From b6f9eb800ae83d0cd269c10ee3f1838a563ddb42 Mon Sep 17 00:00:00 2001 From: William Scott Date: Mon, 3 Sep 2018 11:53:32 -0700 Subject: [PATCH 1/6] fix-met.prop: correct metFormulas This updates the list of metabolites that previously had no formulas. ardicdavis and I found formulas for some metabolites and furthermore added metabolite ids, and sources. --- .../Missingmetaboliteformulas.tsv | 37 +++++++++++++++ .../modelCuration/updateMetaboliteFormula.m | 45 +++++++++++++++++++ 2 files changed, 82 insertions(+) create mode 100644 ComplementaryData/modelCuration/Missingmetaboliteformulas.tsv create mode 100644 ComplementaryScripts/modelCuration/updateMetaboliteFormula.m diff --git a/ComplementaryData/modelCuration/Missingmetaboliteformulas.tsv b/ComplementaryData/modelCuration/Missingmetaboliteformulas.tsv new file mode 100644 index 00000000..868c228c --- /dev/null +++ b/ComplementaryData/modelCuration/Missingmetaboliteformulas.tsv @@ -0,0 +1,37 @@ +Met ID Met Name Met Formula Source +s_0330[er]' 6-(alpha-D-glucosaminyl)-O-acyl-1-phosphatidyl-1D-myo-inositol [endoplasmic reticulum]' missing in source +s_0334[er]' 6-O-[alpha-D-mannosyl-(1->4)-alpha-D-glucosaminyl]-O-acyl-1-phosphatidyl-1D-myo-inositol [endoplasmic reticulum]' missing in source +s_0337[er]' 6-O-{2-O-[(2-aminoethyl)phosphoryl]-alpha-D-mannosyl-(1->4)-alpha-D-glucosaminyl}-O-acyl-1-phosphatidyl-1D-myo-inositol [endoplasmic reticulum]' missing in source +s_0338[er]' 6-O-{alpha-D-mannosyl-(1->2)-alpha-D-mannosyl-(1->6)-2-O-[(2-aminoethyl)phosphoryl]-alpha-D-mannosyl-(1->4)-alpha-D-glucosaminyl}-O-acyl-1-phosphatidyl-1D-myo-inositol [endoplasmic reticulum]' missing in source +s_0339[er]' 6-O-{alpha-D-mannosyl-(1->6)-2-O-[(2-aminoethyl)phosphoryl]-alpha-D-mannosyl-(1->4)-alpha-D-glucosaminyl}-O-acyl-1-phosphatidyl-1D-myo-inositol [endoplasmic reticulum]' missing in source +s_0450[c]' biomass [cytoplasm]' +s_0694[c]' fatty acid backbone [cytoplasm]' +s_0709[m]' ferricytochrome c [mitochondrion]' C42H44FeN8O8S2R4 https://www.genome.jp/dbget-bin/www_bget?cpd:C00125 +s_0710[m]' ferrocytochrome c [mitochondrion]' C42H44FeN8O8S2R4 https://www.genome.jp/dbget-bin/www_bget?cpd:C00126 +s_0773[c]' glycogen [cytoplasm]' C24H42O21 https://www.genome.jp/dbget-bin/www_bget?C00182 +s_0774[v]' glycogen [vacuole]' C24H42O21 https://www.genome.jp/dbget-bin/www_bget?C00182 +s_1096[c]' lipid [cytoplasm]' +s_1107[c]' mannan [cytoplasm]' C12H21O10(C12H20O11)n https://www.genome.jp/dbget-bin/www_bget?cpd:C04276 +s_1108[er]' mannan [endoplasmic reticulum]' C12H21O10(C12H20O11)n https://www.genome.jp/dbget-bin/www_bget?cpd:C04276 +s_1845[m]' ACP1 [mitochondrion]' +s_2775[m]' 3-hydroxybutanoyl-ACP [mitochondrion]' C4H7O2SR https://www.genome.jp/dbget-bin/www_bget?C04618 +s_2778[m]' trans-but-2-enoyl-ACP [mitochondrion]' C4H5OS https://www.ebi.ac.uk/chebi/searchId.do?chebiId=132146 +s_2779[m]' trans-hex-2-enoyl-ACP [mitochondrion]' C6H9OSR https://www.genome.jp/dbget-bin/www_bget?C05748 +s_2780[m]' trans-oct-2-enoyl-ACP [mitochondrion]' C8H13OSR https://www.genome.jp/dbget-bin/www_bget?C05751 +s_2812[erm]' trans-icos-2-enoyl-CoA [endoplasmic reticulum membrane]' C41H72N7O17P3S http://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:75061 +s_2889[p]' trans-icos-2-enoyl-CoA [peroxisome]' C41H72N7O17P3S http://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:75061 +s_2896[p]' "trans-2,cis-5-dodecadienoyl-CoA [peroxisome]'" C35H54N7O17P3S http://mousecyc.jax.org/META/NEW-IMAGE?type=COMPOUND&object=CPD0-1162 +s_2904[p]' (R)-3-hydroxyoctanoyl-CoA [peroxisome]' C29H50N7O18P3S https://www.genome.jp/dbget-bin/www_bget?cpd:C05278 +s_2909[p]' (R)-3-hydroxy-cis-tetradec-7-enoyl-CoA [peroxisome]' Missing source and formula +s_2910[p]' (R)-3-hydroxy-cis-dodec-5-enoyl-CoA [peroxisome]' Missing source and formula +s_2922[p]' 3-oxo-cis-dodec-5-enoyl-CoA [peroxisome]' Missing source and formula +s_3479[ce]' 1-acylglycerophosphoserine (16:0) [cell envelope]' C22H44NP10 Found by elemental balance +s_3481[ce]' 1-acylglycerophosphoserine (16:1) [cell envelope]' C22H42NP10 Found by elemental balance +s_3483[ce]' 1-acylglycerophosphoserine (18:0) [cell envelope]' C24H48NP10 Found by elemental balance +s_3485[ce]' 1-acylglycerophosphoserine (18:1) [cell envelope]' C24H46NP10 Found by elemental balance +s_3717[c]' protein [cytoplasm]' +s_3718[c]' carbohydrate [cytoplasm]' +s_3719[c]' RNA [cytoplasm]' +s_3720[c]' DNA [cytoplasm]' +s_3746[c]' lipid - backbones [cytoplasm]' +s_3747[c]' lipid - tails [cytoplasm]' diff --git a/ComplementaryScripts/modelCuration/updateMetaboliteFormula.m b/ComplementaryScripts/modelCuration/updateMetaboliteFormula.m new file mode 100644 index 00000000..7737407f --- /dev/null +++ b/ComplementaryScripts/modelCuration/updateMetaboliteFormula.m @@ -0,0 +1,45 @@ +%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% +% model = updateMetaboliteFormula(model) +% +% Reads the data file and updates the metabolite formula information in the model +% +% +% William T. Scott, Jr. +% Last Update: 2018-08-23 +%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% + + +% Load model +cd .. +model = loadYeastModel; + +%Correct some of the metabolite fomulae from most recent info +%Load data: +fid = fopen('../ComplementaryData/modelCuration/Missingmetaboliteformulas.tsv','r'); +metaboliteData = textscan(fid,'%s %s %s %s %f32 %s','Delimiter','\t','HeaderLines',1); +fclose(fid); + +for i = 1:length(metaboliteData{1}) + for j = 1:length(model.mets) + %Find name: + if startsWith(model.metNames{j},[metaboliteData{2}{i} ' [']) %metabolite name + metName = model.metNames{j}; + comp = metName(strfind(metName,' ['):end); + metName = [metaboliteData{2}{i} comp]; + model.metNames{j} = metName; + end + + %Update other fields: + if startsWith(model.metNames{j},[metaboliteData{2}{i} ' [']) %new name + model.model.metFormulas{j} = metaboliteData{3}{i}; %new formulas + end + end +end + +% Save model + +saveYeastModel(model) +cd modelCuration + + +%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% \ No newline at end of file From 275ed3ee3088d1e8b5898998c4bf5f8cea6daf4d Mon Sep 17 00:00:00 2001 From: William Scott Date: Fri, 14 Sep 2018 09:54:16 -0700 Subject: [PATCH 2/6] fix-met.prop: correct metFormulas --- ModelFiles/dependencies.txt | 4 ++-- README.md | 2 +- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/ModelFiles/dependencies.txt b/ModelFiles/dependencies.txt index e5fb14da..bf8abad5 100644 --- a/ModelFiles/dependencies.txt +++ b/ModelFiles/dependencies.txt @@ -1,7 +1,7 @@ MATLAB 9.4.0.813654 (R2018a) libSBML 5.17.0 -RAVEN_toolbox unknown -COBRA_toolbox commit ef3990e +RAVEN_toolbox 2.0.1 +COBRA_toolbox commit unknown SBML_level 3 SBML_version 1 fbc_version 2 diff --git a/README.md b/README.md index 6c958bf1..305987c0 100644 --- a/README.md +++ b/README.md @@ -10,7 +10,7 @@ This repository contains the current consensus genome-scale metabolic model of _ **GEM Category:** Species; **Utilisation:** predictive simulation, multi-omics integrative analysis, _in silico_ strain design, model template; **Field:** metabolic-network reconstruction; **Type of Model:** curated, reconstruction; **Model Source:** [Yeast 7.6](https://sourceforge.net/projects/yeast/); **Taxonomy:** _Saccharomyces cerevisiae_; **Metabolic System:** General Metabolism; **Condition:** aerobic, glucose-limited, defined media, maximization of growth. -* Last update: 2018-08-30 +* Last update: 2018-09-14 * Main Model Descriptors: From 3326a813292833f8c3c63a35c319f73861c9666f Mon Sep 17 00:00:00 2001 From: William Scott Date: Fri, 28 Sep 2018 12:30:16 -0700 Subject: [PATCH 3/6] fix-met.prop: correct metFormula --- ModelFiles/dependencies.txt | 2 +- README.md | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/ModelFiles/dependencies.txt b/ModelFiles/dependencies.txt index bf8abad5..0ef8d979 100644 --- a/ModelFiles/dependencies.txt +++ b/ModelFiles/dependencies.txt @@ -1,7 +1,7 @@ MATLAB 9.4.0.813654 (R2018a) libSBML 5.17.0 RAVEN_toolbox 2.0.1 -COBRA_toolbox commit unknown +COBRA_toolbox commit d7ce7d6 SBML_level 3 SBML_version 1 fbc_version 2 diff --git a/README.md b/README.md index 305987c0..e3e7f355 100644 --- a/README.md +++ b/README.md @@ -10,7 +10,7 @@ This repository contains the current consensus genome-scale metabolic model of _ **GEM Category:** Species; **Utilisation:** predictive simulation, multi-omics integrative analysis, _in silico_ strain design, model template; **Field:** metabolic-network reconstruction; **Type of Model:** curated, reconstruction; **Model Source:** [Yeast 7.6](https://sourceforge.net/projects/yeast/); **Taxonomy:** _Saccharomyces cerevisiae_; **Metabolic System:** General Metabolism; **Condition:** aerobic, glucose-limited, defined media, maximization of growth. -* Last update: 2018-09-14 +* Last update: 2018-09-28 * Main Model Descriptors: From 9451f05a81ac5f7f117079eb0c9fece22fab3f4d Mon Sep 17 00:00:00 2001 From: benjasanchez Date: Thu, 6 Dec 2018 19:51:46 +0100 Subject: [PATCH 4/6] fix-data: empty rows * remove rows with no formulas (redundant) * remove undesired ' characters * some bugs in function --- .../Missingmetaboliteformulas.tsv | 54 +++++++------------ .../modelCuration/updateMetaboliteFormula.m | 25 +++------ 2 files changed, 24 insertions(+), 55 deletions(-) diff --git a/ComplementaryData/modelCuration/Missingmetaboliteformulas.tsv b/ComplementaryData/modelCuration/Missingmetaboliteformulas.tsv index 868c228c..fc1fe6d1 100644 --- a/ComplementaryData/modelCuration/Missingmetaboliteformulas.tsv +++ b/ComplementaryData/modelCuration/Missingmetaboliteformulas.tsv @@ -1,37 +1,19 @@ Met ID Met Name Met Formula Source -s_0330[er]' 6-(alpha-D-glucosaminyl)-O-acyl-1-phosphatidyl-1D-myo-inositol [endoplasmic reticulum]' missing in source -s_0334[er]' 6-O-[alpha-D-mannosyl-(1->4)-alpha-D-glucosaminyl]-O-acyl-1-phosphatidyl-1D-myo-inositol [endoplasmic reticulum]' missing in source -s_0337[er]' 6-O-{2-O-[(2-aminoethyl)phosphoryl]-alpha-D-mannosyl-(1->4)-alpha-D-glucosaminyl}-O-acyl-1-phosphatidyl-1D-myo-inositol [endoplasmic reticulum]' missing in source -s_0338[er]' 6-O-{alpha-D-mannosyl-(1->2)-alpha-D-mannosyl-(1->6)-2-O-[(2-aminoethyl)phosphoryl]-alpha-D-mannosyl-(1->4)-alpha-D-glucosaminyl}-O-acyl-1-phosphatidyl-1D-myo-inositol [endoplasmic reticulum]' missing in source -s_0339[er]' 6-O-{alpha-D-mannosyl-(1->6)-2-O-[(2-aminoethyl)phosphoryl]-alpha-D-mannosyl-(1->4)-alpha-D-glucosaminyl}-O-acyl-1-phosphatidyl-1D-myo-inositol [endoplasmic reticulum]' missing in source -s_0450[c]' biomass [cytoplasm]' -s_0694[c]' fatty acid backbone [cytoplasm]' -s_0709[m]' ferricytochrome c [mitochondrion]' C42H44FeN8O8S2R4 https://www.genome.jp/dbget-bin/www_bget?cpd:C00125 -s_0710[m]' ferrocytochrome c [mitochondrion]' C42H44FeN8O8S2R4 https://www.genome.jp/dbget-bin/www_bget?cpd:C00126 -s_0773[c]' glycogen [cytoplasm]' C24H42O21 https://www.genome.jp/dbget-bin/www_bget?C00182 -s_0774[v]' glycogen [vacuole]' C24H42O21 https://www.genome.jp/dbget-bin/www_bget?C00182 -s_1096[c]' lipid [cytoplasm]' -s_1107[c]' mannan [cytoplasm]' C12H21O10(C12H20O11)n https://www.genome.jp/dbget-bin/www_bget?cpd:C04276 -s_1108[er]' mannan [endoplasmic reticulum]' C12H21O10(C12H20O11)n https://www.genome.jp/dbget-bin/www_bget?cpd:C04276 -s_1845[m]' ACP1 [mitochondrion]' -s_2775[m]' 3-hydroxybutanoyl-ACP [mitochondrion]' C4H7O2SR https://www.genome.jp/dbget-bin/www_bget?C04618 -s_2778[m]' trans-but-2-enoyl-ACP [mitochondrion]' C4H5OS https://www.ebi.ac.uk/chebi/searchId.do?chebiId=132146 -s_2779[m]' trans-hex-2-enoyl-ACP [mitochondrion]' C6H9OSR https://www.genome.jp/dbget-bin/www_bget?C05748 -s_2780[m]' trans-oct-2-enoyl-ACP [mitochondrion]' C8H13OSR https://www.genome.jp/dbget-bin/www_bget?C05751 -s_2812[erm]' trans-icos-2-enoyl-CoA [endoplasmic reticulum membrane]' C41H72N7O17P3S http://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:75061 -s_2889[p]' trans-icos-2-enoyl-CoA [peroxisome]' C41H72N7O17P3S http://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:75061 -s_2896[p]' "trans-2,cis-5-dodecadienoyl-CoA [peroxisome]'" C35H54N7O17P3S http://mousecyc.jax.org/META/NEW-IMAGE?type=COMPOUND&object=CPD0-1162 -s_2904[p]' (R)-3-hydroxyoctanoyl-CoA [peroxisome]' C29H50N7O18P3S https://www.genome.jp/dbget-bin/www_bget?cpd:C05278 -s_2909[p]' (R)-3-hydroxy-cis-tetradec-7-enoyl-CoA [peroxisome]' Missing source and formula -s_2910[p]' (R)-3-hydroxy-cis-dodec-5-enoyl-CoA [peroxisome]' Missing source and formula -s_2922[p]' 3-oxo-cis-dodec-5-enoyl-CoA [peroxisome]' Missing source and formula -s_3479[ce]' 1-acylglycerophosphoserine (16:0) [cell envelope]' C22H44NP10 Found by elemental balance -s_3481[ce]' 1-acylglycerophosphoserine (16:1) [cell envelope]' C22H42NP10 Found by elemental balance -s_3483[ce]' 1-acylglycerophosphoserine (18:0) [cell envelope]' C24H48NP10 Found by elemental balance -s_3485[ce]' 1-acylglycerophosphoserine (18:1) [cell envelope]' C24H46NP10 Found by elemental balance -s_3717[c]' protein [cytoplasm]' -s_3718[c]' carbohydrate [cytoplasm]' -s_3719[c]' RNA [cytoplasm]' -s_3720[c]' DNA [cytoplasm]' -s_3746[c]' lipid - backbones [cytoplasm]' -s_3747[c]' lipid - tails [cytoplasm]' +s_0709[m] ferricytochrome c [mitochondrion] C42H44FeN8O8S2R4 https://www.genome.jp/dbget-bin/www_bget?cpd:C00125 +s_0710[m] ferrocytochrome c [mitochondrion] C42H44FeN8O8S2R4 https://www.genome.jp/dbget-bin/www_bget?cpd:C00126 +s_0773[c] glycogen [cytoplasm] C24H42O21 https://www.genome.jp/dbget-bin/www_bget?C00182 +s_0774[v] glycogen [vacuole] C24H42O21 https://www.genome.jp/dbget-bin/www_bget?C00182 +s_1107[c] mannan [cytoplasm] C12H21O10(C12H20O11)n https://www.genome.jp/dbget-bin/www_bget?cpd:C04276 +s_1108[er] mannan [endoplasmic reticulum] C12H21O10(C12H20O11)n https://www.genome.jp/dbget-bin/www_bget?cpd:C04276 +s_2775[m] 3-hydroxybutanoyl-ACP [mitochondrion] C4H7O2SR https://www.genome.jp/dbget-bin/www_bget?C04618 +s_2778[m] trans-but-2-enoyl-ACP [mitochondrion] C4H5OS https://www.ebi.ac.uk/chebi/searchId.do?chebiId=132146 +s_2779[m] trans-hex-2-enoyl-ACP [mitochondrion] C6H9OSR https://www.genome.jp/dbget-bin/www_bget?C05748 +s_2780[m] trans-oct-2-enoyl-ACP [mitochondrion] C8H13OSR https://www.genome.jp/dbget-bin/www_bget?C05751 +s_2812[erm] trans-icos-2-enoyl-CoA [endoplasmic reticulum membrane] C41H72N7O17P3S http://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:75061 +s_2889[p] trans-icos-2-enoyl-CoA [peroxisome] C41H72N7O17P3S http://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:75061 +s_2896[p] trans-2,cis-5-dodecadienoyl-CoA [peroxisome] C35H54N7O17P3S http://mousecyc.jax.org/META/NEW-IMAGE?type=COMPOUND&object=CPD0-1162 +s_2904[p] (R)-3-hydroxyoctanoyl-CoA [peroxisome] C29H50N7O18P3S https://www.genome.jp/dbget-bin/www_bget?cpd:C05278 +s_3479[ce] 1-acylglycerophosphoserine (16:0) [cell envelope] C22H44NP10 Found by elemental balance +s_3481[ce] 1-acylglycerophosphoserine (16:1) [cell envelope] C22H42NP10 Found by elemental balance +s_3483[ce] 1-acylglycerophosphoserine (18:0) [cell envelope] C24H48NP10 Found by elemental balance +s_3485[ce] 1-acylglycerophosphoserine (18:1) [cell envelope] C24H46NP10 Found by elemental balance diff --git a/ComplementaryScripts/modelCuration/updateMetaboliteFormula.m b/ComplementaryScripts/modelCuration/updateMetaboliteFormula.m index 7737407f..48936662 100644 --- a/ComplementaryScripts/modelCuration/updateMetaboliteFormula.m +++ b/ComplementaryScripts/modelCuration/updateMetaboliteFormula.m @@ -3,43 +3,30 @@ % % Reads the data file and updates the metabolite formula information in the model % -% % William T. Scott, Jr. % Last Update: 2018-08-23 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% - % Load model cd .. model = loadYeastModel; - -%Correct some of the metabolite fomulae from most recent info + %Load data: fid = fopen('../ComplementaryData/modelCuration/Missingmetaboliteformulas.tsv','r'); metaboliteData = textscan(fid,'%s %s %s %s %f32 %s','Delimiter','\t','HeaderLines',1); fclose(fid); - + +%Update formulas: for i = 1:length(metaboliteData{1}) for j = 1:length(model.mets) - %Find name: - if startsWith(model.metNames{j},[metaboliteData{2}{i} ' [']) %metabolite name - metName = model.metNames{j}; - comp = metName(strfind(metName,' ['):end); - metName = [metaboliteData{2}{i} comp]; - model.metNames{j} = metName; - end - - %Update other fields: - if startsWith(model.metNames{j},[metaboliteData{2}{i} ' [']) %new name - model.model.metFormulas{j} = metaboliteData{3}{i}; %new formulas + if strcmp(model.metNames{j},metaboliteData{2}{i}) + model.metFormulas{j} = metaboliteData{3}{i}; end end end % Save model - saveYeastModel(model) cd modelCuration - -%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% \ No newline at end of file +%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% From 5c4f58d0c923e060bee4c6a61bde4499f7b24913 Mon Sep 17 00:00:00 2001 From: benjasanchez Date: Thu, 6 Dec 2018 20:09:03 +0100 Subject: [PATCH 5/6] fix-data: carbohydrate formulas as complex carbohydrates have varying length, it's best to use the monomeric form --- .../modelCuration/Missingmetaboliteformulas.tsv | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/ComplementaryData/modelCuration/Missingmetaboliteformulas.tsv b/ComplementaryData/modelCuration/Missingmetaboliteformulas.tsv index fc1fe6d1..50566b17 100644 --- a/ComplementaryData/modelCuration/Missingmetaboliteformulas.tsv +++ b/ComplementaryData/modelCuration/Missingmetaboliteformulas.tsv @@ -1,10 +1,10 @@ Met ID Met Name Met Formula Source s_0709[m] ferricytochrome c [mitochondrion] C42H44FeN8O8S2R4 https://www.genome.jp/dbget-bin/www_bget?cpd:C00125 s_0710[m] ferrocytochrome c [mitochondrion] C42H44FeN8O8S2R4 https://www.genome.jp/dbget-bin/www_bget?cpd:C00126 -s_0773[c] glycogen [cytoplasm] C24H42O21 https://www.genome.jp/dbget-bin/www_bget?C00182 -s_0774[v] glycogen [vacuole] C24H42O21 https://www.genome.jp/dbget-bin/www_bget?C00182 -s_1107[c] mannan [cytoplasm] C12H21O10(C12H20O11)n https://www.genome.jp/dbget-bin/www_bget?cpd:C04276 -s_1108[er] mannan [endoplasmic reticulum] C12H21O10(C12H20O11)n https://www.genome.jp/dbget-bin/www_bget?cpd:C04276 +s_0773[c] glycogen [cytoplasm] C6H12O6 Monomeric form = glucose +s_0774[v] glycogen [vacuole] C6H12O6 Monomeric form = glucose +s_1107[c] mannan [cytoplasm] C6H12O6 Monomeric form = mannose +s_1108[er] mannan [endoplasmic reticulum] C6H12O6 Monomeric form = mannose s_2775[m] 3-hydroxybutanoyl-ACP [mitochondrion] C4H7O2SR https://www.genome.jp/dbget-bin/www_bget?C04618 s_2778[m] trans-but-2-enoyl-ACP [mitochondrion] C4H5OS https://www.ebi.ac.uk/chebi/searchId.do?chebiId=132146 s_2779[m] trans-hex-2-enoyl-ACP [mitochondrion] C6H9OSR https://www.genome.jp/dbget-bin/www_bget?C05748 From 763a9fd8301ce40979d4189fff6fab4bf980cab8 Mon Sep 17 00:00:00 2001 From: benjasanchez Date: Thu, 6 Dec 2018 20:29:52 +0100 Subject: [PATCH 6/6] feat-met.prop: chemical formulas --- ModelFiles/xml/yeastGEM.xml | 36 ++++++++++++++++++------------------ ModelFiles/yml/yeastGEM.yml | 18 ++++++++++++++++++ 2 files changed, 36 insertions(+), 18 deletions(-) diff --git a/ModelFiles/xml/yeastGEM.xml b/ModelFiles/xml/yeastGEM.xml index 4b630f01..9100d499 100644 --- a/ModelFiles/xml/yeastGEM.xml +++ b/ModelFiles/xml/yeastGEM.xml @@ -10660,7 +10660,7 @@ - + @@ -10680,7 +10680,7 @@ - + @@ -11580,7 +11580,7 @@ - + @@ -11600,7 +11600,7 @@ - + @@ -17324,7 +17324,7 @@ - + @@ -17344,7 +17344,7 @@ - + @@ -25271,7 +25271,7 @@ - + @@ -25328,7 +25328,7 @@ - + @@ -25346,7 +25346,7 @@ - + @@ -25366,7 +25366,7 @@ - + @@ -25994,7 +25994,7 @@ - + @@ -27429,7 +27429,7 @@ - + @@ -27535,7 +27535,7 @@ - + @@ -27673,7 +27673,7 @@ - + @@ -37036,7 +37036,7 @@ - + @@ -37062,7 +37062,7 @@ - + @@ -37093,7 +37093,7 @@ - + @@ -37124,7 +37124,7 @@ - + diff --git a/ModelFiles/yml/yeastGEM.yml b/ModelFiles/yml/yeastGEM.yml index e0f766a0..3738e7e8 100644 --- a/ModelFiles/yml/yeastGEM.yml +++ b/ModelFiles/yml/yeastGEM.yml @@ -5818,6 +5818,7 @@ - id: s_0709 - name: ferricytochrome c - compartment: m + - formula: C42H44FeN8O8S2R4 - charge: 0 - annotation: !!omap - chebi: CHEBI:15991 @@ -5828,6 +5829,7 @@ - id: s_0710 - name: ferrocytochrome c - compartment: m + - formula: C42H44FeN8O8S2R4 - charge: 0 - annotation: !!omap - chebi: CHEBI:16928 @@ -6322,6 +6324,7 @@ - id: s_0773 - name: glycogen - compartment: c + - formula: C6H12O6 - charge: 0 - annotation: !!omap - chebi: CHEBI:28087 @@ -6332,6 +6335,7 @@ - id: s_0774 - name: glycogen - compartment: v + - formula: C6H12O6 - charge: 0 - annotation: !!omap - chebi: CHEBI:28087 @@ -9443,6 +9447,7 @@ - id: s_1107 - name: mannan - compartment: c + - formula: C6H12O6 - charge: 0 - annotation: !!omap - chebi: CHEBI:28808 @@ -9453,6 +9458,7 @@ - id: s_1108 - name: mannan - compartment: er + - formula: C6H12O6 - charge: 0 - annotation: !!omap - chebi: CHEBI:28808 @@ -13780,6 +13786,7 @@ - id: s_2775 - name: 3-hydroxybutanoyl-ACP - compartment: m + - formula: C4H7O2SR - charge: 0 - annotation: !!omap - kegg.compound: C04618 @@ -13809,6 +13816,7 @@ - id: s_2778 - name: trans-but-2-enoyl-ACP - compartment: m + - formula: C4H5OS - charge: 0 - annotation: !!omap - chebi: CHEBI:132146 @@ -13817,6 +13825,7 @@ - id: s_2779 - name: trans-hex-2-enoyl-ACP - compartment: m + - formula: C6H9OSR - charge: 0 - annotation: !!omap - chebi: CHEBI:10727 @@ -13827,6 +13836,7 @@ - id: s_2780 - name: trans-oct-2-enoyl-ACP - compartment: m + - formula: C8H13OSR - charge: 0 - annotation: !!omap - kegg.compound: C05751 @@ -14166,6 +14176,7 @@ - id: s_2812 - name: trans-icos-2-enoyl-CoA - compartment: erm + - formula: C41H72N7O17P3S - charge: 0 - annotation: !!omap - sbo: SBO:0000247 @@ -14951,6 +14962,7 @@ - id: s_2889 - name: trans-icos-2-enoyl-CoA - compartment: p + - formula: C41H72N7O17P3S - charge: 0 - annotation: !!omap - sbo: SBO:0000247 @@ -15009,6 +15021,7 @@ - id: s_2896 - name: trans-2,cis-5-dodecadienoyl-CoA - compartment: p + - formula: C35H54N7O17P3S - charge: 0 - annotation: !!omap - sbo: SBO:0000247 @@ -15082,6 +15095,7 @@ - id: s_2904 - name: (R)-3-hydroxyoctanoyl-CoA - compartment: p + - formula: C29H50N7O18P3S - charge: 0 - annotation: !!omap - chebi: CHEBI:28573 @@ -20186,6 +20200,7 @@ - id: s_3479 - name: 1-acylglycerophosphoserine (16:0) - compartment: ce + - formula: C22H44NP10 - charge: 0 - annotation: !!omap - sbo: SBO:0000247 @@ -20201,6 +20216,7 @@ - id: s_3481 - name: 1-acylglycerophosphoserine (16:1) - compartment: ce + - formula: C22H42NP10 - charge: 0 - annotation: !!omap - sbo: SBO:0000247 @@ -20217,6 +20233,7 @@ - id: s_3483 - name: 1-acylglycerophosphoserine (18:0) - compartment: ce + - formula: C24H48NP10 - charge: 0 - annotation: !!omap - sbo: SBO:0000247 @@ -20233,6 +20250,7 @@ - id: s_3485 - name: 1-acylglycerophosphoserine (18:1) - compartment: ce + - formula: C24H46NP10 - charge: 0 - annotation: !!omap - sbo: SBO:0000247