From 91d349662eb7b3c87c9df959e84340d2607fbe96 Mon Sep 17 00:00:00 2001 From: Devlin-Moyer Date: Fri, 8 Dec 2023 09:07:03 -0500 Subject: [PATCH 1/6] fix: remove MAR06329 for being redundant with MAR03149 + MAR03150 + MAR03151 + MAR03153 --- .../deprecatedReactions.tsv | 1 + model/Human-GEM.yml | 24 ------------------- model/reactions.tsv | 9 ++++--- 3 files changed, 5 insertions(+), 29 deletions(-) diff --git a/data/deprecatedIdentifiers/deprecatedReactions.tsv b/data/deprecatedIdentifiers/deprecatedReactions.tsv index c726bad6..d06bf72b 100644 --- a/data/deprecatedIdentifiers/deprecatedReactions.tsv +++ b/data/deprecatedIdentifiers/deprecatedReactions.tsv @@ -262,3 +262,4 @@ rxns rxnKEGGID rxnBiGGID rxnEHMNID rxnHepatoNET1ID rxnREACTOMEID rxnRecon3DID rx "MAR04239" "R01933" "2OXOADOXm" "R01933M" "r0448" "" "2OXOADOXm" "MNXR94818" "HMR_4239" "RCR11332" "" 0 "RHEA:30796" "RHEA:30795" "HMR_4239" "MAR04940" "" "" "" "r0885" "" "r0885" "MNXR105402" "HMR_4940" "RCR20265" "2.A.29.2.7" 0 "" "" "HMR_4940" "MAR06391" "" "" "" "r2520" "" "r2520" "MNXR106328" "HMR_6391" "RCR20063" "" 0 "" "" "HMR_6391" +"MAR06329" "" "FAOXC8C6m" "" "" "" "FAOXC8C6m" "" "" "" "" 0 "" "" "FAOXC8C6m" diff --git a/model/Human-GEM.yml b/model/Human-GEM.yml index 460f88a5..b8473686 100644 --- a/model/Human-GEM.yml +++ b/model/Human-GEM.yml @@ -242032,30 +242032,6 @@ - subsystem: - "Fatty acid oxidation" - confidence_score: 0 - - !!omap - - id: "MAR06329" - - name: "Fatty Acid Beta Oxidation (C8->C6), Mitochondrial" - - metabolites: !!omap - - MAM01261m: 1 - - MAM01597m: -1 - - MAM01802m: -1 - - MAM01803m: 1 - - MAM02039m: 1 - - MAM02040m: -1 - - MAM02122m: 1 - - MAM02552m: -1 - - MAM02553m: 1 - - MAM02644m: -1 - - lower_bound: 0 - - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000117054 and ENSG00000127884 and ENSG00000138796 and ENSG00000167315" - - rxnNotes: "" - - rxnFrom: "Recon3D" - - eccodes: "" - - references: "PMID:20195903;PMID:20490924;PMID:17143551" - - subsystem: - - "Fatty acid oxidation" - - confidence_score: 0 - !!omap - id: "MAR06344" - name: "Fatty Acid Beta Oxidation (C8->C6), Peroxisomal" diff --git a/model/reactions.tsv b/model/reactions.tsv index 7c808f4e..fe82f984 100644 --- a/model/reactions.tsv +++ b/model/reactions.tsv @@ -2649,10 +2649,10 @@ rxns rxnKEGGID rxnBiGGID rxnEHMNID rxnHepatoNET1ID rxnREACTOMEID rxnRecon3DID rx "MAR03143" "R04744" "" "R04744X" "r0728" "" "r0728" "MNXR97889" "HMR_3143" "RCR12646" "" 0 "" "RHEA:31191" "HMR_3143" "MAR03144" "R04743" "" "R04743X" "r0726" "" "r0726" "MNXR100545" "HMR_3144" "RCR12647" "" 0 "" "RHEA:31187" "HMR_3144" "MAR03146" "R03778" "" "R03778X" "r0634" "" "r0634" "MNXR95198" "HMR_3146" "RCR12648" "" 0 "RHEA:31089" "RHEA:31087" "HMR_3146" -"MAR03149" "R03777" "r1448" "" "" "R-HSA-77338" "HMR_3149;r1448" "MNXR95304" "HMR_3149" "RCR12649" "" 0 "" "RHEA:30943" "HMR_3149;r1448;MAR02369" -"MAR03150" "R04746" "" "R04746M" "r0731" "" "r0731" "MNXR97888" "HMR_3150" "RCR12650" "" 0 "" "RHEA:31199" "HMR_3150" -"MAR03151" "R04745" "" "R04745M" "r0730" "" "r0730" "MNXR100544" "HMR_3151" "RCR12651" "" 0 "" "RHEA:31195" "HMR_3151" -"MAR03153" "R04747" "" "R04747M" "r0732" "" "r0732" "MNXR109092" "HMR_3153" "RCR12652" "" 0 "RHEA:31205" "RHEA:31203" "HMR_3153" +"MAR03149" "R03777" "r1448;FAOXC8C6m" "" "" "R-HSA-77338" "HMR_3149;r1448i;FAOXC6C8m" "MNXR95304" "HMR_3149" "RCR12649" "" 0 "" "RHEA:30943" "HMR_3149;r1448;MAR02369;FAOXC8C6m;MAR06329" +"MAR03150" "R04746" "FAOXC8C6m" "R04746M" "r0731" "" "r0731;FAOXC8C6m" "MNXR97888" "HMR_3150" "RCR12650" "" 0 "" "RHEA:31199" "HMR_3150;FAOXC6C8m;MAR06329" +"MAR03151" "R04745" "FAOXC8C6m" "R04745M" "r0730" "" "r0730;FAOXC8C6m" "MNXR100544" "HMR_3151" "RCR12651" "" 0 "" "RHEA:31195" "HMR_3151;FAOXC8C6m;MAR06329" +"MAR03153" "R04747" "FAOXC8C6m" "R04747M" "r0732" "" "r0732;FAOXC8C6m" "MNXR109092" "HMR_3153" "RCR12652" "" 0 "RHEA:31205" "RHEA:31203" "HMR_3153;FAOXC8C6m;MAR06329" "MAR03156" "R04751" "r1450" "" "" "R-HSA-77327" "HMR_3156;r1450" "MNXR109093" "HMR_3156" "RCR12653" "" 0 "" "RHEA:31207" "HMR_3156;r1450;MAR02372" "MAR03157" "R04749" "" "R04749M" "r0734" "" "r0734" "MNXR97886" "HMR_3157" "RCR12654" "" 0 "" "RHEA:30547" "HMR_3157" "MAR03158" "R04748" "" "R04748M" "r0733" "R-HSA-77323" "r0733" "MNXR100543" "HMR_3158" "RCR12655" "" 0 "" "RHEA:31143" "HMR_3158" @@ -9363,7 +9363,6 @@ rxns rxnKEGGID rxnBiGGID rxnEHMNID rxnHepatoNET1ID rxnREACTOMEID rxnRecon3DID rx "MAR06319" "" "FAOXC7C5m" "" "" "" "FAOXC7C5m" "" "" "" "" 0 "" "" "FAOXC7C5m" "MAR06320" "" "FAOXC81C61m" "" "" "" "FAOXC81C61m" "" "" "" "" 0 "" "" "FAOXC81C61m" "MAR06322" "" "FAOXC81C61x" "" "" "" "FAOXC81C61x" "" "" "" "" 0 "" "" "FAOXC81C61x" -"MAR06329" "" "FAOXC8C6m" "" "" "" "FAOXC8C6m" "" "" "" "" 0 "" "" "FAOXC8C6m" "MAR06344" "" "FAOXC8C6x" "" "" "" "FAOXC8C6x" "" "" "" "" 0 "" "" "FAOXC8C6x" "MAR06345" "" "FAOXC8DCC6DCx" "" "" "" "FAOXC8DCC6DCx" "" "" "" "" 0 "" "" "FAOXC8DCC6DCx" "MAR06346" "" "" "" "" "" "FAOXC9BRC7BRm" "" "" "" "" 0 "" "" "FAOXC9BRC7BRm" From 9955c41e4d1731b4a1f8e741f2aef08134ccd6aa Mon Sep 17 00:00:00 2001 From: Devlin-Moyer Date: Fri, 8 Dec 2023 09:20:34 -0500 Subject: [PATCH 2/6] fix: remove MAR06283 for being redundant with MAR03156 + MAR03157 + MAR03158 + MAR03160 --- .../deprecatedReactions.tsv | 1 + model/Human-GEM.yml | 24 ------------------- model/reactions.tsv | 9 ++++--- 3 files changed, 5 insertions(+), 29 deletions(-) diff --git a/data/deprecatedIdentifiers/deprecatedReactions.tsv b/data/deprecatedIdentifiers/deprecatedReactions.tsv index d06bf72b..c62b1d75 100644 --- a/data/deprecatedIdentifiers/deprecatedReactions.tsv +++ b/data/deprecatedIdentifiers/deprecatedReactions.tsv @@ -263,3 +263,4 @@ rxns rxnKEGGID rxnBiGGID rxnEHMNID rxnHepatoNET1ID rxnREACTOMEID rxnRecon3DID rx "MAR04940" "" "" "" "r0885" "" "r0885" "MNXR105402" "HMR_4940" "RCR20265" "2.A.29.2.7" 0 "" "" "HMR_4940" "MAR06391" "" "" "" "r2520" "" "r2520" "MNXR106328" "HMR_6391" "RCR20063" "" 0 "" "" "HMR_6391" "MAR06329" "" "FAOXC8C6m" "" "" "" "FAOXC8C6m" "" "" "" "" 0 "" "" "FAOXC8C6m" +"MAR06283" "" "FAOXC6C4m" "" "" "" "FAOXC6C4m" "" "" "" "" 0 "" "" "FAOXC6C4m" diff --git a/model/Human-GEM.yml b/model/Human-GEM.yml index b8473686..d5910666 100644 --- a/model/Human-GEM.yml +++ b/model/Human-GEM.yml @@ -241888,30 +241888,6 @@ - subsystem: - "Fatty acid oxidation" - confidence_score: 0 - - !!omap - - id: "MAR06283" - - name: "Fatty Acid Beta Oxidation (C6->C4), Mitochondrial" - - metabolites: !!omap - - MAM01261m: 1 - - MAM01412m: 1 - - MAM01597m: -1 - - MAM01802m: -1 - - MAM01803m: 1 - - MAM02039m: 1 - - MAM02040m: -1 - - MAM02122m: -1 - - MAM02552m: -1 - - MAM02553m: 1 - - lower_bound: 0 - - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000117054 and ENSG00000127884 and ENSG00000138796 and ENSG00000167315" - - rxnNotes: "" - - rxnFrom: "Recon3D" - - eccodes: "" - - references: "PMID:20195903;PMID:20490924;PMID:17143551" - - subsystem: - - "Fatty acid oxidation" - - confidence_score: 0 - !!omap - id: "MAR06284" - name: "Fatty Acid Beta Oxidation (C6->C4), Peroxisomal" diff --git a/model/reactions.tsv b/model/reactions.tsv index fe82f984..fd185ee9 100644 --- a/model/reactions.tsv +++ b/model/reactions.tsv @@ -2653,10 +2653,10 @@ rxns rxnKEGGID rxnBiGGID rxnEHMNID rxnHepatoNET1ID rxnREACTOMEID rxnRecon3DID rx "MAR03150" "R04746" "FAOXC8C6m" "R04746M" "r0731" "" "r0731;FAOXC8C6m" "MNXR97888" "HMR_3150" "RCR12650" "" 0 "" "RHEA:31199" "HMR_3150;FAOXC6C8m;MAR06329" "MAR03151" "R04745" "FAOXC8C6m" "R04745M" "r0730" "" "r0730;FAOXC8C6m" "MNXR100544" "HMR_3151" "RCR12651" "" 0 "" "RHEA:31195" "HMR_3151;FAOXC8C6m;MAR06329" "MAR03153" "R04747" "FAOXC8C6m" "R04747M" "r0732" "" "r0732;FAOXC8C6m" "MNXR109092" "HMR_3153" "RCR12652" "" 0 "RHEA:31205" "RHEA:31203" "HMR_3153;FAOXC8C6m;MAR06329" -"MAR03156" "R04751" "r1450" "" "" "R-HSA-77327" "HMR_3156;r1450" "MNXR109093" "HMR_3156" "RCR12653" "" 0 "" "RHEA:31207" "HMR_3156;r1450;MAR02372" -"MAR03157" "R04749" "" "R04749M" "r0734" "" "r0734" "MNXR97886" "HMR_3157" "RCR12654" "" 0 "" "RHEA:30547" "HMR_3157" -"MAR03158" "R04748" "" "R04748M" "r0733" "R-HSA-77323" "r0733" "MNXR100543" "HMR_3158" "RCR12655" "" 0 "" "RHEA:31143" "HMR_3158" -"MAR03160" "R01177" "" "R01177M" "r0287" "R-HSA-77321" "r0287" "MNXR95196" "HMR_3160" "RCR12656" "" 0 "" "RHEA:31111" "HMR_3160" +"MAR03156" "R04751" "r1450;FAOXC6C4m" "" "" "R-HSA-77327" "HMR_3156;r1450;FAOXC6C4m" "MNXR109093" "HMR_3156" "RCR12653" "" 0 "" "RHEA:31207" "HMR_3156;r1450;MAR02372;FAOXC6C4m;MAR06283" +"MAR03157" "R04749" "FAOXC6C4m" "R04749M" "r0734" "" "r0734;FAOXC6C4m" "MNXR97886" "HMR_3157" "RCR12654" "" 0 "" "RHEA:30547" "HMR_3157;FAOXC6C4m;MAR06283" +"MAR03158" "R04748" "FAOXC6C4m" "R04748M" "r0733" "R-HSA-77323" "r0733;FAOXC6C4m" "MNXR100543" "HMR_3158" "RCR12655" "" 0 "" "RHEA:31143" "HMR_3158;FAOXC6C4m;MAR06283" +"MAR03160" "R01177" "FAOXC6C4m" "R01177M" "r0287" "R-HSA-77321" "r0287;FAOXC6C4m" "MNXR95196" "HMR_3160" "RCR12656" "" 0 "" "RHEA:31111" "HMR_3160;FAOXC6C4m;MAR03160" "MAR03398" "" "HMR_3398" "" "" "" "HMR_3398" "" "HMR_3398" "RCR12657" "" 0 "" "" "HMR_3398" "MAR03406" "" "HMR_3406" "" "" "" "HMR_3406" "" "HMR_3406" "RCR12658" "" 0 "" "" "HMR_3406" "MAR03407" "" "" "" "" "" "HMR_3407" "" "HMR_3407" "RCR12659" "" 0 "" "" "HMR_3407" @@ -9357,7 +9357,6 @@ rxns rxnKEGGID rxnBiGGID rxnEHMNID rxnHepatoNET1ID rxnREACTOMEID rxnRecon3DID rx "MAR06280" "" "FAOXC61C4x" "" "" "" "FAOXC61C4x" "" "" "" "" 0 "" "" "FAOXC61C4x" "MAR06281" "" "FAOXC61m" "" "" "" "FAOXC61m" "" "" "" "" 0 "" "" "FAOXC61m" "MAR06282" "" "FAOXC61x" "" "" "" "FAOXC61x" "" "" "" "" 0 "" "" "FAOXC61x" -"MAR06283" "" "FAOXC6C4m" "" "" "" "FAOXC6C4m" "" "" "" "" 0 "" "" "FAOXC6C4m" "MAR06284" "" "FAOXC6C4x" "" "" "" "FAOXC6C4x" "" "" "" "" 0 "" "" "FAOXC6C4x" "MAR06285" "" "FAOXC6DCC4DCx" "" "" "" "FAOXC6DCC4DCx" "" "" "" "" 0 "" "" "FAOXC6DCC4DCx" "MAR06319" "" "FAOXC7C5m" "" "" "" "FAOXC7C5m" "" "" "" "" 0 "" "" "FAOXC7C5m" From b281b49d10525e0dfdcf53ddb5af47ea41e414bc Mon Sep 17 00:00:00 2001 From: Devlin-Moyer Date: Fri, 8 Dec 2023 09:24:16 -0500 Subject: [PATCH 3/6] fix: remove MAR06279 for being redundant with MAR03157 + MAR03158 + MAR03160 --- .../deprecatedReactions.tsv | 1 + model/Human-GEM.yml | 22 ------------------- model/reactions.tsv | 7 +++--- 3 files changed, 4 insertions(+), 26 deletions(-) diff --git a/data/deprecatedIdentifiers/deprecatedReactions.tsv b/data/deprecatedIdentifiers/deprecatedReactions.tsv index c62b1d75..08900b8f 100644 --- a/data/deprecatedIdentifiers/deprecatedReactions.tsv +++ b/data/deprecatedIdentifiers/deprecatedReactions.tsv @@ -264,3 +264,4 @@ rxns rxnKEGGID rxnBiGGID rxnEHMNID rxnHepatoNET1ID rxnREACTOMEID rxnRecon3DID rx "MAR06391" "" "" "" "r2520" "" "r2520" "MNXR106328" "HMR_6391" "RCR20063" "" 0 "" "" "HMR_6391" "MAR06329" "" "FAOXC8C6m" "" "" "" "FAOXC8C6m" "" "" "" "" 0 "" "" "FAOXC8C6m" "MAR06283" "" "FAOXC6C4m" "" "" "" "FAOXC6C4m" "" "" "" "" 0 "" "" "FAOXC6C4m" +"MAR06279" "" "FAOXC61C4m" "" "" "" "FAOXC61C4m" "" "" "" "" 0 "" "" "FAOXC61C4m" diff --git a/model/Human-GEM.yml b/model/Human-GEM.yml index d5910666..152e6955 100644 --- a/model/Human-GEM.yml +++ b/model/Human-GEM.yml @@ -241812,28 +241812,6 @@ - subsystem: - "Fatty acid oxidation" - confidence_score: 0 - - !!omap - - id: "MAR06279" - - name: "Fatty Acid Beta Oxidation (C6:1->C4:0), Mitochondrial" - - metabolites: !!omap - - MAM00053m: -1 - - MAM01261m: 1 - - MAM01412m: 1 - - MAM01597m: -1 - - MAM02039m: 1 - - MAM02040m: -1 - - MAM02552m: -1 - - MAM02553m: 1 - - lower_bound: 0 - - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000127884 and ENSG00000138796 and ENSG00000167315" - - rxnNotes: "" - - rxnFrom: "Recon3D" - - eccodes: "" - - references: "PMID:20195903;PMID:20490924;PMID:17143551" - - subsystem: - - "Fatty acid oxidation" - - confidence_score: 0 - !!omap - id: "MAR06280" - name: "Fatty Acid Beta Oxidation (C6:1->C4:0), Peroxisomal" diff --git a/model/reactions.tsv b/model/reactions.tsv index fd185ee9..86f49446 100644 --- a/model/reactions.tsv +++ b/model/reactions.tsv @@ -2654,9 +2654,9 @@ rxns rxnKEGGID rxnBiGGID rxnEHMNID rxnHepatoNET1ID rxnREACTOMEID rxnRecon3DID rx "MAR03151" "R04745" "FAOXC8C6m" "R04745M" "r0730" "" "r0730;FAOXC8C6m" "MNXR100544" "HMR_3151" "RCR12651" "" 0 "" "RHEA:31195" "HMR_3151;FAOXC8C6m;MAR06329" "MAR03153" "R04747" "FAOXC8C6m" "R04747M" "r0732" "" "r0732;FAOXC8C6m" "MNXR109092" "HMR_3153" "RCR12652" "" 0 "RHEA:31205" "RHEA:31203" "HMR_3153;FAOXC8C6m;MAR06329" "MAR03156" "R04751" "r1450;FAOXC6C4m" "" "" "R-HSA-77327" "HMR_3156;r1450;FAOXC6C4m" "MNXR109093" "HMR_3156" "RCR12653" "" 0 "" "RHEA:31207" "HMR_3156;r1450;MAR02372;FAOXC6C4m;MAR06283" -"MAR03157" "R04749" "FAOXC6C4m" "R04749M" "r0734" "" "r0734;FAOXC6C4m" "MNXR97886" "HMR_3157" "RCR12654" "" 0 "" "RHEA:30547" "HMR_3157;FAOXC6C4m;MAR06283" -"MAR03158" "R04748" "FAOXC6C4m" "R04748M" "r0733" "R-HSA-77323" "r0733;FAOXC6C4m" "MNXR100543" "HMR_3158" "RCR12655" "" 0 "" "RHEA:31143" "HMR_3158;FAOXC6C4m;MAR06283" -"MAR03160" "R01177" "FAOXC6C4m" "R01177M" "r0287" "R-HSA-77321" "r0287;FAOXC6C4m" "MNXR95196" "HMR_3160" "RCR12656" "" 0 "" "RHEA:31111" "HMR_3160;FAOXC6C4m;MAR03160" +"MAR03157" "R04749" "FAOXC6C4m;FAOXC61C4m" "R04749M" "r0734" "" "r0734;FAOXC6C4m;FAOXC61C4m" "MNXR97886" "HMR_3157" "RCR12654" "" 0 "" "RHEA:30547" "HMR_3157;FAOXC6C4m;MAR06283;FAOXC61C4m;MAR06279" +"MAR03158" "R04748" "FAOXC6C4m;FAOXC61C4m" "R04748M" "r0733" "R-HSA-77323" "r0733;FAOXC6C4m;FAOXC61C4m" "MNXR100543" "HMR_3158" "RCR12655" "" 0 "" "RHEA:31143" "HMR_3158;FAOXC6C4m;MAR06283;FAOXC61C4m;MAR06279" +"MAR03160" "R01177" "FAOXC6C4m;FAOXC61C4m" "R01177M" "r0287" "R-HSA-77321" "r0287;FAOXC6C4m;FAOXC61C4m" "MNXR95196" "HMR_3160" "RCR12656" "" 0 "" "RHEA:31111" "HMR_3160;FAOXC6C4m;MAR03160;FAOXC61C4m;MAR06279" "MAR03398" "" "HMR_3398" "" "" "" "HMR_3398" "" "HMR_3398" "RCR12657" "" 0 "" "" "HMR_3398" "MAR03406" "" "HMR_3406" "" "" "" "HMR_3406" "" "HMR_3406" "RCR12658" "" 0 "" "" "HMR_3406" "MAR03407" "" "" "" "" "" "HMR_3407" "" "HMR_3407" "RCR12659" "" 0 "" "" "HMR_3407" @@ -9353,7 +9353,6 @@ rxns rxnKEGGID rxnBiGGID rxnEHMNID rxnHepatoNET1ID rxnREACTOMEID rxnRecon3DID rx "MAR05991" "" "FAOXC5C5DCc" "" "" "" "FAOXC5C5DCc" "" "" "" "" 0 "" "" "FAOXC5C5DCc" "MAR05999" "" "FAOXC5C5OHm" "" "" "" "FAOXC5C5OHm" "" "" "" "" 0 "RHEA:31081" "RHEA:31079" "FAOXC5C5OHm" "MAR06278" "" "FAOXC5OHc" "" "" "" "FAOXC5OHc" "" "" "" "" 0 "" "" "FAOXC5OHc" -"MAR06279" "" "FAOXC61C4m" "" "" "" "FAOXC61C4m" "" "" "" "" 0 "" "" "FAOXC61C4m" "MAR06280" "" "FAOXC61C4x" "" "" "" "FAOXC61C4x" "" "" "" "" 0 "" "" "FAOXC61C4x" "MAR06281" "" "FAOXC61m" "" "" "" "FAOXC61m" "" "" "" "" 0 "" "" "FAOXC61m" "MAR06282" "" "FAOXC61x" "" "" "" "FAOXC61x" "" "" "" "" 0 "" "" "FAOXC61x" From df8c0721fcf1a5b5205d4f9ab6b4cf29bd0b11d6 Mon Sep 17 00:00:00 2001 From: Devlin-Moyer Date: Fri, 8 Dec 2023 09:29:26 -0500 Subject: [PATCH 4/6] fix: remove MAR05449 for being redundant with MAR03163 + MAR03164 + MAR03166 + MAR03885 --- .../deprecatedReactions.tsv | 1 + model/Human-GEM.yml | 23 ------------------- model/reactions.tsv | 9 ++++---- 3 files changed, 5 insertions(+), 28 deletions(-) diff --git a/data/deprecatedIdentifiers/deprecatedReactions.tsv b/data/deprecatedIdentifiers/deprecatedReactions.tsv index 08900b8f..f7610e91 100644 --- a/data/deprecatedIdentifiers/deprecatedReactions.tsv +++ b/data/deprecatedIdentifiers/deprecatedReactions.tsv @@ -265,3 +265,4 @@ rxns rxnKEGGID rxnBiGGID rxnEHMNID rxnHepatoNET1ID rxnREACTOMEID rxnRecon3DID rx "MAR06329" "" "FAOXC8C6m" "" "" "" "FAOXC8C6m" "" "" "" "" 0 "" "" "FAOXC8C6m" "MAR06283" "" "FAOXC6C4m" "" "" "" "FAOXC6C4m" "" "" "" "" 0 "" "" "FAOXC6C4m" "MAR06279" "" "FAOXC61C4m" "" "" "" "FAOXC61C4m" "" "" "" "" 0 "" "" "FAOXC61C4m" +"MAR05449" "" "FAOXC4020m" "" "" "" "FAOXC4C2m" "MNXR99368" "" "" "" 0 "" "" "FAOXC4C2m" diff --git a/model/Human-GEM.yml b/model/Human-GEM.yml index 152e6955..df1c6b03 100644 --- a/model/Human-GEM.yml +++ b/model/Human-GEM.yml @@ -241693,29 +241693,6 @@ - subsystem: - "Fatty acid oxidation" - confidence_score: 0 - - !!omap - - id: "MAR05449" - - name: "Fatty Acid Beta Oxidation (C4->C2), Mitochondrial" - - metabolites: !!omap - - MAM01261m: 2 - - MAM01412m: -1 - - MAM01597m: -1 - - MAM01802m: -1 - - MAM01803m: 1 - - MAM02039m: 1 - - MAM02040m: -1 - - MAM02552m: -1 - - MAM02553m: 1 - - lower_bound: 0 - - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000122971 and ENSG00000127884 and ENSG00000138796 and ENSG00000167315" - - rxnNotes: "" - - rxnFrom: "Recon3D" - - eccodes: "" - - references: "PMID:20195903;PMID:20490924;PMID:17143551" - - subsystem: - - "Fatty acid oxidation" - - confidence_score: 0 - !!omap - id: "MAR05456" - name: "Succ->C4Dcc" diff --git a/model/reactions.tsv b/model/reactions.tsv index 86f49446..48e866d4 100644 --- a/model/reactions.tsv +++ b/model/reactions.tsv @@ -178,7 +178,7 @@ rxns rxnKEGGID rxnBiGGID rxnEHMNID rxnHepatoNET1ID rxnREACTOMEID rxnRecon3DID rx "MAR00719" "R08198" "" "" "" "" "HMR_0719" "MNXR111769" "HMR_0719" "RCR11097" "" 0 "" "RHEA:13449" "HMR_0719" "MAR01434" "R00238" "ACACT1r" "R00238M" "r0069" "" "ACACT1r" "MNXR95194" "HMR_1434" "RCR10465" "" 0 "RHEA:21039" "RHEA:21036" "HMR_1434" "MAR01436" "R01357" "AACOAT" "R01357M" "r0320" "" "AACOAT" "MNXR95136" "HMR_1436" "RCR10466" "" 0 "RHEA:16118" "RHEA:16117" "HMR_1436" -"MAR03163" "R01175" "ACOAD1fm" "" "" "R-HSA-77319" "ACOAD1fm" "MNXR95302" "HMR_3163" "RCR11098" "" 0 "" "RHEA:24004" "HMR_3163" +"MAR03163" "R01175" "ACOAD1fm;FAOXC4020m" "" "" "R-HSA-77319" "ACOAD1fm;FAOXC4C2m" "MNXR95302" "HMR_3163" "RCR11098" "" 0 "" "RHEA:24004" "HMR_3163;FAOXC4C2m;MAR05449" "MAR04461" "R01361" "BDHm" "R01361C" "r0323" "" "BDHm" "MNXR96232" "HMR_4461" "RCR10467" "" 0 "RHEA:20524" "RHEA:20521" "HMR_4461" "MAR04604" "R01978" "" "R01978C" "r0463" "" "r0463" "MNXR100660;MNXR107257" "HMR_4604" "RCR11099" "" 0 "" "RHEA:10188" "HMR_4604" "MAR05351" "R01000" "" "" "" "" "2HBO" "MNXR94796" "HMR_5351" "RCR10152" "" 0 "" "RHEA:36371" "HMR_5351" @@ -740,9 +740,9 @@ rxns rxnKEGGID rxnBiGGID rxnEHMNID rxnHepatoNET1ID rxnREACTOMEID rxnRecon3DID rx "MAR08026" "" "LYSMTF2n" "" "" "" "LYSMTF2n" "MNXR101260" "HMR_8026" "RCR11349" "" 0 "" "" "HMR_8026" "MAR08027" "R04867" "LYSMTF3n" "" "" "" "LYSMTF3n" "MNXR101261" "HMR_8027" "RCR11350" "" 0 "" "RHEA:54200" "HMR_8027" "MAR08029" "" "PLYSPSer" "" "" "" "PLYSPSer" "MNXR103039" "HMR_8029" "RCR14338" "" 0 "" "" "HMR_8029" -"MAR03164" "R03026" "ECOAH1m" "R03026M" "r0588" "" "ECOAH1m" "MNXR97883" "HMR_3164" "RCR11351" "" 0 "" "RHEA:26558" "HMR_3164" -"MAR03166" "R01975" "HACD1m" "R01975M" "r0460" "" "HACD1m" "MNXR100541" "HMR_3166" "RCR11352" "" 0 "" "RHEA:30799" "HMR_3166" -"MAR03885" "R00238" "ACACT1m" "R00238M" "r0070" "" "ACACT1rm" "MNXR95194" "HMR_3885" "RCR10247" "" 0 "RHEA:21039" "RHEA:21036" "HMR_3885" +"MAR03164" "R03026" "ECOAH1m;FAOXC4020m" "R03026M" "r0588" "" "ECOAH1m;FAOXC4C2m" "MNXR97883" "HMR_3164" "RCR11351" "" 0 "" "RHEA:26558" "HMR_3164;FAOXC4C2m;MAR05449" +"MAR03166" "R01975" "HACD1m;FAOXC4020m" "R01975M" "r0460" "" "HACD1m;FAOXC4C2m" "MNXR100541" "HMR_3166" "RCR11352" "" 0 "" "RHEA:30799" "HMR_3166;FAOXC4C2m;MAR05449" +"MAR03885" "R00238" "ACACT1m;FAOXC4020m" "R00238M" "r0070" "" "ACACT1rm;FAOXC4C2m" "MNXR95194" "HMR_3885" "RCR10247" "" 0 "RHEA:21039" "RHEA:21036" "HMR_3885;FAOXC4C2m;MAR05449" "MAR04250" "R04293" "QUILSYN" "" "r0675" "" "QUILSYN" "MNXR103396" "HMR_4250" "RCR11353" "" 1 "" "RHEA:25147" "HMR_4250" "MAR08091" "" "3HXKYNDCL" "" "" "" "3HXKYNDCL" "MNXR94906" "HMR_8091" "RCR11354" "" 0 "" "" "HMR_8091" "MAR08092" "R04907" "3HXKYNOXDA" "" "" "" "3HXKYNOXDA" "MNXR94907" "HMR_8092" "RCR11355" "" 0 "" "" "HMR_8092" @@ -9347,7 +9347,6 @@ rxns rxnKEGGID rxnBiGGID rxnEHMNID rxnHepatoNET1ID rxnREACTOMEID rxnRecon3DID rx "MAR05427" "" "FAOXC22OHC22r" "" "" "" "FAOXC22OHC22r" "" "" "" "" 0 "" "" "FAOXC22OHC22r" "MAR05428" "" "FAOXC241C221x" "" "" "" "FAOXC241C221x" "" "" "" "" 0 "" "" "FAOXC241C221x" "MAR05431" "" "FAOXC24C22x" "" "" "" "FAOXC24C22x" "" "" "" "" 0 "" "" "FAOXC24C22x" -"MAR05449" "" "FAOXC4020m" "" "" "" "FAOXC4C2m" "MNXR99368" "" "" "" 0 "" "" "FAOXC4C2m" "MAR05456" "" "FAOXC4C4DCc" "" "" "" "FAOXC4C4DCc" "" "" "" "" 0 "" "" "FAOXC4C4DCc" "MAR05988" "" "FAOXC5C3x" "" "" "" "FAOXC5C3x" "" "" "" "" 0 "" "" "FAOXC5C3x" "MAR05991" "" "FAOXC5C5DCc" "" "" "" "FAOXC5C5DCc" "" "" "" "" 0 "" "" "FAOXC5C5DCc" From 08aa570a3ebf13cf2422bf27cd8d8b9c2aa4d54f Mon Sep 17 00:00:00 2001 From: Devlin-Moyer Date: Fri, 8 Dec 2023 09:37:49 -0500 Subject: [PATCH 5/6] fix: remove MAR01009 for being redundant with MAR03885 and MAR03149,50,51,53,56,57,58,60,63,64,66 --- .../deprecatedReactions.tsv | 1 + model/Human-GEM.yml | 23 ----------------- model/reactions.tsv | 25 +++++++++---------- 3 files changed, 13 insertions(+), 36 deletions(-) diff --git a/data/deprecatedIdentifiers/deprecatedReactions.tsv b/data/deprecatedIdentifiers/deprecatedReactions.tsv index f7610e91..7a07508c 100644 --- a/data/deprecatedIdentifiers/deprecatedReactions.tsv +++ b/data/deprecatedIdentifiers/deprecatedReactions.tsv @@ -266,3 +266,4 @@ rxns rxnKEGGID rxnBiGGID rxnEHMNID rxnHepatoNET1ID rxnREACTOMEID rxnRecon3DID rx "MAR06283" "" "FAOXC6C4m" "" "" "" "FAOXC6C4m" "" "" "" "" 0 "" "" "FAOXC6C4m" "MAR06279" "" "FAOXC61C4m" "" "" "" "FAOXC61C4m" "" "" "" "" 0 "" "" "FAOXC61C4m" "MAR05449" "" "FAOXC4020m" "" "" "" "FAOXC4C2m" "MNXR99368" "" "" "" 0 "" "" "FAOXC4C2m" +"MAR01009" "" "FAOXC80" "" "" "" "FAOXC80" "MNXR99373" "" "" "" 0 "" "" "FAOXC80" diff --git a/model/Human-GEM.yml b/model/Human-GEM.yml index df1c6b03..3ffcbca4 100644 --- a/model/Human-GEM.yml +++ b/model/Human-GEM.yml @@ -222432,29 +222432,6 @@ - subsystem: - "Fatty acid oxidation" - confidence_score: 0 - - !!omap - - id: "MAR01009" - - name: "Beta Oxidation of Med/Long Chain Fatty Acid" - - metabolites: !!omap - - MAM01261m: 4 - - MAM01597m: -3 - - MAM01802m: -3 - - MAM01803m: 3 - - MAM02039m: 3 - - MAM02040m: -3 - - MAM02552m: -3 - - MAM02553m: 3 - - MAM02644m: -1 - - lower_bound: 0 - - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000117054 or ENSG00000122971" - - rxnNotes: "" - - rxnFrom: "Recon3D" - - eccodes: "1.3.99.3" - - references: "PMID:2565344;PMID:3035565" - - subsystem: - - "Fatty acid oxidation" - - confidence_score: 0 - !!omap - id: "MAR01012" - name: "Fatty Acyl Coenzyme A Synthase (N-C10:0CoA)" diff --git a/model/reactions.tsv b/model/reactions.tsv index 48e866d4..b4084e75 100644 --- a/model/reactions.tsv +++ b/model/reactions.tsv @@ -178,7 +178,7 @@ rxns rxnKEGGID rxnBiGGID rxnEHMNID rxnHepatoNET1ID rxnREACTOMEID rxnRecon3DID rx "MAR00719" "R08198" "" "" "" "" "HMR_0719" "MNXR111769" "HMR_0719" "RCR11097" "" 0 "" "RHEA:13449" "HMR_0719" "MAR01434" "R00238" "ACACT1r" "R00238M" "r0069" "" "ACACT1r" "MNXR95194" "HMR_1434" "RCR10465" "" 0 "RHEA:21039" "RHEA:21036" "HMR_1434" "MAR01436" "R01357" "AACOAT" "R01357M" "r0320" "" "AACOAT" "MNXR95136" "HMR_1436" "RCR10466" "" 0 "RHEA:16118" "RHEA:16117" "HMR_1436" -"MAR03163" "R01175" "ACOAD1fm;FAOXC4020m" "" "" "R-HSA-77319" "ACOAD1fm;FAOXC4C2m" "MNXR95302" "HMR_3163" "RCR11098" "" 0 "" "RHEA:24004" "HMR_3163;FAOXC4C2m;MAR05449" +"MAR03163" "R01175" "ACOAD1fm;FAOXC4020m;FAOXC80" "" "" "R-HSA-77319" "ACOAD1fm;FAOXC4C2m;FAOXC80" "MNXR95302" "HMR_3163" "RCR11098" "" 0 "" "RHEA:24004" "HMR_3163;FAOXC4C2m;MAR05449;FAOXC80;MAR01009" "MAR04461" "R01361" "BDHm" "R01361C" "r0323" "" "BDHm" "MNXR96232" "HMR_4461" "RCR10467" "" 0 "RHEA:20524" "RHEA:20521" "HMR_4461" "MAR04604" "R01978" "" "R01978C" "r0463" "" "r0463" "MNXR100660;MNXR107257" "HMR_4604" "RCR11099" "" 0 "" "RHEA:10188" "HMR_4604" "MAR05351" "R01000" "" "" "" "" "2HBO" "MNXR94796" "HMR_5351" "RCR10152" "" 0 "" "RHEA:36371" "HMR_5351" @@ -740,9 +740,9 @@ rxns rxnKEGGID rxnBiGGID rxnEHMNID rxnHepatoNET1ID rxnREACTOMEID rxnRecon3DID rx "MAR08026" "" "LYSMTF2n" "" "" "" "LYSMTF2n" "MNXR101260" "HMR_8026" "RCR11349" "" 0 "" "" "HMR_8026" "MAR08027" "R04867" "LYSMTF3n" "" "" "" "LYSMTF3n" "MNXR101261" "HMR_8027" "RCR11350" "" 0 "" "RHEA:54200" "HMR_8027" "MAR08029" "" "PLYSPSer" "" "" "" "PLYSPSer" "MNXR103039" "HMR_8029" "RCR14338" "" 0 "" "" "HMR_8029" -"MAR03164" "R03026" "ECOAH1m;FAOXC4020m" "R03026M" "r0588" "" "ECOAH1m;FAOXC4C2m" "MNXR97883" "HMR_3164" "RCR11351" "" 0 "" "RHEA:26558" "HMR_3164;FAOXC4C2m;MAR05449" -"MAR03166" "R01975" "HACD1m;FAOXC4020m" "R01975M" "r0460" "" "HACD1m;FAOXC4C2m" "MNXR100541" "HMR_3166" "RCR11352" "" 0 "" "RHEA:30799" "HMR_3166;FAOXC4C2m;MAR05449" -"MAR03885" "R00238" "ACACT1m;FAOXC4020m" "R00238M" "r0070" "" "ACACT1rm;FAOXC4C2m" "MNXR95194" "HMR_3885" "RCR10247" "" 0 "RHEA:21039" "RHEA:21036" "HMR_3885;FAOXC4C2m;MAR05449" +"MAR03164" "R03026" "ECOAH1m;FAOXC4020m;FAOXC80" "R03026M" "r0588" "" "ECOAH1m;FAOXC4C2m;FAOXC80" "MNXR97883" "HMR_3164" "RCR11351" "" 0 "" "RHEA:26558" "HMR_3164;FAOXC4C2m;MAR05449;FAOXC80;MAR01009" +"MAR03166" "R01975" "HACD1m;FAOXC4020m;FAOXC80" "R01975M" "r0460" "" "HACD1m;FAOXC4C2m;FAOXC80" "MNXR100541" "HMR_3166" "RCR11352" "" 0 "" "RHEA:30799" "HMR_3166;FAOXC4C2m;MAR05449;FAOXC80;MAR01009" +"MAR03885" "R00238" "ACACT1m;FAOXC4020m;FAOXC80" "R00238M" "r0070" "" "ACACT1rm;FAOXC4C2m;FAOXC80" "MNXR95194" "HMR_3885" "RCR10247" "" 0 "RHEA:21039" "RHEA:21036" "HMR_3885;FAOXC4C2m;MAR05449;FAOXC80;MAR01009" "MAR04250" "R04293" "QUILSYN" "" "r0675" "" "QUILSYN" "MNXR103396" "HMR_4250" "RCR11353" "" 1 "" "RHEA:25147" "HMR_4250" "MAR08091" "" "3HXKYNDCL" "" "" "" "3HXKYNDCL" "MNXR94906" "HMR_8091" "RCR11354" "" 0 "" "" "HMR_8091" "MAR08092" "R04907" "3HXKYNOXDA" "" "" "" "3HXKYNOXDA" "MNXR94907" "HMR_8092" "RCR11355" "" 0 "" "" "HMR_8092" @@ -2649,14 +2649,14 @@ rxns rxnKEGGID rxnBiGGID rxnEHMNID rxnHepatoNET1ID rxnREACTOMEID rxnRecon3DID rx "MAR03143" "R04744" "" "R04744X" "r0728" "" "r0728" "MNXR97889" "HMR_3143" "RCR12646" "" 0 "" "RHEA:31191" "HMR_3143" "MAR03144" "R04743" "" "R04743X" "r0726" "" "r0726" "MNXR100545" "HMR_3144" "RCR12647" "" 0 "" "RHEA:31187" "HMR_3144" "MAR03146" "R03778" "" "R03778X" "r0634" "" "r0634" "MNXR95198" "HMR_3146" "RCR12648" "" 0 "RHEA:31089" "RHEA:31087" "HMR_3146" -"MAR03149" "R03777" "r1448;FAOXC8C6m" "" "" "R-HSA-77338" "HMR_3149;r1448i;FAOXC6C8m" "MNXR95304" "HMR_3149" "RCR12649" "" 0 "" "RHEA:30943" "HMR_3149;r1448;MAR02369;FAOXC8C6m;MAR06329" -"MAR03150" "R04746" "FAOXC8C6m" "R04746M" "r0731" "" "r0731;FAOXC8C6m" "MNXR97888" "HMR_3150" "RCR12650" "" 0 "" "RHEA:31199" "HMR_3150;FAOXC6C8m;MAR06329" -"MAR03151" "R04745" "FAOXC8C6m" "R04745M" "r0730" "" "r0730;FAOXC8C6m" "MNXR100544" "HMR_3151" "RCR12651" "" 0 "" "RHEA:31195" "HMR_3151;FAOXC8C6m;MAR06329" -"MAR03153" "R04747" "FAOXC8C6m" "R04747M" "r0732" "" "r0732;FAOXC8C6m" "MNXR109092" "HMR_3153" "RCR12652" "" 0 "RHEA:31205" "RHEA:31203" "HMR_3153;FAOXC8C6m;MAR06329" -"MAR03156" "R04751" "r1450;FAOXC6C4m" "" "" "R-HSA-77327" "HMR_3156;r1450;FAOXC6C4m" "MNXR109093" "HMR_3156" "RCR12653" "" 0 "" "RHEA:31207" "HMR_3156;r1450;MAR02372;FAOXC6C4m;MAR06283" -"MAR03157" "R04749" "FAOXC6C4m;FAOXC61C4m" "R04749M" "r0734" "" "r0734;FAOXC6C4m;FAOXC61C4m" "MNXR97886" "HMR_3157" "RCR12654" "" 0 "" "RHEA:30547" "HMR_3157;FAOXC6C4m;MAR06283;FAOXC61C4m;MAR06279" -"MAR03158" "R04748" "FAOXC6C4m;FAOXC61C4m" "R04748M" "r0733" "R-HSA-77323" "r0733;FAOXC6C4m;FAOXC61C4m" "MNXR100543" "HMR_3158" "RCR12655" "" 0 "" "RHEA:31143" "HMR_3158;FAOXC6C4m;MAR06283;FAOXC61C4m;MAR06279" -"MAR03160" "R01177" "FAOXC6C4m;FAOXC61C4m" "R01177M" "r0287" "R-HSA-77321" "r0287;FAOXC6C4m;FAOXC61C4m" "MNXR95196" "HMR_3160" "RCR12656" "" 0 "" "RHEA:31111" "HMR_3160;FAOXC6C4m;MAR03160;FAOXC61C4m;MAR06279" +"MAR03149" "R03777" "r1448;FAOXC8C6m;FAOXC80" "" "" "R-HSA-77338" "HMR_3149;r1448i;FAOXC6C8m;FAOXC80" "MNXR95304" "HMR_3149" "RCR12649" "" 0 "" "RHEA:30943" "HMR_3149;r1448;MAR02369;FAOXC8C6m;MAR06329;FAOXC80;MAR01009" +"MAR03150" "R04746" "FAOXC8C6m;FAOXC80" "R04746M" "r0731" "" "r0731;FAOXC8C6m;FAOXC80" "MNXR97888" "HMR_3150" "RCR12650" "" 0 "" "RHEA:31199" "HMR_3150;FAOXC6C8m;MAR06329;FAOXC80;MAR01009" +"MAR03151" "R04745" "FAOXC8C6m;FAOXC80" "R04745M" "r0730" "" "r0730;FAOXC8C6m;FAOXC80" "MNXR100544" "HMR_3151" "RCR12651" "" 0 "" "RHEA:31195" "HMR_3151;FAOXC8C6m;MAR06329;FAOXC80;MAR01009" +"MAR03153" "R04747" "FAOXC8C6m;FAOXC80" "R04747M" "r0732" "" "r0732;FAOXC8C6m;FAOXC80" "MNXR109092" "HMR_3153" "RCR12652" "" 0 "RHEA:31205" "RHEA:31203" "HMR_3153;FAOXC8C6m;MAR06329;FAOXC80;MAR01009" +"MAR03156" "R04751" "r1450;FAOXC6C4m;FAOXC80" "" "" "R-HSA-77327" "HMR_3156;r1450;FAOXC6C4m;FAOXC80" "MNXR109093" "HMR_3156" "RCR12653" "" 0 "" "RHEA:31207" "HMR_3156;r1450;MAR02372;FAOXC6C4m;MAR06283;FAOXC80;MAR01009" +"MAR03157" "R04749" "FAOXC6C4m;FAOXC61C4m;FAOXC80" "R04749M" "r0734" "" "r0734;FAOXC6C4m;FAOXC61C4m;FAOXC80" "MNXR97886" "HMR_3157" "RCR12654" "" 0 "" "RHEA:30547" "HMR_3157;FAOXC6C4m;MAR06283;FAOXC61C4m;MAR06279;FAOXC80;MAR01009" +"MAR03158" "R04748" "FAOXC6C4m;FAOXC61C4m;FAOXC80" "R04748M" "r0733" "R-HSA-77323" "r0733;FAOXC6C4m;FAOXC61C4m;FAOXC80" "MNXR100543" "HMR_3158" "RCR12655" "" 0 "" "RHEA:31143" "HMR_3158;FAOXC6C4m;MAR06283;FAOXC61C4m;MAR06279;FAOXC80;MAR01009" +"MAR03160" "R01177" "FAOXC6C4m;FAOXC61C4m;FAOXC80" "R01177M" "r0287" "R-HSA-77321" "r0287;FAOXC6C4m;FAOXC61C4m;FAOXC80" "MNXR95196" "HMR_3160" "RCR12656" "" 0 "" "RHEA:31111" "HMR_3160;FAOXC6C4m;MAR03160;FAOXC61C4m;MAR06279;FAOXC80;MAR01009" "MAR03398" "" "HMR_3398" "" "" "" "HMR_3398" "" "HMR_3398" "RCR12657" "" 0 "" "" "HMR_3398" "MAR03406" "" "HMR_3406" "" "" "" "HMR_3406" "" "HMR_3406" "RCR12658" "" 0 "" "" "HMR_3406" "MAR03407" "" "" "" "" "" "HMR_3407" "" "HMR_3407" "RCR12659" "" 0 "" "" "HMR_3407" @@ -8291,7 +8291,6 @@ rxns rxnKEGGID rxnBiGGID rxnEHMNID rxnHepatoNET1ID rxnREACTOMEID rxnRecon3DID rx "MAR00982" "" "FAOXC2452256x" "" "" "" "FAOXC2452256x" "MNXR99365" "" "" "" 0 "" "" "FAOXC2452256x" "MAR01001" "" "FAOXC246226x" "" "" "" "FAOXC246226x" "MNXR99366" "" "" "" 0 "" "" "FAOXC246226x" "MAR01005" "" "FAOXC260240x" "" "" "" "FAOXC260240x" "MNXR99367" "" "" "" 0 "" "" "FAOXC260240x" -"MAR01009" "" "FAOXC80" "" "" "" "FAOXC80" "MNXR99373" "" "" "" 0 "" "" "FAOXC80" "MAR01012" "" "FAS100COA" "" "" "" "FAS100COA" "MNXR99385" "" "" "" 0 "" "" "FAS100COA" "MAR01019" "" "FAS120COA" "" "" "" "FAS120COA" "MNXR99389" "" "" "" 0 "" "" "FAS120COA" "MAR01024" "" "FAS140COA" "" "" "" "FAS140COA" "MNXR99393" "" "" "" 0 "" "" "FAS140COA" From 702fa11764a34804738dda243def3e3208abbed6 Mon Sep 17 00:00:00 2001 From: Hao Wang Date: Fri, 22 Dec 2023 13:05:17 +0100 Subject: [PATCH 6/6] doc: update rxnRetired column for MAR03160 --- model/reactions.tsv | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/model/reactions.tsv b/model/reactions.tsv index 2534439f..36b7eb40 100644 --- a/model/reactions.tsv +++ b/model/reactions.tsv @@ -2654,7 +2654,7 @@ rxns rxnKEGGID rxnBiGGID rxnEHMNID rxnHepatoNET1ID rxnREACTOMEID rxnRecon3DID rx "MAR03156" "R04751" "r1450;FAOXC6C4m;FAOXC80" "" "" "R-HSA-77327" "HMR_3156;r1450;FAOXC6C4m;FAOXC80;HMR_3422" "MNXR109093" "HMR_3156;HMR_3422" "RCR12653;RCR12667" "" 0 "" "RHEA:31207" "HMR_3156;r1450;MAR02372;FAOXC6C4m;MAR06283;FAOXC80;MAR01009;HMR_3422;MAR03422" "MAR03157" "R04749" "FAOXC6C4m;FAOXC61C4m;FAOXC80;HMR_3426" "R04749M" "r0734" "" "r0734;FAOXC6C4m;FAOXC61C4m;FAOXC80;HMR_3422;HMR_3426" "MNXR97886" "HMR_3157;HMR_3422;HMR_3426" "RCR12654;RCR12667;RCR12671" "" 0 "" "RHEA:30547" "HMR_3157;FAOXC6C4m;MAR06283;FAOXC61C4m;MAR06279;FAOXC80;MAR01009;HMR_3422;MAR03422;HMR_3426;MAR03426" "MAR03158" "R04748" "FAOXC6C4m;FAOXC61C4m;FAOXC80;HMR_3426" "R04748M" "r0733" "R-HSA-77323" "r0733;FAOXC6C4m;FAOXC61C4m;FAOXC80;HMR_3422;HMR_3426" "MNXR100543" "HMR_3158;HMR_3422;HMR_3426" "RCR12655;RCR12667;RCR12671" "" 0 "" "RHEA:31143" "HMR_3158;FAOXC6C4m;MAR06283;FAOXC61C4m;MAR06279;FAOXC80;MAR01009;HMR_3422;MAR03422;HMR_3426;MAR03426" -"MAR03160" "R01177" "FAOXC6C4m;FAOXC61C4m;FAOXC80;HMR_3426" "R01177M" "r0287" "R-HSA-77321" "r0287;FAOXC6C4m;FAOXC61C4m;FAOXC80;HMR_3422;HMR_3426" "MNXR95196" "HMR_3160;HMR_3422;HMR_3426" "RCR12656;RCR12667;RCR12671" "" 0 "" "RHEA:31111" "HMR_3160;FAOXC6C4m;MAR03160;FAOXC61C4m;MAR06279;FAOXC80;MAR01009;HMR_3422;MAR03422;HMR_3426;MAR03426" +"MAR03160" "R01177" "FAOXC6C4m;FAOXC61C4m;FAOXC80;HMR_3426" "R01177M" "r0287" "R-HSA-77321" "r0287;FAOXC6C4m;FAOXC61C4m;FAOXC80;HMR_3422;HMR_3426" "MNXR95196" "HMR_3160;HMR_3422;HMR_3426" "RCR12656;RCR12667;RCR12671" "" 0 "" "RHEA:31111" "HMR_3160;FAOXC6C4m;MAR06283;FAOXC61C4m;MAR06279;FAOXC80;MAR01009;HMR_3422;MAR03422;HMR_3426;MAR03426" "MAR03398" "" "HMR_3398" "" "" "" "HMR_3398" "" "HMR_3398" "RCR12657" "" 0 "" "" "HMR_3398" "MAR03406" "" "HMR_3406" "" "" "" "HMR_3406" "" "HMR_3406" "RCR12658" "" 0 "" "" "HMR_3406" "MAR03407" "" "" "" "" "" "HMR_3407" "" "HMR_3407" "RCR12659" "" 0 "" "" "HMR_3407"