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

@@ -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');
+

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"