diff --git a/met4j-toolbox/src/main/java/fr/inrae/toulouse/metexplore/met4j_toolbox/attributes/ExtractPathways.java b/met4j-toolbox/src/main/java/fr/inrae/toulouse/metexplore/met4j_toolbox/attributes/ExtractPathways.java
new file mode 100644
index 0000000000000000000000000000000000000000..fdac9589509d4e8b93c263aed3c0e0b96269673d
--- /dev/null
+++ b/met4j-toolbox/src/main/java/fr/inrae/toulouse/metexplore/met4j_toolbox/attributes/ExtractPathways.java
@@ -0,0 +1,99 @@
+package fr.inrae.toulouse.metexplore.met4j_toolbox.attributes;
+
+import fr.inrae.toulouse.metexplore.met4j_core.biodata.*;
+import fr.inrae.toulouse.metexplore.met4j_core.biodata.collection.BioCollection;
+import fr.inrae.toulouse.metexplore.met4j_io.jsbml.reader.JsbmlReader;
+import fr.inrae.toulouse.metexplore.met4j_io.jsbml.reader.Met4jSbmlReaderException;
+import fr.inrae.toulouse.metexplore.met4j_io.jsbml.writer.JsbmlWriter;
+import fr.inrae.toulouse.metexplore.met4j_io.jsbml.writer.Met4jSbmlWriterException;
+import fr.inrae.toulouse.metexplore.met4j_toolbox.generic.AbstractMet4jApplication;
+import org.kohsuke.args4j.Option;
+
+import java.io.IOException;
+
+public class ExtractPathways extends AbstractMet4jApplication {
+
+ @Option(name = "-i", usage = "input SBML file", required = true)
+ public String inputPath = null;
+
+ @Option(name = "-o", usage = "output SBML file", required = true)
+ public String outputPath = null;
+
+ @Option(name = "-p", usage = "pathway identifiers, separated by \"+\" sign if more than one", required = true)
+ public String pathwayId = null;
+
+ public static void main(String[] args) throws IOException, Met4jSbmlReaderException, Met4jSbmlWriterException {
+
+ ExtractPathways app = new ExtractPathways();
+
+ app.parseArguments(args);
+
+ app.run();
+
+ }
+
+
+ public void run() throws IOException, Met4jSbmlReaderException, Met4jSbmlWriterException {
+ //read smbl
+ JsbmlReader reader = new JsbmlReader(this.inputPath);
+ BioNetwork network = reader.read();
+ System.out.println("Number of reactions in original network: "+network.getReactionsView().size());
+ System.out.println("Number of species in original network: "+network.getMetabolitesView().size());
+ System.out.println("Number of genes in original network: "+network.getGenesView().size());
+
+
+ //get all reactions & metabolites
+ BioCollection<BioReaction> reactions = new BioCollection<>(network.getReactionsView());
+ BioCollection<BioMetabolite> metabolites = new BioCollection<>(network.getMetabolitesView());
+ BioCollection<BioGene> genes = new BioCollection<>(network.getGenesView());
+
+ //get pathways
+ BioCollection<BioPathway> pathways = new BioCollection<>();
+ for(String id : pathwayId.split("\\+")){
+ BioPathway pathway = network.getPathwaysView().get(id);
+ if(pathway!=null){
+ pathways.add(pathway);
+ System.out.println("Number of reactions in pathway "+pathway.getName()+" ("+id+"): "+network.getReactionsFromPathways(pathway).size());
+ System.out.println("Number of species in pathway "+pathway.getName()+" ("+id+"): "+network.getMetabolitesFromPathway(pathway).size());
+ System.out.println("Number of genes in pathway "+pathway.getName()+" ("+id+"): "+network.getGenesFromPathways(pathway).size());
+ }else{
+ System.out.println("Error: Pathway "+id+" not found in network, please check sbml file.");
+ }
+ }
+
+ //remove pathway's reactions and metabolites from list
+ BioCollection<BioReaction> pathwaysReactions = network.getReactionsFromPathways(pathways);
+ reactions.removeAll(pathwaysReactions);
+ metabolites.removeAll(network.getMetabolitesFromReactions(pathwaysReactions));
+ genes.removeAll(network.getGenesFromReactions(pathwaysReactions));
+
+ //remove remaining reactions
+ network.removeOnCascade(reactions);
+ network.removeOnCascade(metabolites);
+ network.removeOnCascade(genes);
+ System.out.println("Number of reactions in network: "+network.getReactionsView().size());
+ System.out.println("Number of species in network: "+network.getMetabolitesView().size());
+ System.out.println("Number of genes in network: "+network.getGenesView().size());
+
+ //export network
+ JsbmlWriter w = new JsbmlWriter(outputPath, network);
+ w.write();
+ System.err.println("network exported.");
+ return;
+ }
+
+ @Override
+ public String getLabel() {
+ return this.getClass().getSimpleName();
+ }
+
+ @Override
+ public String getLongDescription() {
+ return "\"Extract pathway(s) from GSMN: From a SBML file, Create a sub-network SBML file including only a selection of pathways";
+ }
+
+ @Override
+ public String getShortDescription() {
+ return "Extract pathway(s) from GSMN";
+ }
+}
diff --git a/met4j-toolbox/src/main/java/fr/inrae/toulouse/metexplore/met4j_toolbox/attributes/ExtractSbmlAnnot.java b/met4j-toolbox/src/main/java/fr/inrae/toulouse/metexplore/met4j_toolbox/attributes/ExtractSbmlAnnot.java
new file mode 100644
index 0000000000000000000000000000000000000000..34a659f176949b4e6c7d7a10784dc0cf425e443f
--- /dev/null
+++ b/met4j-toolbox/src/main/java/fr/inrae/toulouse/metexplore/met4j_toolbox/attributes/ExtractSbmlAnnot.java
@@ -0,0 +1,120 @@
+package fr.inrae.toulouse.metexplore.met4j_toolbox.attributes;
+
+import fr.inrae.toulouse.metexplore.met4j_core.biodata.BioEntity;
+import fr.inrae.toulouse.metexplore.met4j_core.biodata.BioNetwork;
+import fr.inrae.toulouse.metexplore.met4j_core.biodata.BioRef;
+import fr.inrae.toulouse.metexplore.met4j_core.biodata.collection.BioCollection;
+import fr.inrae.toulouse.metexplore.met4j_io.jsbml.reader.JsbmlReader;
+import fr.inrae.toulouse.metexplore.met4j_io.jsbml.reader.Met4jSbmlReaderException;
+import fr.inrae.toulouse.metexplore.met4j_toolbox.generic.AbstractMet4jApplication;
+import org.kohsuke.args4j.Option;
+
+import java.io.FileWriter;
+import java.io.IOException;
+import java.util.*;
+
+public class ExtractSbmlAnnot extends AbstractMet4jApplication {
+
+ @Option(name = "-i", usage = "input SBML file", required = true)
+ public String inputPath = null;
+
+ @Option(name = "-o", usage = "output file path", required = true)
+ public String outputPath = null;
+
+ enum entity { METABOLITE,REACTION,GENE}
+
+ @Option(name="-export", usage = "the type of entity to extract annotation, either metabolite, reaction, or gene", required = true)
+ public entity export;
+
+ @Option(name="-db", usage = "name of the referenced database to export annotations from, as listed in notes or identifiers.org base uri", required = true)
+ public String db;
+
+ @Option(name="-uniq", usage = "keep only one identifier if multiple are referenced for the same entity", required = false)
+ public Boolean uniq = false;
+
+ @Option(name="-skip", usage = "Skip entities without the selected annotations, by default output them with NA value", required = false)
+ public Boolean skip = false;
+
+ public String sep = "\t";
+
+
+ public static void main(String[] args) throws IOException, Met4jSbmlReaderException {
+
+ ExtractSbmlAnnot app = new ExtractSbmlAnnot();
+
+ app.parseArguments(args);
+
+ app.run();
+
+ }
+
+ private void run() throws IOException, Met4jSbmlReaderException {
+ //open file
+ FileWriter fw = new FileWriter(outputPath);
+
+ //read smbl
+ JsbmlReader reader = new JsbmlReader(this.inputPath);
+ BioNetwork network = reader.read();
+
+ BioCollection<? extends BioEntity> entities = new BioCollection<>();
+ if(export==entity.METABOLITE){
+ entities=network.getMetabolitesView();
+ }else if(export==entity.REACTION){
+ entities=network.getReactionsView();
+ }else if(export==entity.GENE){
+ entities=network.getGenesView();
+ }
+
+ //write header
+ fw.write(export.name()+sep+db.toUpperCase()+"\n");
+
+ //export annotations
+ //keep track of successful export
+ int i = 0;
+ for(BioEntity e : entities){
+
+ Set<BioRef> refSet = e.getRefs(db);
+ if(refSet!=null){
+ i+=1;
+ if(uniq)refSet= new HashSet<BioRef>(Arrays.asList(refSet.iterator().next()));
+ for(BioRef ref : refSet){
+ StringBuffer sb = new StringBuffer();
+ sb.append(e.getId());
+ sb.append(sep);
+ sb.append(ref.getId());
+ sb.append("\n");
+ fw.write(sb.toString());
+ }
+ }else if(!skip){
+ StringBuffer sb = new StringBuffer();
+ sb.append(e.getId());
+ sb.append(sep);
+ sb.append("NA\n");
+ fw.write(sb.toString());
+ }
+
+ }
+ fw.close();
+ System.out.println("annotations found for "+i+"/"+entities.size()+" "+export.name().toLowerCase()+((i>1)?"s":""));
+
+ }
+
+ @Override
+ public String getLabel() {
+ return this.getClass().getSimpleName();
+ }
+
+ @Override
+ public String getLongDescription() {
+ return "Extract databases' references from SBML annotations or notes. " +
+ "The references are exported as a tabulated file with one column with the SBML compound, " +
+ "reaction or gene identifiers, and one column with the corresponding database identifier." +
+ "The name of the targeted database need to be provided under the same form than the one used " +
+ "in the notes field or the identifiers.org uri";
+ }
+
+ @Override
+ public String getShortDescription() {
+ return "Extract databases' references from SBML annotations or notes.";
+ }
+}