diff --git a/.classpath b/.classpath
index 7e29bb7..f830608 100644
--- a/.classpath
+++ b/.classpath
@@ -21,10 +21,10 @@
 			<attribute name="maven.pomderived" value="true"/>
 		</attributes>
 	</classpathentry>
-	<classpathentry kind="lib" path="target/Libraries/align.jar"/>
-	<classpathentry kind="lib" path="target/Libraries/alignsvc.jar"/>
-	<classpathentry kind="lib" path="target/Libraries/ontowrap.jar"/>
-	<classpathentry kind="lib" path="target/Libraries/procalign.jar"/>
-	<classpathentry kind="lib" path="target/Libraries/spmf.jar"/>
+	<classpathentry kind="lib" path="lib/align.jar"/>
+	<classpathentry kind="lib" path="lib/alignsvc.jar"/>
+	<classpathentry kind="lib" path="lib/ontowrap.jar"/>
+	<classpathentry kind="lib" path="lib/procalign.jar"/>
+	<classpathentry kind="lib" path="lib/spmf.jar"/>
 	<classpathentry kind="output" path="target/classes"/>
 </classpath>
diff --git a/.gitignore b/.gitignore
index c71ea97..9eeaefc 100644
--- a/.gitignore
+++ b/.gitignore
@@ -1 +1,2 @@
 /.apt_generated/
+target/
diff --git a/README.md b/README.md
index aa1ffde..02b3df6 100644
--- a/README.md
+++ b/README.md
@@ -10,9 +10,28 @@ An automatic data linking tool developed by [DOREMUS][3].
 3. **Indexing and Instance matching**: We apply standard NLP techniques to index the instance profiles by using a term frequency vector model. The threshold value of Legato applies to the similarity computed at this stage. Low thresholds are recommended to ensure high recall (default 0.2). 
 4. **Link repairing**: A post-processing step to repair erroneous links generated in the matching step by clustering highly similar instances together and applying a key-identification adn ranking algorthims.
 
-<b> How to run <i> Legato </i> </b>
+<b> How to build <i> Legato </i> </b>
 ========
-For running <b> <i> Legato </i> </b> through the GUI, please run the "main.java" class in the "legato" package. Then, select the source, the target and a reference alignement (if availble). Then, you can choose between two treatment's modes:
+### Using Maven
+The first time you build this project, run the following command to generate Maven dependencies:
+```
+mvn initialize
+```
+Then, everytime you want to build:
+```
+mvn clean package
+```
+To run:
+```
+mvn exec:java
+```
+
+### Manually
+For running <b> <i> Legato </i> </b> through the GUI, please run the "main.java" class in the "legato" package.
+
+<b> How to use <i> Legato </i> </b>
+========
+Select the source, the target and a reference alignement (if availble). Then, you can choose between two treatment's modes:
 - Automatic allows to filter resources by fixing only the classes to compare.
 - Manual allows to filter resources by classe and comparate by a set of selected properties.
 The field "threshold value" allows to define Legato's threshold in the Instance matching step. Legato will consider only resources with a similarity higher than the threshold value.
diff --git a/target/Libraries/align.jar b/lib/align.jar
old mode 100644
new mode 100755
similarity index 100%
rename from target/Libraries/align.jar
rename to lib/align.jar
diff --git a/target/Libraries/alignsvc.jar b/lib/alignsvc.jar
old mode 100644
new mode 100755
similarity index 100%
rename from target/Libraries/alignsvc.jar
rename to lib/alignsvc.jar
diff --git a/target/Libraries/ontowrap.jar b/lib/ontowrap.jar
old mode 100644
new mode 100755
similarity index 100%
rename from target/Libraries/ontowrap.jar
rename to lib/ontowrap.jar
diff --git a/target/Libraries/procalign.jar b/lib/procalign.jar
old mode 100644
new mode 100755
similarity index 100%
rename from target/Libraries/procalign.jar
rename to lib/procalign.jar
diff --git a/target/Libraries/spmf.jar b/lib/spmf.jar
old mode 100644
new mode 100755
similarity index 100%
rename from target/Libraries/spmf.jar
rename to lib/spmf.jar
diff --git a/pom.xml b/pom.xml
index 3431e3c..47adc7b 100644
--- a/pom.xml
+++ b/pom.xml
@@ -18,6 +18,134 @@
           <target>1.8</target>
         </configuration>
       </plugin>
+      <plugin>
+        <groupId>org.codehaus.mojo</groupId>
+        <artifactId>exec-maven-plugin</artifactId>
+        <version>1.6.0</version>
+        <executions>
+          <execution>
+          <goals>
+            <goal>java</goal>
+          </goals>
+          </execution>
+        </executions>
+        <configuration>
+          <mainClass>legato.Main</mainClass>
+        </configuration>
+      </plugin>
+      <plugin>
+        <groupId>org.apache.maven.plugins</groupId>
+        <artifactId>maven-shade-plugin</artifactId>
+        <version>3.1.1</version>
+        <executions>
+          <execution>
+            <phase>package</phase>
+            <goals>
+              <goal>shade</goal>
+            </goals>
+          </execution>
+        </executions>
+      </plugin>
+      <plugin>
+        <groupId>org.apache.maven.plugins</groupId>
+        <artifactId>maven-jar-plugin</artifactId>
+        <version>2.4</version>
+        <configuration>
+          <archive>
+            <manifest>
+              <mainClass>legato.Main</mainClass>
+              <addClasspath>true</addClasspath>
+              <classpathPrefix>libs/</classpathPrefix>
+            </manifest>
+          </archive>
+        </configuration>
+      </plugin>
+      <plugin>
+        <groupId>org.apache.maven.plugins</groupId>
+        <artifactId>maven-install-plugin</artifactId>
+        <version>2.5.2</version>
+        <executions>
+          <!-- SPMF -->
+          <execution>
+            <id>install-spmf</id>
+            <phase>initialize</phase>
+            <goals>
+              <goal>install-file</goal>
+            </goals>
+            <configuration>
+              <file>lib/spmf.jar</file>
+              <groupId>ca.pfv.spmf</groupId>
+              <artifactId>SPMF</artifactId>
+              <version>1.0</version>
+              <packaging>jar</packaging>
+            </configuration>
+          </execution>
+
+          <!-- align -->
+          <execution>
+            <id>install-align</id>
+            <phase>initialize</phase>
+            <goals>
+              <goal>install-file</goal>
+            </goals>
+            <configuration>
+              <file>lib/align.jar</file>
+              <groupId>org.semanticweb.owl</groupId>
+              <artifactId>align</artifactId>
+              <version>1.0</version>
+              <packaging>jar</packaging>
+            </configuration>
+          </execution>
+
+          <!-- alignsvc -->
+          <execution>
+            <id>install-alignsvc</id>
+            <phase>initialize</phase>
+            <goals>
+              <goal>install-file</goal>
+            </goals>
+            <configuration>
+              <file>lib/alignsvc.jar</file>
+              <groupId>org.semanticweb.owl</groupId>
+              <artifactId>alignsvc</artifactId>
+              <version>1.0</version>
+              <packaging>jar</packaging>
+            </configuration>
+          </execution>
+
+          <!-- ontowrap -->
+          <execution>
+            <id>install-ontowrap</id>
+            <phase>initialize</phase>
+            <goals>
+              <goal>install-file</goal>
+            </goals>
+            <configuration>
+              <file>lib/ontowrap.jar</file>
+              <groupId>org.semanticweb.owl</groupId>
+              <artifactId>ontowrap</artifactId>
+              <version>1.0</version>
+              <packaging>jar</packaging>
+            </configuration>
+          </execution>
+
+          <!-- proc-align -->
+          <execution>
+            <id>install-proc-align</id>
+            <phase>initialize</phase>
+            <goals>
+              <goal>install-file</goal>
+            </goals>
+            <configuration>
+              <file>lib/procalign.jar</file>
+              <groupId>org.semanticweb.owl</groupId>
+              <artifactId>proc-align</artifactId>
+              <version>1.0</version>
+              <packaging>jar</packaging>
+            </configuration>
+          </execution>
+        </executions>
+      </plugin>
     </plugins>
   </build>
   
@@ -119,6 +247,41 @@
 	</dependency>
 	
 
+	<!-- lib/spmf.jar -->
+	<dependency>
+	<groupId>ca.pfv.spmf</groupId>
+	<artifactId>SPMF</artifactId>
+	<version>1.0</version>
+	</dependency>
+
+	<!-- lib/align.jar -->
+	<dependency>
+	<groupId>org.semanticweb.owl</groupId>
+	<artifactId>align</artifactId>
+	<version>1.0</version>
+	</dependency>
+
+	<!-- lib/alignsvc.jar -->
+	<dependency>
+	<groupId>org.semanticweb.owl</groupId>
+	<artifactId>alignsvc</artifactId>
+	<version>1.0</version>
+	</dependency>
+
+	<!-- lib/ontowrap.jar -->
+	<dependency>
+	<groupId>org.semanticweb.owl</groupId>
+	<artifactId>ontowrap</artifactId>
+	<version>1.0</version>
+	</dependency>
+
+	<!-- lib/procalign.jar -->
+	<dependency>
+	<groupId>org.semanticweb.owl</groupId>
+	<artifactId>proc-align</artifactId>
+	<version>1.0</version>
+	</dependency>
+
   </dependencies>
 
 </project>
\ No newline at end of file
diff --git a/src/legato/indexer/VectorGenerator.java b/src/legato/indexer/VectorGenerator.java
index cf8d6aa..32f64d5 100644
--- a/src/legato/indexer/VectorGenerator.java
+++ b/src/legato/indexer/VectorGenerator.java
@@ -42,7 +42,7 @@ public DocVector[] GetDocumentVectors() throws IOException {
         for (int docId = 0; docId < totalNoOfDocumentInIndex; docId++) {
             Terms vector = indexReader.getTermVector(docId, LEGATO.getInstance().FIELD_CONTENT);
             TermsEnum termsEnum = null;
-            //Verification integrité de vector
+            //Verification integrité de vector
             try
             {
             	termsEnum = vector.iterator(termsEnum);
diff --git a/target/Libraries/pom.xml b/target/Libraries/pom.xml
deleted file mode 100644
index 3431e3c..0000000
--- a/target/Libraries/pom.xml
+++ /dev/null
@@ -1,124 +0,0 @@
-<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
-  
-  <modelVersion>4.0.0</modelVersion>
-  <groupId>org.doremus.legato</groupId>
-  <artifactId>legato</artifactId>
-  <version>0.0.1-SNAPSHOT</version>
-  <name>Legato</name>
-  <description>Disambiguating and Linking Heterogeneous Entities Across RDF Graphs</description>
-  
-  <build>
-    <sourceDirectory>src</sourceDirectory>
-    <plugins>
-      <plugin>
-        <artifactId>maven-compiler-plugin</artifactId>
-        <version>3.5.1</version>
-        <configuration>
-          <source>1.8</source>
-          <target>1.8</target>
-        </configuration>
-      </plugin>
-    </plugins>
-  </build>
-  
-  <dependencies>
-    <!-- https://mvnrepository.com/artifact/org.apache.jena/jena -->
-	<dependency>
-    	<groupId>org.apache.jena</groupId>
-    	<artifactId>jena</artifactId>
-    	<version>3.0.0</version>
-    	<type>pom</type>
-	</dependency>
-	
-	<!-- https://mvnrepository.com/artifact/org.apache.commons/commons-lang3 -->
-	<dependency>
-    	<groupId>org.apache.commons</groupId>
-    	<artifactId>commons-lang3</artifactId>
-    	<version>3.3.2</version>
-	</dependency>
-	
-	
-	<!-- https://mvnrepository.com/artifact/org.apache.lucene/lucene-core -->
-	<dependency>
-    	<groupId>org.apache.lucene</groupId>
-    	<artifactId>lucene-core</artifactId>
-    	<version>4.10.2</version>
-	</dependency>
-	
-	<!-- https://mvnrepository.com/artifact/org.apache.lucene/lucene-analyzers-common -->
-	<dependency>
-    	<groupId>org.apache.lucene</groupId>
-    	<artifactId>lucene-analyzers-common</artifactId>
-    	<version>4.10.2</version>
-	</dependency>
-	
-	<!-- https://mvnrepository.com/artifact/org.apache.commons/commons-math3 -->
-	<dependency>
-    	<groupId>org.apache.commons</groupId>
-    	<artifactId>commons-math3</artifactId>
-    	<version>3.6.1</version>
-	</dependency>
-	
-	<!-- https://mvnrepository.com/artifact/org.apache.commons/commons-math -->
-	<dependency>
-    	<groupId>org.apache.commons</groupId>
-	    <artifactId>commons-math</artifactId>
-    	<version>2.0</version>
-	</dependency>
-	
-	<!-- https://mvnrepository.com/artifact/commons-io/commons-io -->
-	<dependency>
-    	<groupId>commons-io</groupId>
-    	<artifactId>commons-io</artifactId>
-    	<version>2.4</version>
-	</dependency>
-	
-	<!-- https://mvnrepository.com/artifact/com.hermit-reasoner/org.semanticweb.hermit -->
-	<dependency>
-    	<groupId>com.hermit-reasoner</groupId>
-    	<artifactId>org.semanticweb.hermit</artifactId>
-    	<version>1.3.8.1</version>
-	</dependency>
-	
-	<!-- https://mvnrepository.com/artifact/org.apache.jena/jena-arq -->
-	<dependency>
-    	<groupId>org.apache.jena</groupId>
-    	<artifactId>jena-arq</artifactId>
-    	<version>3.0.0</version>
-	</dependency>
-	
-	
-	<!-- https://mvnrepository.com/artifact/net.sourceforge.owlapi/owlapi-distribution -->
-	<dependency>
-    	<groupId>net.sourceforge.owlapi</groupId>
-    	<artifactId>owlapi-distribution</artifactId>
-    	<version>5.0.2</version>
-	</dependency>
-	
-	
-	<!-- https://mvnrepository.com/artifact/junit/junit -->
-	<dependency>
-    	<groupId>junit</groupId>
-    	<artifactId>junit</artifactId>
-    	<version>4.12</version>
-    	<scope>test</scope>
-	</dependency>
-	
-	<!-- https://mvnrepository.com/artifact/com.google.code.gson/gson -->
-	<dependency>
-    	<groupId>com.google.code.gson</groupId>
-    	<artifactId>gson</artifactId>
-    	<version>2.2.2</version>
-	</dependency>
-	
-	<!-- https://mvnrepository.com/artifact/commons-lang/commons-lang -->
-	<dependency>
-    	<groupId>commons-lang</groupId>
-    	<artifactId>commons-lang</artifactId>
-    	<version>2.6</version>
-	</dependency>
-	
-
-  </dependencies>
-
-</project>
\ No newline at end of file
diff --git a/target/classes/.gitignore b/target/classes/.gitignore
deleted file mode 100644
index 7b04817..0000000
--- a/target/classes/.gitignore
+++ /dev/null
@@ -1 +0,0 @@
-/legato/
diff --git a/target/classes/legato/LEGATO.class b/target/classes/legato/LEGATO.class
deleted file mode 100644
index 7798ae8..0000000
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diff --git a/target/classes/legato/Main.class b/target/classes/legato/Main.class
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diff --git a/target/classes/legato/cluster/Cluster.class b/target/classes/legato/cluster/Cluster.class
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diff --git a/target/classes/legato/cluster/ClusterList.class b/target/classes/legato/cluster/ClusterList.class
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diff --git a/target/classes/legato/cluster/Clustering.class b/target/classes/legato/cluster/Clustering.class
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diff --git a/target/classes/legato/cluster/DocVec.class b/target/classes/legato/cluster/DocVec.class
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diff --git a/target/legato-0.0.1-SNAPSHOT.jar b/target/legato-0.0.1-SNAPSHOT.jar
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diff --git a/target/maven-archiver/pom.properties b/target/maven-archiver/pom.properties
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--- a/target/maven-archiver/pom.properties
+++ /dev/null
@@ -1,5 +0,0 @@
-#Generated by Maven
-#Sun Nov 05 00:03:36 CET 2017
-version=0.0.1-SNAPSHOT
-groupId=org.doremus.legato
-artifactId=legato
diff --git a/target/maven-status/maven-compiler-plugin/compile/default-compile/createdFiles.lst b/target/maven-status/maven-compiler-plugin/compile/default-compile/createdFiles.lst
deleted file mode 100644
index 05167eb..0000000
--- a/target/maven-status/maven-compiler-plugin/compile/default-compile/createdFiles.lst
+++ /dev/null
@@ -1,57 +0,0 @@
-legato\gui\GUI$6.class
-legato\cluster\Vecteur.class
-legato\indexer\IndexOpener.class
-legato\indexer\VectorGenerator.class
-legato\gui\DatasetFileChooser$1.class
-legato\document\CBDBuilder.class
-legato\gui\GUI$13.class
-legato\indexer\DocVector.class
-legato\cluster\ClusterList.class
-legato\gui\GUI$3.class
-legato\match\MapList.class
-legato\rdf\PathManager$Path.class
-legato\measures\CosineSimilarity.class
-legato\rdf\PropList.class
-legato\rdf\Prop.class
-legato\keys\Sakey.class
-legato\A.class
-legato\utils\PropertyHandler.class
-legato\cluster\Clustering.class
-legato\gui\GUI$12.class
-legato\rdf\ModelManager.class
-legato\document\DocumentBuilder.class
-legato\rdf\PathManager.class
-legato\gui\GUI$4.class
-legato\gui\GUI$7.class
-legato\utils\A.class
-legato\indexer\Indexer.class
-legato\cluster\Cluster.class
-legato\utils\ValueComparator.class
-legato\gui\GUI$11.class
-legato\keys\def\KeyList.class
-legato\gui\GUI$1.class
-legato\cluster\DocVec.class
-legato\LEGATO.class
-legato\match\Align.class
-legato\keys\KeysClassifier.class
-legato\match\Matchifier.class
-legato\gui\GUI.class
-legato\document\FileManager.class
-legato\match\Map.class
-legato\gui\DatasetFileChooser.class
-legato\gui\GUI$8.class
-legato\Test.class
-legato\gui\GUI$10.class
-legato\cluster\HierarchicalClustering.class
-legato\gui\GUI$5.class
-legato\indexer\AllTerms.class
-legato\utils\Stemmer.class
-legato\keys\def\Key.class
-legato\gui\GUI$2.class
-legato\gui\GUI$9.class
-legato\keys\SilkConfig.class
-legato\utils\StopWords.class
-legato\keys\SupportMergedKeys.class
-legato\keys\SILK.class
-legato\Main.class
-legato\gui\GUI$14.class
diff --git a/target/maven-status/maven-compiler-plugin/compile/default-compile/inputFiles.lst b/target/maven-status/maven-compiler-plugin/compile/default-compile/inputFiles.lst
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--- a/target/maven-status/maven-compiler-plugin/compile/default-compile/inputFiles.lst
+++ /dev/null
@@ -1,41 +0,0 @@
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-C:\eclipse\workspace\legato\src\legato\gui\DatasetFileChooser.java
-C:\eclipse\workspace\legato\src\legato\match\MapList.java
-C:\eclipse\workspace\legato\src\legato\indexer\Indexer.java
-C:\eclipse\workspace\legato\src\legato\rdf\Prop.java
-C:\eclipse\workspace\legato\src\legato\keys\SupportMergedKeys.java
-C:\eclipse\workspace\legato\src\legato\rdf\PropList.java
-C:\eclipse\workspace\legato\src\legato\cluster\HierarchicalClustering.java
-C:\eclipse\workspace\legato\src\legato\utils\PropertyHandler.java
-C:\eclipse\workspace\legato\src\legato\cluster\DocVec.java
-C:\eclipse\workspace\legato\src\legato\match\Matchifier.java
-C:\eclipse\workspace\legato\src\legato\cluster\Clustering.java
-C:\eclipse\workspace\legato\src\legato\rdf\PathManager.java
-C:\eclipse\workspace\legato\src\legato\LEGATO.java
-C:\eclipse\workspace\legato\src\legato\match\Align.java
-C:\eclipse\workspace\legato\src\legato\document\DocumentBuilder.java
-C:\eclipse\workspace\legato\src\legato\Main.java
-C:\eclipse\workspace\legato\src\legato\indexer\DocVector.java
-C:\eclipse\workspace\legato\src\legato\indexer\IndexOpener.java
-C:\eclipse\workspace\legato\src\legato\keys\def\KeyList.java
-C:\eclipse\workspace\legato\src\legato\keys\SILK.java
-C:\eclipse\workspace\legato\src\legato\keys\Sakey.java
-C:\eclipse\workspace\legato\src\legato\rdf\ModelManager.java
-C:\eclipse\workspace\legato\src\legato\Test.java
-C:\eclipse\workspace\legato\src\legato\indexer\AllTerms.java
-C:\eclipse\workspace\legato\src\legato\measures\CosineSimilarity.java
-C:\eclipse\workspace\legato\src\legato\utils\StopWords.java
-C:\eclipse\workspace\legato\src\legato\utils\ValueComparator.java
-C:\eclipse\workspace\legato\src\legato\cluster\Cluster.java
-C:\eclipse\workspace\legato\src\legato\document\CBDBuilder.java
-C:\eclipse\workspace\legato\src\legato\keys\def\Key.java
-C:\eclipse\workspace\legato\src\legato\utils\Stemmer.java
-C:\eclipse\workspace\legato\src\legato\gui\GUI.java
-C:\eclipse\workspace\legato\src\legato\utils\A.java
-C:\eclipse\workspace\legato\src\legato\indexer\VectorGenerator.java
-C:\eclipse\workspace\legato\src\legato\A.java
-C:\eclipse\workspace\legato\src\legato\keys\KeysClassifier.java
-C:\eclipse\workspace\legato\src\legato\cluster\ClusterList.java
-C:\eclipse\workspace\legato\src\legato\match\Map.java
-C:\eclipse\workspace\legato\src\legato\cluster\Vecteur.java
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