Feat/SBOterms

ComplementaryScripts/missingFields/addSBOterms.m

@@ -0,0 +1,61 @@
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+% model = addSBOterms(model)
+%
+% Benjamín J. Sánchez
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
+function model = addSBOterms(model)
+
+%Get RAVEN model for matching names & compartments
+model_r = ravenCobraWrapper(model);
+
+%Add SBO terms for mets:
+model.metSBOTerms = cell(size(model.mets));
+for i = 1:length(model.mets)
+    metName = model_r.metNames{i};
+    if ismember(metName,{'biomass','DNA','RNA','protein','carbohydrate','lipid'}) ...
+            || endsWith(metName,' backbone') || endsWith(metName,' chain')
+        model.metSBOTerms{i} = 'SBO:0000649';     %Biomass
+    else
+        model.metSBOTerms{i} = 'SBO:0000247';     %Simple chemical
+    end
+end
+
+%Add SBO terms for rxns:
+model.rxnSBOTerms = cell(size(model.rxns));
+for i = 1:length(model.rxns)
+    rxnName   = model_r.rxnNames{i};
+    metNames  = model_r.metNames(model.S(:,i) ~= 0);
+    metComps  = model_r.metComps(model.S(:,i) ~= 0);
+    metStoich = model_r.S(model.S(:,i) ~= 0,i);
+
+    if length(metNames) == 1
+        if strcmp(model_r.comps{metComps},'e')
+            model.rxnSBOTerms{i} = 'SBO:0000627';	%Exchange rxn
+
+        elseif metStoich > 0
+            model.rxnSBOTerms{i} = 'SBO:0000628';	%Demand rxn
+        else
+            model.rxnSBOTerms{i} = 'SBO:0000632';	%Sink rxn
+        end
+
+    elseif strcmp(rxnName,'biomass pseudoreaction')
+        model.rxnSBOTerms{i} = 'SBO:0000629';       %Biomass pseudo-rxn
+
+    elseif strcmp(rxnName,'non-growth associated maintenance reaction')
+        model.rxnSBOTerms{i} = 'SBO:0000630';       %ATP maintenance
+
+    elseif contains(rxnName,'pseudoreaction') || contains(rxnName,'SLIME rxn')
+        model.rxnSBOTerms{i} = 'SBO:0000395';       %Encapsulating process
+
+    elseif length(unique(metComps)) > 1 && length(unique(metNames)) < length(metNames)
+        model.rxnSBOTerms{i} = 'SBO:0000655';       %Transport rxn
+
+    else
+        model.rxnSBOTerms{i} = 'SBO:0000176';       %Metabolic rxn
+    end
+end
+
+end
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

ComplementaryScripts/saveYeastModel.m

@@ -20,6 +20,11 @@ function saveYeastModel(model,upDATE)
 scriptFolder = fileparts(which(mfilename));
 currentDir = cd(scriptFolder);
 
+%Update SBO terms in model:
+cd missingFields
+model = addSBOterms(model);
+cd ..
+
 %Check if model is a valid SBML structure:
 writeCbModel(model,'sbml','tempModel.xml');
 [~,errors] = TranslateSBML('tempModel.xml');