Merge branch 'develop' into develop

code/addBoundaryMets.m

@@ -48,10 +48,10 @@
 % add a boundary compartment to the model if it does not yet exist
 if ~ismember('boundary',lower(model.compNames))
     model.compNames(end+1) = {'Boundary'};
-    if ismember('x',model.comps)
-        error('Consider renaming the "x" compartment, or modify this function to use another letter.');
+    if ismember('b',model.comps)
+        error('Consider renaming the "b" compartment, or modify this function to use another letter.');
     else
-        model.comps(end+1) = {'x'};
+        model.comps(end+1) = {'b'};
     end
 end
 
@@ -94,17 +94,17 @@
 % metabolite, with the compartment replaced.
 [~,ref_met_ind] = ismember(add_bound_mets,model.metNames);
 if all(endsWith(model.mets,']'))
-    add_bound_met_IDs = regexprep(model.mets(ref_met_ind),'\[.\]$','[x]');
+    add_bound_met_IDs = regexprep(model.mets(ref_met_ind),'\[.\]$','[b]');
 elseif any(endsWith(model.mets,']'))
     error('All metabolite IDs must use the same format for describing the compartment.');
 else
-    add_bound_met_IDs = regexprep(model.mets(ref_met_ind),'.$','x');
+    add_bound_met_IDs = regexprep(model.mets(ref_met_ind),'.$','b');
 end
 
 % add new boundary mets to the model
 metsToAdd.mets = add_bound_met_IDs;
 metsToAdd.metNames = add_bound_mets;
-metsToAdd.compartments = 'x';
+metsToAdd.compartments = 'b';
 metsToAdd.unconstrained = ones(size(add_bound_mets));
 new_model = addMets(model,metsToAdd);
 

code/io/importYaml.m

@@ -280,9 +280,6 @@
 [~, metIdx] = ismember(model.mets, newMets);
 model.S = S(metIdx, :);
 
-% Now the `unconstrained` field is abandoned in HumanGEM
-%model.unconstrained = double(endsWith(model.mets, 'x'));
-
 if ~silentMode
     fprintf(' Done!\n');
 end

code/modelCuration/changeCompAbbrevs.m

@@ -0,0 +1,44 @@
+% script to change model compartment abbreviations
+%   Extracellular:  s -> e
+%   Boundary:       x -> b
+%   Peroxisome:     p -> x
+
+% specify model name
+modelname = 'Human-GEM';
+
+% load model and other data files
+model = importYaml(fullfile('..', '..', 'model', [modelname '.yml']));
+metAssoc = importTsvFile(fullfile('..', '..', 'model', 'metabolites.tsv'));
+metAssoc_table = struct2table(metAssoc);
+metsDep = importTsvFile(fullfile('..', '..', 'data', 'deprecatedIdentifiers', 'deprecatedMetabolites.tsv'));
+metsDep_table = struct2table(metsDep);
+
+% update comps field
+model.comps(ismember(model.compNames, 'Extracellular')) = {'e'};
+model.comps(ismember(model.compNames, 'Peroxisome')) = {'x'};
+
+% update mets field
+model.mets = regexprep(model.mets, 's$', 'e');
+model.mets = regexprep(model.mets, 'p$', 'x');
+
+% copy deprecated metabolites to deprecated metabolite table
+dep_ind = endsWith(metAssoc.mets, {'s', 'p'});
+metsDep_table = [metsDep_table; metAssoc_table(dep_ind, :)];
+
+% update the metabolite compartments in the annotation file
+metAssoc.mets = regexprep(metAssoc.mets, 's$', 'e');
+metAssoc.mets = regexprep(metAssoc.mets, 'p$', 'x');
+
+% export the new model and files
+exportYaml(model, fullfile('..', '..', 'model', [modelname '.yml']));
+exportTsvFile(metAssoc, fullfile('..', '..', 'model', 'metabolites.tsv'));
+exportTsvFile(metsDep_table, fullfile('..', '..', 'data', 'deprecatedIdentifiers', 'deprecatedMetabolites.tsv'));
+
+
+% other tasks to do in addition to running this script:
+%   - replace all instances of [s], [x], [p], with [e], [b], [x],
+%     respectively, in all metabolic task files
+%   - replace the use of "x" with "b" in the addBoundaryMets function
+
+
+

data/deprecatedIdentifiers/deprecatedReactions.tsv

@@ -9,3 +9,8 @@ rxns	rxnKEGGID	rxnBiGGID	rxnEHMNID	rxnHepatoNET1ID	rxnREACTOMEID	rxnRecon3DID	rx
 "MAR09577"	"R00162"	""	""	""	""	"HMR_9577"	"MNXR106414"	"HMR_9577"	"RCR14832"	""	0	""	""	"HMR_9577"
 "MAR09578"	"R00164"	""	""	""	""	"HMR_9578"	"MNXR106415"	"HMR_9578"	"RCR14833"	""	0	""	""	"HMR_9578"
 "MAR09579"	"R03632"	""	""	""	""	"HMR_9579"	"MNXR108312"	"HMR_9579"	"RCR11010"	""	0	""	""	"HMR_9579"
+"MAR07262"	""	"DOLICHOL_Lter"	""	""	""	""	"MNXR97703"	"HMR_7262"	"RCR20987"	""	0	""	""	"HMR_7262"
+"MAR11269"	""	""	""	""	""	"ELAIDCRNtr"	""	""	""	""	0	""	""	"ELAIDCRNtr"
+"MAR11275"	""	""	""	""	""	"PCRNtr"	""	""	""	""	0	""	""	"PCRNtr"
+"MAR11273"	""	""	""	""	""	"LNLCCRNtr"	""	""	""	""	0	""	""	"LNLCCRNtr"
+"MAR08639"	""	""	""	""	""	"HMR_8639"	""	"HMR_8639"	"RCR21087"	""	0	""	""	"HMR_8639"

data/metabolicTasks/metabolicTasks_CellfieConsensus.txt

@@ -23,8 +23,8 @@
 				ADP[c]	2	2	ATP[c]	2	2								
 				Pi[c]	2	2	NADH[c]	2	2								
 							H2O[c]	2	2								
-	7	Reactive oxygen species detoxification (H2O2 to H2O)		H2O2[s]	2	2	H2O[s]	2	2								
-							O2[s]	1	1								
+	7	Reactive oxygen species detoxification (H2O2 to H2O)		H2O2[e]	2	2	H2O[e]	2	2								
+							O2[e]	1	1								
 	8	Presence of the thioredoxin system through the thioredoxin reductase activity		H+[c]	1	1	NADP+[c]	1	1								
 				NADPH[c]	1	1	thioredoxin[c]	1	1								
 				oxidized thioredoxin[c]	1	1											
@@ -135,16 +135,16 @@
 	21	3'-Phospho-5'-adenylyl sulfate synthesis		sulfate[c]	1	1	PAPS[c]	1	1								
 				ATP[c]	2	2	ADP[c]	1	1								
 				H+[c]	1	1	PPi[c]	1	1								
-	22	Degradation of adenine to urate		adenine[c]	1	1	urate[s]	1	1								
+	22	Degradation of adenine to urate		adenine[c]	1	1	urate[e]	1	1								
 				H2O[c]	2	2	NH4+[c]	1	1								
-				H+[c]	1	1	H2O2[s]	2	2								
-				O2[s]	2	2	ribose-1-phosphate[c]	1	1								
+				H+[c]	1	1	H2O2[e]	2	2								
+				O2[e]	2	2	ribose-1-phosphate[c]	1	1								
 				PRPP[c]	1	1	PPi[c]	1	1								
-				H2O[s]	2	2											
-	23	Degradation of guanine to urate		guanine[c]	1	1	urate[s]	1	1								
-				H2O[s]	1	1	NH4+[c]	1	1								
-				H2O[c]	1	1	NADH[s]	1	1								
-				NAD+[s]	1	1	H+[s]	0	1								
+				H2O[e]	2	2											
+	23	Degradation of guanine to urate		guanine[c]	1	1	urate[e]	1	1								
+				H2O[e]	1	1	NH4+[c]	1	1								
+				H2O[c]	1	1	NADH[e]	1	1								
+				NAD+[e]	1	1	H+[e]	0	1								
 	24	Degradation of cytosine		cytosine[c]	1	1	beta-alanine[c]	1	1								
 				H2O[c]	3	3	CO2[c]	1	1								
 				H+[c]	3	3	NH4+[c]	2	2								
@@ -456,7 +456,7 @@
 							H+[c]	2	2								
 							2-oxobutyrate[c]	1	1								
 							NH4+[c]	1	1								
-	82	Cysteine degradation		cysteine[s]	1	1	H2O[c]										
+	82	Cysteine degradation		cysteine[e]	1	1	H2O[c]										
 				O2[c]			ATP[c]										
 				Pi[c]			CO2[c]										
 				ADP[c]			NH4+[c]										
@@ -583,12 +583,12 @@
 				AKG[m]	1	1	H2O[m]	1	1								
 				H+[m]	1	1	NADP+[m]	1	1								
 				NADPH[m]	1	1											
-	107	Conversion of lysine to L-2-Aminoadipate		lysine[s]	1	1	L-2-aminoadipate[c]	1	1								
-				H2O[s]	2	2	H2O2[s]	2	2								
-				O2[s]	2	2	NH4+[s]	1	1								
-				NADH[s]	1	1	H+[c]	1	1								
-				NAD+[c]	1	1	NAD+[s]	1	1								
-				H+[s]	0	1	NADH[c]	1	1								
+	107	Conversion of lysine to L-2-Aminoadipate		lysine[e]	1	1	L-2-aminoadipate[c]	1	1								
+				H2O[e]	2	2	H2O2[e]	2	2								
+				O2[e]	2	2	NH4+[e]	1	1								
+				NADH[e]	1	1	H+[c]	1	1								
+				NAD+[c]	1	1	NAD+[e]	1	1								
+				H+[e]	0	1	NADH[c]	1	1								
 	108	Methionine degradation		methionine[c]	1	1	cysteine[c]	1	1								
 				serine[c]	1	2	propanoyl-CoA[c]	1	1								
 				ATP[c]	2	2	ATP[m]	1	1								
@@ -996,70 +996,70 @@
 				CoA[c]	1	1	PPi[c]	4	4								
 				HCO3-[c]	7	7	H+[m]	8									
 				H+[c]	8												
-	167	Taurochenodeoxycholate synthesis		cholesterol[r]	1	1	taurochenodeoxycholate[s]	1	1								
-				taurine[s]	1	1	propanoyl-CoA[s]	1	1								
-				CoA[s]	1	1	AMP[s]	1	1								
-				ATP[s]	1	1	PPi[s]	1	1								
+	167	Taurochenodeoxycholate synthesis		cholesterol[r]	1	1	taurochenodeoxycholate[e]	1	1								
+				taurine[e]	1	1	propanoyl-CoA[e]	1	1								
+				CoA[e]	1	1	AMP[e]	1	1								
+				ATP[e]	1	1	PPi[e]	1	1								
 				O2[r]	1	1	NADP+[m]	3	3								
-				O2[s]	1	1	NADP+[r]	1	1								
+				O2[e]	1	1	NADP+[r]	1	1								
 				O2[m]	3	3	NADH[r]	1	1								
 				NAD+[r]	1	1	NADP+[c]	1	1								
 				H+[c]	2	2	NAD+[c]	1	1								
 				H+[m]	2	2	H2O[m]	3	3								
 				NADH[c]	1	1	H2O[r]	1	1								
-				NADPH[c]	1	1	H2O[s]	1	1								
+				NADPH[c]	1	1	H2O[e]	1	1								
 				NADPH[m]	3	3											
 				NADPH[r]	1	1											
-	168	Glycochenodeoxycholate synthesis		cholesterol[r]	1	1	glycochenodeoxycholate[s]	1	1								
-				glycine[s]	1	1	propanoyl-CoA[s]	1	1								
-				ATP[s]	1	1	AMP[s]	1	1								
-				FADH2[s]	1	1	PPi[s]	1	1								
-				CoA[s]	1	1	FAD[s]	1	1								
+	168	Glycochenodeoxycholate synthesis		cholesterol[r]	1	1	glycochenodeoxycholate[e]	1	1								
+				glycine[e]	1	1	propanoyl-CoA[e]	1	1								
+				ATP[e]	1	1	AMP[e]	1	1								
+				FADH2[e]	1	1	PPi[e]	1	1								
+				CoA[e]	1	1	FAD[e]	1	1								
 				NADPH[r]	1	1	H2O[r]	1	1								
-				NADPH[c]	1	1	H2O[s]	3	3								
+				NADPH[c]	1	1	H2O[e]	3	3								
 				NADPH[m]	3	3	H2O[m]	5	5								
-				NADPH[s]	1	1	NADP+[r]	1	1								
-				NAD+[r]	1	1	NADP+[s]	1	1								
+				NADPH[e]	1	1	NADP+[r]	1	1								
+				NAD+[r]	1	1	NADP+[e]	1	1								
 				NADH[c]	1	1	NADP+[c]	1	1								
 				H+[m]	2	2	NADP+[m]	3	3								
-				H+[s]	1	1	NADH[r]	1	1								
+				H+[e]	1	1	NADH[r]	1	1								
 				H+[c]	2	2	NAD+[c]	1	1								
 				O2[m]	3	3											
 				O2[r]	1	1											
-				O2[s]	2	2											
-	169	tauro-cholate synthesis		cholesterol[r]	1	1	taurocholate[s]	1	1								
-				taurine[s]	1	1	propanoyl-CoA[s]	1	1								
-				CoA[s]	1	1	AMP[s]	1	1								
-				ATP[s]	1	1	PPi[s]	1	1								
-				FADH2[s]	1	1	FAD[s]	1	1								
+				O2[e]	2	2											
+	169	tauro-cholate synthesis		cholesterol[r]	1	1	taurocholate[e]	1	1								
+				taurine[e]	1	1	propanoyl-CoA[e]	1	1								
+				CoA[e]	1	1	AMP[e]	1	1								
+				ATP[e]	1	1	PPi[e]	1	1								
+				FADH2[e]	1	1	FAD[e]	1	1								
 				NADPH[r]	1	4	NADPH[m]	1	2								
-				NADPH[s]	1	1	NADP+[r]	1	1								
+				NADPH[e]	1	1	NADP+[r]	1	1								
 				NADPH[m]	0	2	NADP+[c]	1	2								
 				NADPH[c]	0	1	NADP+[m]	2	2								
-				NADH[c]	1	1	NADP+[s]	1	1								
+				NADH[c]	1	1	NADP+[e]	1	1								
 				NADP+[m]	0	1	NAD+[c]	1	1								
 				O2[r]	2	2	H2O[m]	2	2								
 				O2[m]	2	2	H2O[r]	2	2								
-				O2[s]	2	2	H2O[s]	3	3								
+				O2[e]	2	2	H2O[e]	3	3								
 				H+[r]	1	1											
 				H+[c]	2	2											
-				H+[s]	1	1											
-	170	glyco-cholate synthesis		cholesterol[r]	1	1	glycocholate[s]	1	1								
-				glycine[s]	1	1	propanoyl-CoA[s]	1	1								
-				ATP[s]	1	1	AMP[s]	1	1								
-				FADH2[s]	1	1	PPi[s]	1	1								
-				CoA[s]	1	1	FAD[s]	1	1								
+				H+[e]	1	1											
+	170	glyco-cholate synthesis		cholesterol[r]	1	1	glycocholate[e]	1	1								
+				glycine[e]	1	1	propanoyl-CoA[e]	1	1								
+				ATP[e]	1	1	AMP[e]	1	1								
+				FADH2[e]	1	1	PPi[e]	1	1								
+				CoA[e]	1	1	FAD[e]	1	1								
 				NADPH[r]	1	1	NADP+[m]	1	1								
-				NADPH[s]	1	1	NADP+[r]	1	1								
+				NADPH[e]	1	1	NADP+[r]	1	1								
 				NADPH[m]	1	1	NADP+[c]	1	1								
-				NADPH[c]	1	1	NADP+[s]	1	1								
+				NADPH[c]	1	1	NADP+[e]	1	1								
 				NADH[c]	1	1	NAD+[c]	1	1								
 				H+[r]	1	1	H2O[m]	2	2								
-				H+[s]	1	1	H2O[s]	3	3								
+				H+[e]	1	1	H2O[e]	3	3								
 				H+[c]	2	2	H2O[r]	2	2								
 				O2[r]	2	2											
 				O2[m]	2	2											
-				O2[s]	2	2											
+				O2[e]	2	2											
 	171	Synthesis of thromboxane from arachidonate		arachidonate[r]	1	1	thromboxane A2[r]	1	1								
 				O2[r]	2	2	H2O[r]	1	1								
 				NADPH[r]	1	1	NADP+[r]	1	1