml | 20 ------------------- model/reactions.tsv | 3 +-- 3 files changed, 2 insertions(+), 22 deletions(-) diff --git a/data/deprecatedIdentifiers/deprecatedReactions.tsv b/data/deprecatedIdentifiers/deprecatedReactions.tsv index 71108f9c..044e6f14 100644 --- a/data/deprecatedIdentifiers/deprecatedReactions.tsv +++ b/data/deprecatedIdentifiers/deprecatedReactions.tsv @@ -142,3 +142,4 @@ 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" diff --git a/model/Human-GEM.yml b/model/Human-GEM.yml index 88682ac7..1b1d0505 100644 --- a/model/Human-GEM.yml +++ b/model/Human-GEM.yml @@ -172647,26 +172647,6 @@ - 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: "" diff --git a/model/reactions.tsv b/model/reactions.tsv index af0d5802..bff02b45 100644 --- a/model/reactions.tsv +++ b/model/reactions.tsv @@ -5411,7 +5411,6 @@ 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" @@ -6294,7 +6293,7 @@ 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" "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" From ccdb77f459e370a37f6493d6fe7e307bd894d855 Mon Sep 17 00:00:00 2001 From: Devlin-Moyer Date: Tue, 20 Jun 2023 17:26:44 -0400 Subject: [PATCH 2/5] fix: replaces inaccurate GPRs of MAR06380 and MAR09887 with accurate ones --- model/Human-GEM.yml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/model/Human-GEM.yml b/model/Human-GEM.yml index 1b1d0505..b17d0798 100644 --- a/model/Human-GEM.yml +++ b/model/Human-GEM.yml @@ -189482,7 +189482,7 @@ - MAM02519e: -1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000017483 or ENSG00000111371 or ENSG00000134294 or ENSG00000139209" + - gene_reaction_rule: "ENSG00000017483 or ENSG00000188338" - rxnNotes: "" - rxnFrom: "HMRdatabase" - eccodes: "" @@ -249795,7 +249795,7 @@ - MAM02519e: -1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000147003 and ENSG00000164363" + - gene_reaction_rule: "ENSG00000268104" - rxnNotes: "" - rxnFrom: "Recon3D" - eccodes: "" From 100ce85226d3355ffbccd55679f3f96cbd8215e9 Mon Sep 17 00:00:00 2001 From: Devlin-Moyer Date: Tue, 27 Jun 2023 17:24:57 -0400 Subject: [PATCH 3/5] fix: add MAR05310 to rxnRetired column for MAR06380 in model/reactions.tsv --- model/reactions.tsv | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/model/reactions.tsv b/model/reactions.tsv index c4327d68..80341e81 100644 --- a/model/reactions.tsv +++ b/model/reactions.tsv @@ -6274,7 +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;GLNtN1" "" "r2477" "" "GLNtN1" "MNXR100261;MNXR100263" "HMR_6380;HMR_5310" "RCR41528;RCR41006" "2.A.18.6.2" 0 "" "" "HMR_6380;HMR_5310" +"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" From d604989e7304ee5f6fbb3c6801fc944c86c5621e Mon Sep 17 00:00:00 2001 From: Devlin-Moyer Date: Wed, 5 Jul 2023 16:24:32 -0400 Subject: [PATCH 4/5] make MAR06380 reversible --- model/Human-GEM.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/model/Human-GEM.yml b/model/Human-GEM.yml index a1b76c65..02b9bb74 100644 --- a/model/Human-GEM.yml +++ b/model/Human-GEM.yml @@ -188958,7 +188958,7 @@ - MAM02039e: 1 - MAM02519c: 1 - MAM02519e: -1 - - lower_bound: 0 + - lower_bound: -1000 - upper_bound: 1000 - gene_reaction_rule: "ENSG00000017483 or ENSG00000188338" - rxnNotes: "" From 2d59575cb132ea242dc7ec7bb204b6c4ef295e47 Mon Sep 17 00:00:00 2001 From: Devlin-Moyer Date: Wed, 5 Jul 2023 16:27:11 -0400 Subject: [PATCH 5/5] fix: remove MAR09887 and merge annotations into MAR06896 --- .../deprecatedReactions.tsv | 1 + model/Human-GEM.yml | 20 ------------------- model/reactions.tsv | 3 +-- 3 files changed, 2 insertions(+), 22 deletions(-) diff --git a/data/deprecatedIdentifiers/deprecatedReactions.tsv b/data/deprecatedIdentifiers/deprecatedReactions.tsv index 3a1e6114..e6fe86d2 100644 --- a/data/deprecatedIdentifiers/deprecatedReactions.tsv +++ b/data/deprecatedIdentifiers/deprecatedReactions.tsv @@ -188,3 +188,4 @@ 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 02b9bb74..1048c1c8 100644 --- a/model/Human-GEM.yml +++ b/model/Human-GEM.yml @@ -248862,26 +248862,6 @@ - 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: "ENSG00000268104" - - 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 80341e81..2c502d8c 100644 --- a/model/reactions.tsv +++ b/model/reactions.tsv @@ -9504,7 +9504,7 @@ 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 +9740,6 @@ 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"