From 1f992aec3290a29b9ae1078cefd3c3ff29957bc0 Mon Sep 17 00:00:00 2001 From: Hao Wang Date: Wed, 2 Nov 2022 13:24:58 +0100 Subject: [PATCH] feat: add cis-aconitate decarboxylase reaction catalyzed by ACOD1 (IRG1) - this is to add reaction catalyzed by ACOD1 (IRG1), according to Mouse-GEM issue #20 --- code/modelCuration/addRxnACOD1_20221102.m | 33 +++++++++++++++++++++ data/modelCuration/addRxnACOD1_20221102.tsv | 2 ++ 2 files changed, 35 insertions(+) create mode 100644 code/modelCuration/addRxnACOD1_20221102.m create mode 100644 data/modelCuration/addRxnACOD1_20221102.tsv diff --git a/code/modelCuration/addRxnACOD1_20221102.m b/code/modelCuration/addRxnACOD1_20221102.m new file mode 100644 index 00000000..2c4f38e7 --- /dev/null +++ b/code/modelCuration/addRxnACOD1_20221102.m @@ -0,0 +1,33 @@ +% load model and new reaction info +ihuman = importYaml('../../model/Human-GEM.yml'); +rxnsToAdd = importTsvFile('../../data/modelCuration/addRxnACOD1_20221102.tsv'); + +% add new genes to Human-GEM +newGEM = ihuman; +newGEM.genes = [newGEM.genes; rxnsToAdd.grRules]; +newGEM.rxnGeneMat(:, end+1) = 0; + +% reformat subsystem +if ~iscell(rxnsToAdd.subSystems{1}) + rxnsToAdd.subSystems = cellfun(@(s) {{s}}, rxnsToAdd.subSystems); +end +% add new reaction +newGEM = addRxns(newGEM, rxnsToAdd, 3); + +% add reaction annotation +rxnAssoc = importTsvFile('../../model/reactions.tsv'); +annoNames = fieldnames(rxnAssoc); +for i=1:length(annoNames) + if ismember(annoNames{i}, fieldnames(rxnsToAdd)) + rxnAssoc.(annoNames{i}) = [rxnAssoc.(annoNames{i}); rxnsToAdd.(annoNames{i})]; + elseif isequal(annoNames{i},'spontaneous') + rxnAssoc.(annoNames{i}) = [rxnAssoc.(annoNames{i}); 0]; + else + rxnAssoc.(annoNames{i}) = [rxnAssoc.(annoNames{i}); {''}]; + end +end + +% update yaml model and reaction association file +exportYaml(newGEM, '../../model/Human-GEM.yml'); +exportTsvFile(rxnAssoc,'../../model/reactions.tsv'); + diff --git a/data/modelCuration/addRxnACOD1_20221102.tsv b/data/modelCuration/addRxnACOD1_20221102.tsv new file mode 100644 index 00000000..675491ab --- /dev/null +++ b/data/modelCuration/addRxnACOD1_20221102.tsv @@ -0,0 +1,2 @@ +rxns equations ub lb eccodes subSystems grRules rxnReferences rxnConfidenceScores rxnKEGGID rxnMetaCycID rxnMetaNetXID rxnRheaID rxnRheaMasterID +"MAR13087" "cis-aconitate[m] + H+[m] => CO2[m] + itaconate[m]" 1000 0 "4.1.1.6" "C5-branched dibasic acid metabolism" "ENSG00000102794" "PMID:23610393;PMID:31548418" 4 "R02243" "ACONITATE-DECARBOXYLASE-RXN" "MNXR107402" "RHEA:15254" "RHEA:15253" \ No newline at end of file