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Fix: Amend #403 by merging additional model fields from duplicated rxns #405

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merged 2 commits into from
Jul 28, 2022
Merged

Fix: Amend #403 by merging additional model fields from duplicated rxns #405

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c5e262c
feat: update script to merge eccodes and rxnReferences model fields
JonathanRob Jul 27, 2022
192bded
feat: merge rxn eccode and rxnReference fields from duplicated rxns
JonathanRob Jul 27, 2022
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13 changes: 13 additions & 0 deletions code/modelCuration/removeDuplicateRxns_issue345.m
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Original file line number Diff line number Diff line change
Expand Up @@ -92,6 +92,19 @@
rxnAssocTable = struct2table(rxnAssoc);
exportTsvFile([deprecRxnsTable; rxnAssocTable(rxn_indx(:,2), :)], depRxnFile);

% merge additional model fields from duplicate rxns with the kept rxns
mergeFields = {'eccodes'; 'rxnReferences'};
for i = 1:size(rxns, 1)
for f = 1:numel(mergeFields)
entry1 = strsplit(model.(mergeFields{f}){rxn_indx(i,1)}, ';');
entry2 = strsplit(model.(mergeFields{f}){rxn_indx(i,2)}, ';');
merged_entry = setdiff(union(entry1, entry2), {''});
if ~isempty(merged_entry)
model.(mergeFields{f}){rxn_indx(i,1)} = strjoin(merged_entry, ';');
end
end
end

% delete reactions from model and annotation file
model = removeReactions(model, rxns(:,2));
exportYaml(model, '../../model/Human-GEM.yml');
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86 changes: 43 additions & 43 deletions model/Human-GEM.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -4,7 +4,7 @@
short_name: "Human-GEM"
full_name: "Generic genome-scale metabolic model of Homo sapiens"
version: ""
date: "2022-07-21"
date: "2022-07-27"
authors: "Jonathan Robinson, Hao Wang, Pierre-Etienne Cholley, Pinar Kocabas"
email: "jonrob@chalmers.se"
organization: "Chalmers University of Technology"
Expand Down Expand Up @@ -219680,7 +219680,7 @@
- rxnNotes: ""
- rxnFrom: "Recon3D"
- eccodes: "4.3.2.1"
- references: "PMID:14598172"
- references: "PMID:14598172;PMID:8132483"
- subsystem:
- "Transport reactions"
- confidence_score: 0
Expand Down Expand Up @@ -220084,7 +220084,7 @@
- rxnNotes: ""
- rxnFrom: "Recon3D"
- eccodes: "1.3.1.70"
- references: "PMID:16784888"
- references: "PMID:11969204;PMID:16784888;PMID:7946524"
- subsystem:
- "Cholesterol metabolism"
- confidence_score: 0
Expand Down Expand Up @@ -220446,7 +220446,7 @@
- rxnNotes: ""
- rxnFrom: "Recon3D"
- eccodes: "2.7.7.41"
- references: ""
- references: "PMID:1330695;PMID:9370329"
- subsystem:
- "Glycerophospholipid metabolism"
- confidence_score: 0
Expand Down Expand Up @@ -229798,7 +229798,7 @@
- rxnNotes: ""
- rxnFrom: "Recon3D"
- eccodes: "5.3.3.5"
- references: "PMID:12133002;PMID:4475632;PMID:5810070"
- references: "PMID:10391219;PMID:12133002;PMID:4475632;PMID:5810070"
- subsystem:
- "Cholesterol metabolism"
- confidence_score: 0
Expand Down Expand Up @@ -247391,8 +247391,8 @@
- gene_reaction_rule: "ENSG00000160211"
- rxnNotes: "Harpers illustrated Biochemistry (2009) 28th edition pages 174-183, ISBN:9781282335806"
- rxnFrom: "Recon3D"
- eccodes: ""
- references: "PMID:4382012;PMID:13575411"
- eccodes: "1.1.1.49"
- references: "PMID:13575411;PMID:15774558;PMID:16756494;PMID:2753047;PMID:4169027;PMID:4382012"
- subsystem:
- "Pentose phosphate pathway"
- confidence_score: 0
Expand Down Expand Up @@ -248222,7 +248222,7 @@
- rxnNotes: ""
- rxnFrom: "Recon3D"
- eccodes: ""
- references: ""
- references: "PMID:21749321"
- subsystem:
- "Transport reactions"
- confidence_score: 0
Expand Down Expand Up @@ -270782,7 +270782,7 @@
- rxnNotes: ""
- rxnFrom: "Recon3D"
- eccodes: ""
- references: ""
- references: "PMID:11489939;PMID:17347912;PMID:20157782"
- subsystem:
- "Transport reactions"
- confidence_score: 0
Expand All @@ -270798,7 +270798,7 @@
- rxnNotes: ""
- rxnFrom: "Recon3D"
- eccodes: ""
- references: ""
- references: "PMID:15535801"
- subsystem:
- "Transport reactions"
- confidence_score: 0
Expand All @@ -270814,7 +270814,7 @@
- rxnNotes: ""
- rxnFrom: "Recon3D"
- eccodes: ""
- references: ""
- references: "PMID:19720082"
- subsystem:
- "Transport reactions"
- confidence_score: 0
Expand All @@ -270830,7 +270830,7 @@
- rxnNotes: ""
- rxnFrom: "Recon3D"
- eccodes: ""
- references: ""
- references: "PMID:19720082"
- subsystem:
- "Transport reactions"
- confidence_score: 0
Expand All @@ -270846,7 +270846,7 @@
- rxnNotes: ""
- rxnFrom: "Recon3D"
- eccodes: ""
- references: ""
- references: "PMID:19720082"
- subsystem:
- "Transport reactions"
- confidence_score: 0
Expand All @@ -270862,7 +270862,7 @@
- rxnNotes: ""
- rxnFrom: "Recon3D"
- eccodes: ""
- references: ""
- references: "PMID:19720082"
- subsystem:
- "Transport reactions"
- confidence_score: 0
Expand Down Expand Up @@ -270894,7 +270894,7 @@
- rxnNotes: ""
- rxnFrom: "Recon3D"
- eccodes: ""
- references: ""
- references: "PMID:19720082"
- subsystem:
- "Transport reactions"
- confidence_score: 0
Expand All @@ -270910,7 +270910,7 @@
- rxnNotes: ""
- rxnFrom: "Recon3D"
- eccodes: ""
- references: ""
- references: "PMID:19720082"
- subsystem:
- "Transport reactions"
- confidence_score: 0
Expand All @@ -270926,7 +270926,7 @@
- rxnNotes: ""
- rxnFrom: "Recon3D"
- eccodes: ""
- references: ""
- references: "PMID:20583174"
- subsystem:
- "Transport reactions"
- confidence_score: 0
Expand All @@ -270942,7 +270942,7 @@
- rxnNotes: ""
- rxnFrom: "Recon3D"
- eccodes: ""
- references: ""
- references: "PMID:21281499"
- subsystem:
- "Transport reactions"
- confidence_score: 0
Expand All @@ -270958,7 +270958,7 @@
- rxnNotes: ""
- rxnFrom: "Recon3D"
- eccodes: ""
- references: ""
- references: "PMID:21281499"
- subsystem:
- "Transport reactions"
- confidence_score: 0
Expand All @@ -270974,7 +270974,7 @@
- rxnNotes: ""
- rxnFrom: "Recon3D"
- eccodes: ""
- references: ""
- references: "PMID:21281499"
- subsystem:
- "Transport reactions"
- confidence_score: 0
Expand Down Expand Up @@ -271006,7 +271006,7 @@
- rxnNotes: ""
- rxnFrom: "Recon3D"
- eccodes: ""
- references: ""
- references: "PMID:19720082"
- subsystem:
- "Transport reactions"
- confidence_score: 0
Expand All @@ -271022,7 +271022,7 @@
- rxnNotes: ""
- rxnFrom: "Recon3D"
- eccodes: ""
- references: ""
- references: "PMID:19720082"
- subsystem:
- "Transport reactions"
- confidence_score: 0
Expand All @@ -271038,7 +271038,7 @@
- rxnNotes: ""
- rxnFrom: "Recon3D"
- eccodes: ""
- references: ""
- references: "PMID:3119938;PMID:6959231"
- subsystem:
- "Transport reactions"
- confidence_score: 0
Expand All @@ -271054,7 +271054,7 @@
- rxnNotes: ""
- rxnFrom: "Recon3D"
- eccodes: ""
- references: ""
- references: "PMID:16146704"
- subsystem:
- "Transport reactions"
- confidence_score: 0
Expand All @@ -271070,7 +271070,7 @@
- rxnNotes: ""
- rxnFrom: "Recon3D"
- eccodes: ""
- references: ""
- references: "PMID:2064600"
- subsystem:
- "Transport reactions"
- confidence_score: 0
Expand All @@ -271086,7 +271086,7 @@
- rxnNotes: ""
- rxnFrom: "Recon3D"
- eccodes: ""
- references: ""
- references: "PMID:19720082"
- subsystem:
- "Transport reactions"
- confidence_score: 0
Expand All @@ -271101,8 +271101,8 @@
- gene_reaction_rule: ""
- rxnNotes: ""
- rxnFrom: "Recon3D"
- eccodes: ""
- references: ""
- eccodes: "1.1.1.62"
- references: "PMID:19720082"
- subsystem:
- "Transport reactions"
- confidence_score: 0
Expand All @@ -271118,7 +271118,7 @@
- rxnNotes: ""
- rxnFrom: "Recon3D"
- eccodes: ""
- references: ""
- references: "PMID:9266369"
- subsystem:
- "Transport reactions"
- confidence_score: 0
Expand All @@ -271134,7 +271134,7 @@
- rxnNotes: ""
- rxnFrom: "Recon3D"
- eccodes: ""
- references: ""
- references: "PMID:20157782"
- subsystem:
- "Transport reactions"
- confidence_score: 0
Expand All @@ -271150,7 +271150,7 @@
- rxnNotes: ""
- rxnFrom: "Recon3D"
- eccodes: ""
- references: ""
- references: "PMID:19720082"
- subsystem:
- "Transport reactions"
- confidence_score: 0
Expand All @@ -271166,7 +271166,7 @@
- rxnNotes: ""
- rxnFrom: "Recon3D"
- eccodes: ""
- references: ""
- references: "PMID:19720082"
- subsystem:
- "Transport reactions"
- confidence_score: 0
Expand All @@ -271182,7 +271182,7 @@
- rxnNotes: ""
- rxnFrom: "Recon3D"
- eccodes: ""
- references: ""
- references: "PMID:19720082"
- subsystem:
- "Transport reactions"
- confidence_score: 0
Expand All @@ -271198,7 +271198,7 @@
- rxnNotes: ""
- rxnFrom: "Recon3D"
- eccodes: ""
- references: ""
- references: "PMID:12828998"
- subsystem:
- "Transport reactions"
- confidence_score: 0
Expand All @@ -271214,7 +271214,7 @@
- rxnNotes: ""
- rxnFrom: "Recon3D"
- eccodes: ""
- references: ""
- references: "PMID:19720082"
- subsystem:
- "Transport reactions"
- confidence_score: 0
Expand All @@ -271230,7 +271230,7 @@
- rxnNotes: ""
- rxnFrom: "Recon3D"
- eccodes: ""
- references: ""
- references: "PMID:6959231"
- subsystem:
- "Transport reactions"
- confidence_score: 0
Expand All @@ -271246,7 +271246,7 @@
- rxnNotes: ""
- rxnFrom: "Recon3D"
- eccodes: ""
- references: ""
- references: "PMID:12828998;PMID:20026021;PMID:21463612;PMID:9498103"
- subsystem:
- "Transport reactions"
- confidence_score: 0
Expand All @@ -271262,7 +271262,7 @@
- rxnNotes: ""
- rxnFrom: "Recon3D"
- eccodes: ""
- references: ""
- references: "PMID:20026021"
- subsystem:
- "Transport reactions"
- confidence_score: 0
Expand All @@ -271278,7 +271278,7 @@
- rxnNotes: ""
- rxnFrom: "Recon3D"
- eccodes: ""
- references: ""
- references: "PMID:21215187"
- subsystem:
- "Transport reactions"
- confidence_score: 0
Expand Down Expand Up @@ -271310,7 +271310,7 @@
- rxnNotes: ""
- rxnFrom: "Recon3D"
- eccodes: ""
- references: ""
- references: "PMID:19720082"
- subsystem:
- "Transport reactions"
- confidence_score: 0
Expand Down Expand Up @@ -271390,7 +271390,7 @@
- rxnNotes: ""
- rxnFrom: "Recon3D"
- eccodes: ""
- references: ""
- references: "PMID:19720082"
- subsystem:
- "Transport reactions"
- confidence_score: 0
Expand All @@ -271406,7 +271406,7 @@
- rxnNotes: ""
- rxnFrom: "Recon3D"
- eccodes: ""
- references: ""
- references: "PMID:19720082"
- subsystem:
- "Transport reactions"
- confidence_score: 0
Expand All @@ -271422,7 +271422,7 @@
- rxnNotes: ""
- rxnFrom: "Recon3D"
- eccodes: ""
- references: ""
- references: "PMID:19720082"
- subsystem:
- "Transport reactions"
- confidence_score: 0
Expand Down