diff --git a/annotation/src/test/java/lcsb/mapviewer/annotation/services/ModelAnnotatorTest.java b/annotation/src/test/java/lcsb/mapviewer/annotation/services/ModelAnnotatorTest.java
index bcfae071542dd5ca67ede482dff9b623d2de0c7d..bba1c52d6fadac7fd0fdf58f326ec4f7b962be1a 100644
--- a/annotation/src/test/java/lcsb/mapviewer/annotation/services/ModelAnnotatorTest.java
+++ b/annotation/src/test/java/lcsb/mapviewer/annotation/services/ModelAnnotatorTest.java
@@ -29,7 +29,6 @@ import lcsb.mapviewer.annotation.services.annotators.AnnotatorException;
 import lcsb.mapviewer.annotation.services.annotators.ElementAnnotator;
 import lcsb.mapviewer.annotation.services.annotators.ReconAnnotator;
 import lcsb.mapviewer.common.IProgressUpdater;
-import lcsb.mapviewer.converter.model.celldesigner.structure.Protein;
 import lcsb.mapviewer.model.map.AnnotatedObject;
 import lcsb.mapviewer.model.map.MiriamData;
 import lcsb.mapviewer.model.map.MiriamRelationType;
diff --git a/console/src/main/java/lcsb/mapviewer/run/ConsoleConverter.java b/console/src/main/java/lcsb/mapviewer/run/ConsoleConverter.java
index bb4a7bea76be4dc73f5a3cbdbdedcec05235e3b5..5aa503bf510522f90d4b5497c9a0643d3637fc99 100644
--- a/console/src/main/java/lcsb/mapviewer/run/ConsoleConverter.java
+++ b/console/src/main/java/lcsb/mapviewer/run/ConsoleConverter.java
@@ -20,7 +20,6 @@ import lcsb.mapviewer.common.exception.InvalidArgumentException;
 import lcsb.mapviewer.common.exception.InvalidStateException;
 import lcsb.mapviewer.converter.InvalidInputDataExecption;
 import lcsb.mapviewer.converter.model.celldesigner.CellDesignerXmlParser;
-import lcsb.mapviewer.converter.model.celldesigner.structure.Element;
 import lcsb.mapviewer.model.graphics.PolylineData;
 import lcsb.mapviewer.model.map.InconsistentModelException;
 import lcsb.mapviewer.model.map.MiriamData;
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/AntisenseRna.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/AntisenseRna.java
index dbe7dc37c591b33bb17686a7c8a3922019b623bf..d1aa4bfb898338751812a0a097861fe6eaf3e4db 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/AntisenseRna.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/AntisenseRna.java
@@ -3,15 +3,7 @@ package lcsb.mapviewer.converter.model.celldesigner.structure;
 import java.util.ArrayList;
 import java.util.List;
 
-import javax.persistence.DiscriminatorValue;
-import javax.persistence.Entity;
-import javax.persistence.OneToMany;
-
 import org.apache.log4j.Logger;
-import org.hibernate.annotations.Cascade;
-import org.hibernate.annotations.CascadeType;
-import org.hibernate.annotations.LazyCollection;
-import org.hibernate.annotations.LazyCollectionOption;
 
 import lcsb.mapviewer.common.exception.NotImplementedException;
 import lcsb.mapviewer.model.map.layout.alias.AntisenseRnaAlias;
@@ -22,8 +14,6 @@ import lcsb.mapviewer.model.map.layout.alias.AntisenseRnaAlias;
  * @author Piotr Gawron
  * 
  */
-@Entity
-@DiscriminatorValue("Antisense RNA")
 public class AntisenseRna extends Species<AntisenseRnaAlias> {
 
 	/**
@@ -40,9 +30,6 @@ public class AntisenseRna extends Species<AntisenseRnaAlias> {
 	/**
 	 * List of antisense rna regions (some rna sequences) in this object.
 	 */
-	@Cascade({ CascadeType.ALL })
-	@OneToMany(mappedBy = "species")
-	@LazyCollection(LazyCollectionOption.FALSE)
 	private List<AntisenseRnaRegion> regions					= new ArrayList<AntisenseRnaRegion>();
 
 	/**
@@ -51,7 +38,7 @@ public class AntisenseRna extends Species<AntisenseRnaAlias> {
 	 * @param species
 	 *          parent species from which we want to copy data
 	 */
-	public AntisenseRna(Species species) {
+	public AntisenseRna(Species<?> species) {
 		super(species);
 		if (species instanceof AntisenseRna) {
 			AntisenseRna asRna = (AntisenseRna) species;
@@ -104,7 +91,7 @@ public class AntisenseRna extends Species<AntisenseRnaAlias> {
 	}
 
 	@Override
-	public void update(Species sp) {
+	public void update(Species<?> sp) {
 		super.update(sp);
 		if (sp instanceof AntisenseRna) {
 			AntisenseRna rna = (AntisenseRna) sp;
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/AntisenseRnaRegion.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/AntisenseRnaRegion.java
index 8966d674256e615fcee50c189a6f96326bf291b4..8ec3bb9181e15d8ca6ce55615dea847b74392812 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/AntisenseRnaRegion.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/AntisenseRnaRegion.java
@@ -2,43 +2,29 @@ package lcsb.mapviewer.converter.model.celldesigner.structure;
 
 import java.io.Serializable;
 
-import javax.persistence.Column;
-import javax.persistence.Entity;
-import javax.persistence.FetchType;
-import javax.persistence.GeneratedValue;
-import javax.persistence.GenerationType;
-import javax.persistence.Id;
-import javax.persistence.JoinColumn;
-import javax.persistence.ManyToOne;
-import javax.persistence.Table;
-
 import org.apache.log4j.Logger;
-import org.hibernate.annotations.Cascade;
-import org.hibernate.annotations.CascadeType;
 
 import lcsb.mapviewer.common.exception.InvalidArgumentException;
 import lcsb.mapviewer.common.exception.NotImplementedException;
 import lcsb.mapviewer.model.map.layout.alias.AntisenseRnaRegionAlias;
-import lcsb.mapviewer.model.map.layout.alias.ModificationState;
 import lcsb.mapviewer.model.map.layout.alias.AntisenseRnaRegionAlias.AntisenseRnaRegionType;
+import lcsb.mapviewer.model.map.layout.alias.ModificationState;
 
 /**
  * This structure contains information about antisense rna region (rna fragment
  * of interest) for a specific
- * {@link lcsb.mapviewer.converter.model.celldesigner.structure.AntisenseRna AntisenseRna}.
+ * {@link lcsb.mapviewer.converter.model.celldesigner.structure.AntisenseRna
+ * AntisenseRna}.
  * 
  * @author Piotr Gawron
  * 
  */
-@Entity
-@Table(name = "antisense_rna_region_table")
-@org.hibernate.annotations.GenericGenerator(name = "test-increment-strategy", strategy = "increment")
 public class AntisenseRnaRegion implements Serializable {
 
 	/**
 	 * 
 	 */
-	private static final long serialVersionUID = 1L;
+	private static final long			 serialVersionUID			= 1L;
 
 	/**
 	 * Default size of the object (in graphical representation).
@@ -54,21 +40,16 @@ public class AntisenseRnaRegion implements Serializable {
 	/**
 	 * Unique identifier in the database.
 	 */
-	@Id
-	@GeneratedValue(strategy = GenerationType.IDENTITY)
-	@Column(name = "iddb", unique = true, nullable = false)
 	private int										 id;
 
 	/**
 	 * String identifier of the element. Unique in the model.
 	 */
-	@Column(name = "idantisensernaregion")
 	private String								 idAntisenseRnaRegion	= "";
 
 	/**
 	 * Name of the region.
 	 */
-	@Column(name = "name")
 	private String								 name									= "";
 
 	/**
@@ -76,7 +57,6 @@ public class AntisenseRnaRegion implements Serializable {
 	 * 
 	 * @see ModificationState
 	 */
-	@Column(name = "state")
 	private ModificationState			 state								= null;
 
 	/**
@@ -87,28 +67,22 @@ public class AntisenseRnaRegion implements Serializable {
 	 * <li>Modification site.</li>
 	 * </ul>
 	 */
-	@Column(name = "type")
 	private AntisenseRnaRegionType type;
 
 	/**
 	 * Size of the region in the graphic representation.
 	 */
-	@Column(name = "size")
 	private double								 size									= DEFAULT_SIZE;
 
 	/**
 	 * Position on the species in graphic representation.
 	 */
-	@Column(name = "pos")
 	private Double								 pos;
 
 	/**
 	 * Defines a species where the region belongs to.
 	 */
-	@Cascade({ CascadeType.ALL })
-	@ManyToOne(fetch = FetchType.LAZY)
-	@JoinColumn(name = "idSpeciesDb")
-	private Species								 species;
+	private AntisenseRna					 species;
 
 	/**
 	 * Default constructor.
@@ -311,7 +285,7 @@ public class AntisenseRnaRegion implements Serializable {
 	 * @return the species
 	 * @see #species
 	 */
-	public Species getSpecies() {
+	public AntisenseRna getSpecies() {
 		return species;
 	}
 
@@ -320,7 +294,7 @@ public class AntisenseRnaRegion implements Serializable {
 	 *          the species to set
 	 * @see #species
 	 */
-	public void setSpecies(Species species) {
+	public void setSpecies(AntisenseRna species) {
 		this.species = species;
 	}
 
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/Chemical.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/Chemical.java
index 0a910c01ac2dafdf6f8953151f95bd4064ee5576..200e0d5882eca33cafc4db75d9e3731b2b09d21b 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/Chemical.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/Chemical.java
@@ -1,9 +1,5 @@
 package lcsb.mapviewer.converter.model.celldesigner.structure;
 
-import javax.persistence.Column;
-import javax.persistence.DiscriminatorValue;
-import javax.persistence.Entity;
-
 import lcsb.mapviewer.model.map.layout.alias.ChemicalAlias;
 
 /**
@@ -12,8 +8,6 @@ import lcsb.mapviewer.model.map.layout.alias.ChemicalAlias;
  * @author Piotr Gawron
  * 
  */
-@Entity
-@DiscriminatorValue("Chemical")
 public abstract class Chemical<T extends ChemicalAlias> extends Species<T> {
 
 	/**
@@ -26,7 +20,6 @@ public abstract class Chemical<T extends ChemicalAlias> extends Species<T> {
 	 * "http://en.wikipedia.org/wiki/Simplified_molecular-input_line-entry_system"
 	 * >Smiles</a> parameter for the chemical.
 	 */
-	@Column(name = "smiles", columnDefinition = "TEXT")
 	private String						smiles;
 
 	/**
@@ -34,7 +27,6 @@ public abstract class Chemical<T extends ChemicalAlias> extends Species<T> {
 	 * InChI</a> parameter for the chemical.
 	 */
 
-	@Column(name = "inchi", columnDefinition = "TEXT")
 	private String						inChI;
 
 	/**
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/Compartment.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/Compartment.java
index 28f3d50deea49eb9e3ef9508441dfb0e88a7ef53..bd710e3e2200ff64be3b52cfb918ab1f44c25436 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/Compartment.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/Compartment.java
@@ -3,11 +3,6 @@ package lcsb.mapviewer.converter.model.celldesigner.structure;
 import java.util.HashSet;
 import java.util.Set;
 
-import javax.persistence.Column;
-import javax.persistence.DiscriminatorValue;
-import javax.persistence.Entity;
-import javax.persistence.OneToMany;
-
 import org.apache.log4j.Logger;
 
 import lcsb.mapviewer.common.exception.NotImplementedException;
@@ -19,8 +14,6 @@ import lcsb.mapviewer.model.map.layout.alias.CompartmentAlias;
  * @author Piotr Gawron
  * 
  */
-@Entity
-@DiscriminatorValue("Compartment")
 public class Compartment extends Element<CompartmentAlias> implements Comparable<Compartment> {
 
 	/**
@@ -37,14 +30,12 @@ public class Compartment extends Element<CompartmentAlias> implements Comparable
 	/**
 	 * Identifier of the compartment. Unique in the model
 	 */
-	@Column(name = "compartmentId")
 	private String						compartmentId		 = "";
 
 	/**
 	 * List of agregated elements.
 	 */
-	@OneToMany(mappedBy = "parent")
-	private Set<Element<?>>			elements				 = new HashSet<>();
+	private Set<Element<?>>		elements				 = new HashSet<>();
 
 	/**
 	 * Default constructor with identifier given as a parameter.
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/ComplexSpecies.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/ComplexSpecies.java
index 387fa80916305f9d17c12a1cf5eacae27c6269ef..2da11f92155642f55a1d34f51422474195f9eb5b 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/ComplexSpecies.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/ComplexSpecies.java
@@ -3,11 +3,6 @@ package lcsb.mapviewer.converter.model.celldesigner.structure;
 import java.util.HashSet;
 import java.util.Set;
 
-import javax.persistence.Column;
-import javax.persistence.DiscriminatorValue;
-import javax.persistence.Entity;
-import javax.persistence.OneToMany;
-
 import org.apache.log4j.Logger;
 
 import lcsb.mapviewer.common.exception.InvalidArgumentException;
@@ -20,8 +15,6 @@ import lcsb.mapviewer.model.map.layout.alias.ComplexAlias;
  * @author Piotr Gawron
  * 
  */
-@Entity
-@DiscriminatorValue("COMPLEX_SPECIES")
 public class ComplexSpecies extends Species<ComplexAlias> {
 
 	/**
@@ -37,13 +30,11 @@ public class ComplexSpecies extends Species<ComplexAlias> {
 	/**
 	 * Elements that exists in this complex.
 	 */
-	@OneToMany(mappedBy = "complex")
 	private Set<Element<?>>		elements				 = new HashSet<>();
 
 	/**
 	 * State of the complex species.
 	 */
-	@Column(name = "structuralState")
 	private String						structuralState	 = null;
 
 	/**
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/Degraded.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/Degraded.java
index 3f4935ffb20becae46bbc2066f59aaccdede2e69..5d0ef0d4c413e5caa4696608059f1a5f99ea4da0 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/Degraded.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/Degraded.java
@@ -1,8 +1,5 @@
 package lcsb.mapviewer.converter.model.celldesigner.structure;
 
-import javax.persistence.DiscriminatorValue;
-import javax.persistence.Entity;
-
 import lcsb.mapviewer.common.exception.NotImplementedException;
 import lcsb.mapviewer.model.map.layout.alias.DegradedAlias;
 
@@ -12,8 +9,6 @@ import lcsb.mapviewer.model.map.layout.alias.DegradedAlias;
  * @author Piotr Gawron
  * 
  */
-@Entity
-@DiscriminatorValue("Degraded")
 public class Degraded extends Species<DegradedAlias> {
 
 	/**
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/Drug.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/Drug.java
index 977bca234dffb0b1abd82ed713ac1ccee050e48e..b3d86a5568964027298a08575252047a9e9a7647 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/Drug.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/Drug.java
@@ -1,8 +1,5 @@
 package lcsb.mapviewer.converter.model.celldesigner.structure;
 
-import javax.persistence.DiscriminatorValue;
-import javax.persistence.Entity;
-
 import lcsb.mapviewer.common.exception.NotImplementedException;
 import lcsb.mapviewer.model.map.layout.alias.DrugAlias;
 
@@ -12,14 +9,12 @@ import lcsb.mapviewer.model.map.layout.alias.DrugAlias;
  * @author Piotr Gawron
  * 
  */
-@Entity
-@DiscriminatorValue("Drug")
 public class Drug extends Species<DrugAlias> {
 
 	/**
 	 * 
 	 */
-	private static final long	serialVersionUID	= 1L;
+	private static final long serialVersionUID = 1L;
 
 	/**
 	 * Constructor that copies the data from species given in the argument.
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/Element.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/Element.java
index fa575b156c106c697bde55098907962e9d1e6e14..fadaa2a65318e11fbc5dcca5986d4ebac3d50d35 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/Element.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/Element.java
@@ -7,28 +7,7 @@ import java.util.HashSet;
 import java.util.List;
 import java.util.Set;
 
-import javax.persistence.CascadeType;
-import javax.persistence.CollectionTable;
-import javax.persistence.Column;
-import javax.persistence.DiscriminatorColumn;
-import javax.persistence.DiscriminatorType;
-import javax.persistence.DiscriminatorValue;
-import javax.persistence.ElementCollection;
-import javax.persistence.Entity;
-import javax.persistence.FetchType;
-import javax.persistence.GeneratedValue;
-import javax.persistence.GenerationType;
-import javax.persistence.Id;
-import javax.persistence.Inheritance;
-import javax.persistence.InheritanceType;
-import javax.persistence.JoinColumn;
-import javax.persistence.ManyToOne;
-import javax.persistence.Table;
-import javax.persistence.Transient;
-
 import org.apache.log4j.Logger;
-import org.hibernate.annotations.Cascade;
-import org.hibernate.annotations.IndexColumn;
 
 import lcsb.mapviewer.common.exception.InvalidArgumentException;
 import lcsb.mapviewer.model.map.MiriamData;
@@ -43,11 +22,6 @@ import lcsb.mapviewer.model.map.model.ModelData;
  * @author Piotr Gawron
  * 
  */
-@Entity
-@Table(name = "species_table")
-@Inheritance(strategy = InheritanceType.SINGLE_TABLE)
-@DiscriminatorColumn(name = "species_type_db", discriminatorType = DiscriminatorType.STRING)
-@DiscriminatorValue("GENERIC_ELEMENT")
 public abstract class Element<T extends Alias> implements Serializable {
 
 	/**
@@ -65,18 +39,9 @@ public abstract class Element<T extends Alias> implements Serializable {
 	 */
 	private static Logger			logger						 = Logger.getLogger(Element.class);
 
-	/**
-	 * Unique identifier in the database.
-	 */
-	@Id
-	@GeneratedValue(strategy = GenerationType.IDENTITY)
-	@Column(name = "idDb", unique = true, nullable = false)
-	private int								id;
-
 	/**
 	 * Notes describing this element.
 	 */
-	@Column(name = "notes", columnDefinition = "TEXT")
 	private String						notes;
 
 	/**
@@ -102,48 +67,37 @@ public abstract class Element<T extends Alias> implements Serializable {
 	/**
 	 * Short name of the element.
 	 */
-	@Column(name = "name")
 	private String						name							 = "";
 
 	/**
 	 * Lists of all synonyms used for describing this element.
 	 */
-	@ElementCollection(fetch = FetchType.EAGER)
-	@CollectionTable(name = "element_synonyms", joinColumns = @JoinColumn(name = "idDb"))
-	@Column(name = "synonym")
-	@IndexColumn(name = "idx")
-	@Cascade({ org.hibernate.annotations.CascadeType.ALL })
-	private List<String>			synonyms					 = new ArrayList<String>();
+	private List<String>			synonyms					 = new ArrayList<>();
 
 	/**
 	 * List of former symbols used to describe this element.
 	 */
-	@Transient
-	private List<String>			formerSymbols			 = new ArrayList<String>();
+	private List<String>			formerSymbols			 = new ArrayList<>();
 
 	/**
 	 * Where this element lies on.
 	 */
-	@ManyToOne(cascade = { CascadeType.ALL })
 	private Compartment				parent;
 
 	/**
 	 * In which complex this element is located.
 	 */
-	@ManyToOne(cascade = { CascadeType.ALL })
 	private ComplexSpecies		complex;
 
 	/**
 	 * In which model this element is located.
 	 */
-	@ManyToOne(fetch = FetchType.LAZY)
 	private ModelData					model;
 
 	/**
 	 * Set of miriam annotations for this element.
 	 */
-	@Transient
-	private Set<MiriamData>		miriamData				 = new HashSet<MiriamData>();
+	private Set<MiriamData>		miriamData				 = new HashSet<>();
 
 	/**
 	 * Default constructor that initialize the data with the information given in
@@ -234,23 +188,6 @@ public abstract class Element<T extends Alias> implements Serializable {
 	 */
 	public abstract String getStringType();
 
-	/**
-	 * @return the id
-	 * @see #id
-	 */
-	public int getId() {
-		return id;
-	}
-
-	/**
-	 * @param id
-	 *          the id to set
-	 * @see #id
-	 */
-	public void setId(int id) {
-		this.id = id;
-	}
-
 	public String getNotes() {
 		return notes;
 	}
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/Gene.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/Gene.java
index bd9660cdbb6f772bf5628ff4efe0e34312971710..d573c97bc977b676784668dc4cd058a8ecc8dbda 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/Gene.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/Gene.java
@@ -3,15 +3,6 @@ package lcsb.mapviewer.converter.model.celldesigner.structure;
 import java.util.ArrayList;
 import java.util.List;
 
-import javax.persistence.DiscriminatorValue;
-import javax.persistence.Entity;
-import javax.persistence.OneToMany;
-
-import org.hibernate.annotations.Cascade;
-import org.hibernate.annotations.CascadeType;
-import org.hibernate.annotations.LazyCollection;
-import org.hibernate.annotations.LazyCollectionOption;
-
 import lcsb.mapviewer.common.exception.NotImplementedException;
 import lcsb.mapviewer.model.map.layout.alias.GeneAlias;
 
@@ -21,22 +12,17 @@ import lcsb.mapviewer.model.map.layout.alias.GeneAlias;
  * @author Piotr Gawron
  * 
  */
-@Entity
-@DiscriminatorValue("Gene")
 public class Gene extends Species<GeneAlias> {
 
 	/**
 	 * 
 	 */
-	private static final long	serialVersionUID	= 1L;
+	private static final long					serialVersionUID		 = 1L;
 
 	/**
 	 * List of modifications for the Gene.
 	 */
-	@Cascade({ CascadeType.ALL })
-	@OneToMany(mappedBy = "species", orphanRemoval = true)
-	@LazyCollection(LazyCollectionOption.FALSE)
-	private List<ModificationResidue>	modificationResidues	= new ArrayList<ModificationResidue>();
+	private List<ModificationResidue>	modificationResidues = new ArrayList<>();
 
 	/**
 	 * Constructor that initializes gene with the data passed in the argument.
@@ -122,15 +108,14 @@ public class Gene extends Species<GeneAlias> {
 		this.modificationResidues = modificationResidues;
 	}
 
-
 	@Override
 	public GeneAlias createAlias(String aliasId) {
 		GeneAlias result = new GeneAlias(aliasId);
 		super.setAliasFields(result);
-		for (ModificationResidue mr: modificationResidues) {
+		for (ModificationResidue mr : modificationResidues) {
 			result.addModificationResidue(mr.createModificationResidueAlias());
 		}
 		return result;
-		
+
 	}
 }
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/GenericProtein.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/GenericProtein.java
index 7161bcfe86e182ebbd7518a3353f7898173581c7..54ba04d6a5faddeee7f62562a76b17be0a8f1e1b 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/GenericProtein.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/GenericProtein.java
@@ -1,8 +1,5 @@
 package lcsb.mapviewer.converter.model.celldesigner.structure;
 
-import javax.persistence.DiscriminatorValue;
-import javax.persistence.Entity;
-
 import lcsb.mapviewer.common.exception.NotImplementedException;
 import lcsb.mapviewer.model.map.layout.alias.GenericProteinAlias;
 
@@ -12,14 +9,12 @@ import lcsb.mapviewer.model.map.layout.alias.GenericProteinAlias;
  * @author Piotr Gawron
  * 
  */
-@Entity
-@DiscriminatorValue("GENERIC_PROTEIN")
 public class GenericProtein extends Protein<GenericProteinAlias> {
 
 	/**
 	 * 
 	 */
-	private static final long	serialVersionUID	= 1L;
+	private static final long serialVersionUID = 1L;
 
 	/**
 	 * Default constructor.
@@ -31,7 +26,8 @@ public class GenericProtein extends Protein<GenericProteinAlias> {
 	/**
 	 * Constructor that creates a copy of species.
 	 * 
-	 * @param species original species 
+	 * @param species
+	 *          original species
 	 */
 	public GenericProtein(Species<?> species) {
 		super(species);
@@ -53,7 +49,7 @@ public class GenericProtein extends Protein<GenericProteinAlias> {
 	public GenericProteinAlias createAlias(String aliasId) {
 		GenericProteinAlias result = new GenericProteinAlias(aliasId);
 		super.setAliasFields(result);
-		
+
 		return result;
 	}
 
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/Ion.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/Ion.java
index 13198e509dd76d72f50f274c7744423e3bff5d07..7fc1abda1d973f31c874729e5b93ac8c005ec698 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/Ion.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/Ion.java
@@ -1,8 +1,5 @@
 package lcsb.mapviewer.converter.model.celldesigner.structure;
 
-import javax.persistence.DiscriminatorValue;
-import javax.persistence.Entity;
-
 import lcsb.mapviewer.common.exception.NotImplementedException;
 import lcsb.mapviewer.model.map.layout.alias.IonAlias;
 
@@ -12,8 +9,6 @@ import lcsb.mapviewer.model.map.layout.alias.IonAlias;
  * @author Piotr Gawron
  * 
  */
-@Entity
-@DiscriminatorValue("Ion")
 public class Ion extends Chemical<IonAlias> {
 
 	/**
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/IonChannelProtein.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/IonChannelProtein.java
index c0189b97eb366ba4f7a41217b4fe7b21ed4ad97f..9bfe21e7d83a0be86ed83bf1e7025152d81129da 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/IonChannelProtein.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/IonChannelProtein.java
@@ -1,8 +1,5 @@
 package lcsb.mapviewer.converter.model.celldesigner.structure;
 
-import javax.persistence.DiscriminatorValue;
-import javax.persistence.Entity;
-
 import lcsb.mapviewer.common.exception.NotImplementedException;
 import lcsb.mapviewer.model.map.layout.alias.IonChannelProteinAlias;
 
@@ -12,8 +9,6 @@ import lcsb.mapviewer.model.map.layout.alias.IonChannelProteinAlias;
  * @author Piotr Gawron
  * 
  */
-@Entity
-@DiscriminatorValue("ION_CHANNEL_PROTEIN")
 public class IonChannelProtein extends Protein<IonChannelProteinAlias> {
 
 	/**
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/ModificationResidue.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/ModificationResidue.java
index 37e568326991dd797b8a65194afb28cd99aa54ee..6d78eb82d1220ea91312aca54dd9452b7d790eb1 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/ModificationResidue.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/ModificationResidue.java
@@ -2,16 +2,6 @@ package lcsb.mapviewer.converter.model.celldesigner.structure;
 
 import java.io.Serializable;
 
-import javax.persistence.Column;
-import javax.persistence.Entity;
-import javax.persistence.FetchType;
-import javax.persistence.GeneratedValue;
-import javax.persistence.GenerationType;
-import javax.persistence.Id;
-import javax.persistence.JoinColumn;
-import javax.persistence.ManyToOne;
-import javax.persistence.Table;
-
 import org.apache.log4j.Logger;
 
 import lcsb.mapviewer.common.exception.InvalidArgumentException;
@@ -27,9 +17,6 @@ import lcsb.mapviewer.model.map.layout.alias.ModificationState;
  * @author Piotr Gawron
  * 
  */
-@Entity
-@Table(name = "modification_residue_table")
-@org.hibernate.annotations.GenericGenerator(name = "test-increment-strategy", strategy = "increment")
 public class ModificationResidue implements Serializable {
 
 	/**
@@ -43,56 +30,40 @@ public class ModificationResidue implements Serializable {
 	@SuppressWarnings("unused")
 	private static Logger			logger								= Logger.getLogger(ModificationResidue.class.getName());
 
-	/**
-	 * Unique identifier in the database.
-	 */
-	@Id
-	@GeneratedValue(strategy = GenerationType.IDENTITY)
-	@Column(name = "iddb", unique = true, nullable = false)
-	private int								id;
-
 	/**
 	 * Identifier of the modification. Must be unique in single map model.
 	 */
-	@Column(name = "idModificationResidue")
 	private String						idModificationResidue	= "";
 
 	/**
 	 * Name of the modification.
 	 */
-	@Column(name = "name")
 	private String						name									= "";
 
 	/**
 	 * Some strange param in CellDesigner. No idea what is it for.
 	 */
-	@Column(name = "side")
 	private String						side									= "";
 
 	/**
 	 * State in which this modification is.
 	 */
-	@Column(name = "state")
 	private ModificationState	state									= null;
 
 	/**
 	 * Where this modification is located (on which side of the border).
 	 */
-	@Column(name = "angle")
 	private Double						angle									= null;
 
 	/**
 	 * How big is this modification (used only for some types of the
 	 * modification).
 	 */
-	@Column(name = "size")
 	private Double						size									= null;
 
 	/**
 	 * Species to which this modification belong to.
 	 */
-	@ManyToOne(fetch = FetchType.LAZY)
-	@JoinColumn(name = "idSpeciesDb", nullable = false)
 	private Species						species;
 
 	/**
@@ -206,23 +177,6 @@ public class ModificationResidue implements Serializable {
 		}
 	}
 
-	/**
-	 * @return the idModificationResidue
-	 * @see #id
-	 */
-	public int getId() {
-		return id;
-	}
-
-	/**
-	 * @param id
-	 *          the idModificationResidue to set
-	 * @see #id
-	 */
-	public void setId(int id) {
-		this.id = id;
-	}
-
 	/**
 	 * @return the id
 	 * @see #idModificationResidue
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/Phenotype.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/Phenotype.java
index b43dac692f171ffae67dd07b46658351f2d482c1..ddb9639f1c205c70d7a62880c4a3b7eeac790e05 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/Phenotype.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/Phenotype.java
@@ -1,8 +1,5 @@
 package lcsb.mapviewer.converter.model.celldesigner.structure;
 
-import javax.persistence.DiscriminatorValue;
-import javax.persistence.Entity;
-
 import lcsb.mapviewer.common.exception.NotImplementedException;
 import lcsb.mapviewer.model.map.layout.alias.PhenotypeAlias;
 
@@ -12,8 +9,6 @@ import lcsb.mapviewer.model.map.layout.alias.PhenotypeAlias;
  * @author Piotr Gawron
  * 
  */
-@Entity
-@DiscriminatorValue("Phenotype")
 public class Phenotype extends Species<PhenotypeAlias> {
 
 	/**
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/Protein.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/Protein.java
index be2562cff67809e4ccb63d82fc42100953fbe8c4..afecc5eb38941edfb5b9cc72a6cba32b83c7086f 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/Protein.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/Protein.java
@@ -3,16 +3,7 @@ package lcsb.mapviewer.converter.model.celldesigner.structure;
 import java.util.ArrayList;
 import java.util.List;
 
-import javax.persistence.Column;
-import javax.persistence.DiscriminatorValue;
-import javax.persistence.Entity;
-import javax.persistence.OneToMany;
-
 import org.apache.log4j.Logger;
-import org.hibernate.annotations.Cascade;
-import org.hibernate.annotations.CascadeType;
-import org.hibernate.annotations.LazyCollection;
-import org.hibernate.annotations.LazyCollectionOption;
 
 import lcsb.mapviewer.common.exception.NotImplementedException;
 import lcsb.mapviewer.model.map.layout.alias.ProteinAlias;
@@ -23,8 +14,6 @@ import lcsb.mapviewer.model.map.layout.alias.ProteinAlias;
  * @author Piotr Gawron
  * 
  */
-@Entity
-@DiscriminatorValue("Protein")
 public class Protein<T extends ProteinAlias> extends Species<T> {
 	/**
 	 * 
@@ -39,15 +28,11 @@ public class Protein<T extends ProteinAlias> extends Species<T> {
 	/**
 	 * State of the protein.
 	 */
-	@Column(name = "structuralState")
 	private String										structuralState			 = null;
 
 	/**
 	 * List of modifications for the Protein.
 	 */
-	@Cascade({ CascadeType.ALL })
-	@OneToMany(mappedBy = "species", orphanRemoval = true)
-	@LazyCollection(LazyCollectionOption.FALSE)
 	private List<ModificationResidue>	modificationResidues = new ArrayList<ModificationResidue>();
 
 	/**
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/ReceptorProtein.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/ReceptorProtein.java
index 82a4e23eb421ca6a8b6628fa884d6b62c476ae6c..a3cb1b0446c6aa8e25b8ad7641a6cdfd171bcacd 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/ReceptorProtein.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/ReceptorProtein.java
@@ -1,8 +1,5 @@
 package lcsb.mapviewer.converter.model.celldesigner.structure;
 
-import javax.persistence.DiscriminatorValue;
-import javax.persistence.Entity;
-
 import lcsb.mapviewer.common.exception.NotImplementedException;
 import lcsb.mapviewer.model.map.layout.alias.ReceptorProteinAlias;
 
@@ -12,8 +9,6 @@ import lcsb.mapviewer.model.map.layout.alias.ReceptorProteinAlias;
  * @author Piotr Gawron
  * 
  */
-@Entity
-@DiscriminatorValue("RECEPTOR_PROTEIN")
 public class ReceptorProtein extends Protein<ReceptorProteinAlias> {
 
 	/**
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/Rna.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/Rna.java
index e0bdfba4dd42e658c69d955803d78867ebba1bf7..95ad0b3e7f5cd8188f6e08515fb070c97d6b60dd 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/Rna.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/Rna.java
@@ -3,15 +3,7 @@ package lcsb.mapviewer.converter.model.celldesigner.structure;
 import java.util.ArrayList;
 import java.util.List;
 
-import javax.persistence.DiscriminatorValue;
-import javax.persistence.Entity;
-import javax.persistence.OneToMany;
-
 import org.apache.log4j.Logger;
-import org.hibernate.annotations.Cascade;
-import org.hibernate.annotations.CascadeType;
-import org.hibernate.annotations.LazyCollection;
-import org.hibernate.annotations.LazyCollectionOption;
 
 import lcsb.mapviewer.common.exception.NotImplementedException;
 import lcsb.mapviewer.model.map.layout.alias.RnaAlias;
@@ -22,8 +14,6 @@ import lcsb.mapviewer.model.map.layout.alias.RnaAlias;
  * @author Piotr Gawron
  * 
  */
-@Entity
-@DiscriminatorValue("RNA")
 public class Rna extends Species<RnaAlias> {
 
 	/**
@@ -40,10 +30,7 @@ public class Rna extends Species<RnaAlias> {
 	/**
 	 * List of rna regions (some rna sequences) in this object.
 	 */
-	@Cascade({ CascadeType.ALL })
-	@OneToMany(mappedBy = "species", orphanRemoval = true)
-	@LazyCollection(LazyCollectionOption.FALSE)
-	private List<RnaRegion>		regions					 = new ArrayList<RnaRegion>();
+	private List<RnaRegion>		regions					 = new ArrayList<>();
 
 	/**
 	 * Constructor that initializes rna with the data passed in the argument.
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/RnaRegion.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/RnaRegion.java
index 128dcfe834ca73f347f4d46bc67d1b885998a937..7846d84e8cdfed0dcb0d190e3429d60463674a2c 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/RnaRegion.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/RnaRegion.java
@@ -2,16 +2,6 @@ package lcsb.mapviewer.converter.model.celldesigner.structure;
 
 import java.io.Serializable;
 
-import javax.persistence.Column;
-import javax.persistence.Entity;
-import javax.persistence.FetchType;
-import javax.persistence.GeneratedValue;
-import javax.persistence.GenerationType;
-import javax.persistence.Id;
-import javax.persistence.JoinColumn;
-import javax.persistence.ManyToOne;
-import javax.persistence.Table;
-
 import org.apache.log4j.Logger;
 
 import lcsb.mapviewer.common.exception.InvalidArgumentException;
@@ -20,14 +10,12 @@ import lcsb.mapviewer.model.map.layout.alias.RnaRegionAlias;
 
 /**
  * This structure contains information about rna region (rna fragment of
- * interest) for a specific {@link lcsb.mapviewer.converter.model.celldesigner.structure.Rna Rna}.
+ * interest) for a specific
+ * {@link lcsb.mapviewer.converter.model.celldesigner.structure.Rna Rna}.
  * 
  * @author Piotr Gawron
  * 
  */
-@Entity
-@Table(name = "rna_region_table")
-@org.hibernate.annotations.GenericGenerator(name = "test-increment-strategy", strategy = "increment")
 public class RnaRegion implements Serializable {
 
 	/**
@@ -46,20 +34,12 @@ public class RnaRegion implements Serializable {
 	@SuppressWarnings("unused")
 	private static Logger				logger					 = Logger.getLogger(RnaRegion.class.getName());
 
-	/**
-	 * Unique identifier in the database.
-	 */
-	@Id
-	@GeneratedValue(strategy = GenerationType.IDENTITY)
-	@Column(name = "iddb", unique = true, nullable = false)
-	private int									id;
-
 	/**
 	 * Identifier of the region. Unique in the
 	 * {@link lcsb.mapviewer.model.map.model.Model}.
 	 */
-	@Column(name = "idrnaregion")
 	private String							idRnaRegion			 = "";
+
 	/**
 	 * Type of the region in the rna. There are three possible values:
 	 * <ul>
@@ -68,8 +48,6 @@ public class RnaRegion implements Serializable {
 	 * <li>Modification site.</li>
 	 * </ul>
 	 */
-
-	@Column(name = "type")
 	private String							type						 = "";
 
 	/**
@@ -77,33 +55,27 @@ public class RnaRegion implements Serializable {
 	 * 
 	 * @see ModificationState
 	 */
-	@Column(name = "state")
 	private ModificationState		state						 = null;
 
 	/**
 	 * Name of the region.
 	 */
-	@Column(name = "name")
 	private String							name						 = "";
 
 	/**
 	 * Size of the region in the graphic representation.
 	 */
-	@Column(name = "size")
 	private double							size						 = DEFAULT_SIZE;
 
 	/**
 	 * Position on the species in graphic representation.
 	 */
-	@Column(name = "pos")
 	private Double							pos;
 
 	/**
 	 * Defines a species where the region belongs to.
 	 */
-	@ManyToOne(fetch = FetchType.LAZY)
-	@JoinColumn(name = "idSpeciesDb")
-	private Species							species;
+	private Rna									species;
 
 	/**
 	 * Default constructor.
@@ -119,7 +91,6 @@ public class RnaRegion implements Serializable {
 	 *          original {@link RnaRegion}
 	 */
 	public RnaRegion(RnaRegion mr) {
-		this.id = mr.id;
 		this.idRnaRegion = mr.idRnaRegion;
 		this.size = mr.size;
 		setPos(mr.getPos());
@@ -189,23 +160,6 @@ public class RnaRegion implements Serializable {
 
 	}
 
-	/**
-	 * @return the idRnaRegion
-	 * @see #idRnaRegion
-	 */
-	public int getId() {
-		return id;
-	}
-
-	/**
-	 * @param id
-	 *          the idRnaRegion to set
-	 * @see #id
-	 */
-	public void setId(int id) {
-		this.id = id;
-	}
-
 	/**
 	 * @return the id
 	 * @see #id
@@ -312,7 +266,7 @@ public class RnaRegion implements Serializable {
 	 * @return the species
 	 * @see #species
 	 */
-	public Species getSpecies() {
+	public Rna getSpecies() {
 		return species;
 	}
 
@@ -321,7 +275,7 @@ public class RnaRegion implements Serializable {
 	 *          the species to set
 	 * @see #species
 	 */
-	public void setSpecies(Species species) {
+	public void setSpecies(Rna species) {
 		this.species = species;
 	}
 
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/SimpleMolecule.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/SimpleMolecule.java
index 64ca650675f8b6c0a88891a7ce396a2de8d41c2d..75f255eaa83d0e635bf3154599daa3cd75ff5086 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/SimpleMolecule.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/SimpleMolecule.java
@@ -1,8 +1,5 @@
 package lcsb.mapviewer.converter.model.celldesigner.structure;
 
-import javax.persistence.DiscriminatorValue;
-import javax.persistence.Entity;
-
 import org.apache.log4j.Logger;
 
 import lcsb.mapviewer.common.exception.NotImplementedException;
@@ -14,8 +11,6 @@ import lcsb.mapviewer.model.map.layout.alias.SimpleMoleculeAlias;
  * @author Piotr Gawron
  * 
  */
-@Entity
-@DiscriminatorValue("SimpleMolecule")
 public class SimpleMolecule extends Chemical<SimpleMoleculeAlias> {
 
 	/**
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/Species.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/Species.java
index 4a79d01566a3bc0476be5c786e3618fae533dcf7..0066fb92ccf1975bdb40b516dc045ece110186d5 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/Species.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/Species.java
@@ -1,10 +1,5 @@
 package lcsb.mapviewer.converter.model.celldesigner.structure;
 
-import javax.persistence.DiscriminatorValue;
-import javax.persistence.Entity;
-import javax.persistence.EnumType;
-import javax.persistence.Enumerated;
-
 import org.apache.log4j.Logger;
 
 import lcsb.mapviewer.common.exception.InvalidArgumentException;
@@ -19,8 +14,6 @@ import lcsb.mapviewer.model.map.layout.alias.SpeciesAlias;
  * @author Piotr Gawron
  * 
  */
-@Entity
-@DiscriminatorValue("SPECIES")
 public class Species<T extends SpeciesAlias> extends Element<T> {
 	/**
 	 * 
@@ -65,7 +58,6 @@ public class Species<T extends SpeciesAlias> extends Element<T> {
 	/**
 	 * Position on the compartment.
 	 */
-	@Enumerated(EnumType.STRING)
 	private PositionToCompartment	positionToCompartment	= null;
 
 	/**
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/TruncatedProtein.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/TruncatedProtein.java
index 2a1ebc5dfed5950eaf13e867e708d5c80b7cdbae..c05d481c5b849a4a4d12280d748f3181080c991e 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/TruncatedProtein.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/TruncatedProtein.java
@@ -1,8 +1,5 @@
 package lcsb.mapviewer.converter.model.celldesigner.structure;
 
-import javax.persistence.DiscriminatorValue;
-import javax.persistence.Entity;
-
 import lcsb.mapviewer.common.exception.NotImplementedException;
 import lcsb.mapviewer.model.map.layout.alias.TruncatedProteinAlias;
 
@@ -12,8 +9,6 @@ import lcsb.mapviewer.model.map.layout.alias.TruncatedProteinAlias;
  * @author Piotr Gawron
  * 
  */
-@Entity
-@DiscriminatorValue("TRUNCATED_PROTEIN")
 public class TruncatedProtein extends Protein {
 
 	/**
@@ -51,7 +46,7 @@ public class TruncatedProtein extends Protein {
 	public TruncatedProteinAlias createAlias(String aliasId) {
 		TruncatedProteinAlias result = new TruncatedProteinAlias(aliasId);
 		super.setAliasFields(result);
-		
+
 		return result;
 	}
 
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/Unknown.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/Unknown.java
index 1c1d8077a9421dd763c42a8a08afbb7bb79f0e66..4fc711dffd3d185e270dddfb07f82f6bd178ef09 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/Unknown.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/Unknown.java
@@ -1,8 +1,5 @@
 package lcsb.mapviewer.converter.model.celldesigner.structure;
 
-import javax.persistence.DiscriminatorValue;
-import javax.persistence.Entity;
-
 import lcsb.mapviewer.common.exception.NotImplementedException;
 import lcsb.mapviewer.model.map.layout.alias.UnknownAlias;
 
@@ -12,8 +9,6 @@ import lcsb.mapviewer.model.map.layout.alias.UnknownAlias;
  * @author Piotr Gawron
  * 
  */
-@Entity
-@DiscriminatorValue("Unknown")
 public class Unknown extends Species<UnknownAlias> {
 	/**
 	 * 
@@ -52,7 +47,7 @@ public class Unknown extends Species<UnknownAlias> {
 
 	@Override
 	public UnknownAlias createAlias(String aliasId) {
-		UnknownAlias  result = new UnknownAlias(aliasId);
+		UnknownAlias result = new UnknownAlias(aliasId);
 		super.setAliasFields(result);
 		return result;
 	}
diff --git a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/species/ModelMock.java b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/species/ModelMock.java
deleted file mode 100644
index 35b82545c20469ada1255ba63f9534a566b7306f..0000000000000000000000000000000000000000
--- a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/species/ModelMock.java
+++ /dev/null
@@ -1,540 +0,0 @@
-package lcsb.mapviewer.converter.model.celldesigner.species;
-
-import java.util.Calendar;
-import java.util.Collection;
-import java.util.HashMap;
-import java.util.List;
-import java.util.Map;
-import java.util.Set;
-
-import org.apache.log4j.Logger;
-
-import lcsb.mapviewer.common.EventStorageLoggerAppender;
-import lcsb.mapviewer.converter.model.celldesigner.structure.Species;
-import lcsb.mapviewer.model.Project;
-import lcsb.mapviewer.model.map.AnnotatedObject;
-import lcsb.mapviewer.model.map.MiriamData;
-import lcsb.mapviewer.model.map.OverviewImage;
-import lcsb.mapviewer.model.map.graph.DataMiningSet;
-import lcsb.mapviewer.model.map.layout.Layout;
-import lcsb.mapviewer.model.map.layout.alias.Alias;
-import lcsb.mapviewer.model.map.layout.alias.AliasGroup;
-import lcsb.mapviewer.model.map.layout.alias.BlockDiagram;
-import lcsb.mapviewer.model.map.layout.alias.CompartmentAlias;
-import lcsb.mapviewer.model.map.layout.alias.ComplexAlias;
-import lcsb.mapviewer.model.map.layout.alias.SpeciesAlias;
-import lcsb.mapviewer.model.map.layout.graphics.Layer;
-import lcsb.mapviewer.model.map.model.Model;
-import lcsb.mapviewer.model.map.model.ModelData;
-import lcsb.mapviewer.model.map.model.ModelSubmodelConnection;
-import lcsb.mapviewer.model.map.model.SubmodelConnection;
-import lcsb.mapviewer.model.map.reaction.Reaction;
-
-public class ModelMock implements Model {
-	private Logger			 logger	 = Logger.getLogger(SpeciesAlias.class.getName());
-
-	Map<String, Species> species = new HashMap<String, Species>();
-
-	public void addSpecies(Species sp) {
-		species.put(sp.getElementId(), sp);
-	}
-
-	@Override
-	public Double getWidth() {
-		logger.error("Not implemented in mock object");
-		return null;
-	}
-
-	@Override
-	public void setWidth(Double width) {
-		logger.error("Not implemented in mock object");
-	}
-
-	@Override
-	public Double getHeight() {
-		logger.error("Not implemented in mock object");
-		return null;
-	}
-
-	@Override
-	public void setHeight(Double height) {
-		logger.error("Not implemented in mock object");
-	}
-
-	@Override
-	public void setWidth(String nodeAttr) {
-		logger.error("Not implemented in mock object");
-	}
-
-	@Override
-	public void setHeight(String nodeAttr) {
-		logger.error("Not implemented in mock object");
-	}
-
-	@Override
-	public Set<Alias> getAliases() {
-		logger.error("Not implemented in mock object");
-		return null;
-	}
-
-	@Override
-	public SpeciesAlias getAliasByAliasId(String idAlias) {
-		logger.error("Not implemented in mock object");
-		return null;
-	}
-
-	@Override
-	public void addReaction(Reaction reaction) {
-		logger.error("Not implemented in mock object");
-	}
-
-	@Override
-	public Set<Reaction> getReactions() {
-		logger.error("Not implemented in mock object");
-		return null;
-	}
-
-	@Override
-	public CompartmentAlias getCompartmentAliasByCompartmentAliasId(String id) {
-		CompartmentAlias alias = new CompartmentAlias(id);
-		return alias;
-	}
-
-	@Override
-	public List<CompartmentAlias> getCompartmentsAliases() {
-		logger.error("Not implemented in mock object");
-		return null;
-	}
-
-	@Override
-	public void addLayer(Layer layer) {
-		logger.error("Not implemented in mock object");
-
-	}
-
-	@Override
-	public Set<Layer> getLayers() {
-		logger.error("Not implemented in mock object");
-		return null;
-	}
-
-	@Override
-	public void addAliases(List<? extends Alias> aliases) {
-		logger.error("Not implemented in mock object");
-	}
-
-	@Override
-	public void setNotes(String notes) {
-		logger.error("Not implemented in mock object");
-
-	}
-
-	@Override
-	public String getNotes() {
-		logger.error("Not implemented in mock object");
-		return null;
-	}
-
-	@Override
-	public Reaction getReactionByReactionId(String idReaction) {
-		logger.error("Not implemented in mock object");
-		return null;
-	}
-
-	@Override
-	public String getMapVersion() {
-		logger.error("Not implemented in mock object");
-		return null;
-	}
-
-	@Override
-	public void setMapVersion(String version) {
-		logger.error("Not implemented in mock object");
-	}
-
-	@Override
-	public void addLayers(Collection<Layer> parseLayers) {
-		logger.error("Not implemented in mock object");
-
-	}
-
-	@Override
-	public void addAliasGroup(AliasGroup aliasGroup) {
-		logger.error("Not implemented in mock object");
-
-	}
-
-	@Override
-	public void addBlockDiagream(BlockDiagram blockDiagram) {
-		logger.error("Not implemented in mock object");
-	}
-
-	@Override
-	public void setSbgnFormat(boolean sbgnFormat) {
-		logger.error("Not implemented in mock object");
-	}
-
-	@Override
-	public void addCreationWarnings(List<String> warnings) {
-		logger.error("Not implemented in mock object");
-	}
-
-	@Override
-	public List<String> getCreationWarnings() {
-		// TODO Auto-generated method stub
-		return null;
-	}
-
-	@Override
-	public void addCreationWarning(String warning) {
-		// TODO Auto-generated method stub
-
-	}
-
-	@Override
-	public void setNotifyEmail(String notifyEmail) {
-		// TODO Auto-generated method stub
-
-	}
-
-	@Override
-	public String getNotifyEmail() {
-		// TODO Auto-generated method stub
-		return null;
-	}
-
-	@Override
-	public void setIdModel(String idModel) {
-		// TODO Auto-generated method stub
-
-	}
-
-	@Override
-	public String getIdModel() {
-		// TODO Auto-generated method stub
-		return null;
-	}
-
-	@Override
-	public void setTileSize(int tileSize) {
-		// TODO Auto-generated method stub
-
-	}
-
-	@Override
-	public int getTileSize() {
-		// TODO Auto-generated method stub
-		return 0;
-	}
-
-	@Override
-	public void setZoomLevels(int zoomLevels) {
-		// TODO Auto-generated method stub
-
-	}
-
-	@Override
-	public int getZoomLevels() {
-		// TODO Auto-generated method stub
-		return 0;
-	}
-
-	@Override
-	public void removeReaction(Reaction reaction) {
-		// TODO Auto-generated method stub
-
-	}
-
-	@Override
-	public void removeAlias(Alias alias) {
-		// TODO Auto-generated method stub
-
-	}
-
-	@Override
-	public List<Reaction> getSortedReactions() {
-		// TODO Auto-generated method stub
-		return null;
-	}
-
-	@Override
-	public List<Alias> getSortedAliases() {
-		// TODO Auto-generated method stub
-		return null;
-	}
-
-	@Override
-	public Collection<SpeciesAlias> getNotComplexSpeciesAliases() {
-		// TODO Auto-generated method stub
-		return null;
-	}
-
-	@Override
-	public Collection<ComplexAlias> getComplexAliases() {
-		// TODO Auto-generated method stub
-		return null;
-	}
-
-	@Override
-	public void addReactions(List<Reaction> reactions2) {
-		// TODO Auto-generated method stub
-
-	}
-
-	@Override
-	public Set<AnnotatedObject> getElementsByAnnotation(MiriamData miriamData) {
-		// TODO Auto-generated method stub
-		return null;
-	}
-
-	@Override
-	public void setHeight(int height) {
-		// TODO Auto-generated method stub
-
-	}
-
-	@Override
-	public void setWidth(int width) {
-		// TODO Auto-generated method stub
-
-	}
-
-	@Override
-	public void addLayout(Layout layout) {
-		// TODO Auto-generated method stub
-
-	}
-
-	@Override
-	public void setLayouts(List<Layout> layouts) {
-		// TODO Auto-generated method stub
-
-	}
-
-	@Override
-	public List<Layout> getLayouts() {
-		// TODO Auto-generated method stub
-		return null;
-	}
-
-	@Override
-	public void setCreationDate(Calendar creationDate) {
-		// TODO Auto-generated method stub
-
-	}
-
-	@Override
-	public Calendar getCreationDate() {
-		// TODO Auto-generated method stub
-		return null;
-	}
-
-	@Override
-	public Alias getAliasByDbId(Integer dbId) {
-		// TODO Auto-generated method stub
-		return null;
-	}
-
-	@Override
-	public Reaction getReactionByDbId(Integer dbId) {
-		// TODO Auto-generated method stub
-		return null;
-	}
-
-	@Override
-	public List<CompartmentAlias> getSortedCompartmentsAliases() {
-		// TODO Auto-generated method stub
-		return null;
-	}
-
-	@Override
-	public List<Alias> getAliasesSortedBySize() {
-		// TODO Auto-generated method stub
-		return null;
-	}
-
-	@Override
-	public void setProject(Project project) {
-		// TODO Auto-generated method stub
-
-	}
-
-	@Override
-	public Project getProject() {
-		// TODO Auto-generated method stub
-		return null;
-	}
-
-	@Override
-	public void setAliases(Set<Alias> aliases) {
-		// TODO Auto-generated method stub
-
-	}
-
-	@Override
-	public ModelData getModelData() {
-		// TODO Auto-generated method stub
-		return null;
-	}
-
-	@Override
-	public Integer getId() {
-		// TODO Auto-generated method stub
-		return 0;
-	}
-
-	@Override
-	public void addSubmodelConnection(ModelSubmodelConnection submodel) {
-		// TODO Auto-generated method stub
-
-	}
-
-	@Override
-	public List<ModelSubmodelConnection> getSubmodelConnections() {
-		// TODO Auto-generated method stub
-		return null;
-	}
-
-	@Override
-	public String getName() {
-		// TODO Auto-generated method stub
-		return null;
-	}
-
-	@Override
-	public void setName(String name) {
-		// TODO Auto-generated method stub
-
-	}
-
-	@Override
-	public Model getSubmodelById(Integer idObject) {
-		// TODO Auto-generated method stub
-		return null;
-	}
-
-	@Override
-	public Collection<SubmodelConnection> getParentModels() {
-		// TODO Auto-generated method stub
-		return null;
-	}
-
-	@Override
-	public Model getSubmodelByConnectionName(String name) {
-		// TODO Auto-generated method stub
-		return null;
-	}
-
-	@Override
-	public SubmodelConnection getSubmodelConnectionById(Integer idObject) {
-		// TODO Auto-generated method stub
-		return null;
-	}
-
-	@Override
-	public Model getSubmodelById(String modelIdentifier) {
-		logger.error("Not implemented in mock object");
-		return null;
-	}
-
-	@Override
-	public Collection<Model> getSubmodels() {
-		logger.error("Not implemented in mock object");
-		return null;
-	}
-
-	@Override
-	public Model getSubmodelByName(String selectedModelString) {
-		logger.error("Not implemented in mock object");
-		return null;
-	}
-
-	@Override
-	public List<OverviewImage> getOverviewImages() {
-		logger.error("Not implemented in mock object");
-		return null;
-	}
-
-	@Override
-	public void addOverviewImage(OverviewImage overviewImage) {
-		logger.error("Not implemented in mock object");
-	}
-
-	@Override
-	public void setOverviewImages(List<OverviewImage> parseOverviewLinks) {
-		logger.error("Not implemented in mock object");
-	}
-
-	@Override
-	public OverviewImage getTopOverviewImage() {
-		logger.error("Not implemented in mock object");
-		return null;
-	}
-
-	@Override
-	public boolean isSbgnFormat() {
-		// TODO Auto-generated method stub
-		return false;
-	}
-
-	@Override
-	public void addLayout(int index, Layout layout) {
-		logger.error("Not implemented in mock object");
-	}
-
-	@Override
-	public void addDataMiningSet(DataMiningSet dataMiningSet) {
-		logger.error("Not implemented in mock object");
-	}
-
-	@Override
-	public List<DataMiningSet> getDataMiningSets() {
-		logger.error("Not implemented in mock object");
-		return null;
-	}
-
-	@Override
-	public void addDataMiningSets(Collection<DataMiningSet> dataMiningSets) {
-		logger.error("Not implemented in mock object");
-	}
-
-	@Override
-	public Layout getLayoutByIdentifier(Integer layoutIdentfier) {
-		logger.error("Not implemented in mock object");
-		return null;
-	}
-
-	@Override
-	public void addAlias(Alias alias) {
-		logger.error("Not implemented in mock object");
-	}
-
-	@Override
-	public void setId(int id) {
-		logger.error("Not implemented in mock object");
-	}
-
-	@Override
-	public List<AnnotatedObject> getAnnotatedObjects() {
-		logger.error("Not implemented in mock object");
-		return null;
-	}
-
-	@Override
-	public void addLoggingInfo(EventStorageLoggerAppender appender) {
-		logger.error("Not implemented in mock object");
-	}
-
-	@Override
-	public List<Alias> getAliasByName(String name) {
-		// TODO Auto-generated method stub
-		return null;
-	}
-
-	@Override
-	public List<SpeciesAlias> getSpeciesAliases() {
-		// TODO Auto-generated method stub
-		return null;
-	}
-
-}
diff --git a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/AntisenseRnaComparatorTest.java b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/AntisenseRnaComparatorTest.java
index fa649ac8af088fa69d9d1b633f305c5096b97eff..842bdd559e22f13a0765b8b8634f890efb04a189 100644
--- a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/AntisenseRnaComparatorTest.java
+++ b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/AntisenseRnaComparatorTest.java
@@ -37,7 +37,7 @@ public class AntisenseRnaComparatorTest {
 			assertEquals(0, comparator.compare(aRna1, aRna2));
 			assertEquals(0, comparator.compare(aRna2, aRna1));
 
-			aRna1.setId(-1);
+			aRna1.setElementId("AAA");
 			assertEquals(0, comparator.compare(aRna1, aRna2));
 			assertEquals(0, comparator.compare(aRna2, aRna1));
 
diff --git a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/AntisenseRnaRegionTest.java b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/AntisenseRnaRegionTest.java
index 0564a8bc982d1c66554dc9e35f00b1831b489525..12841cda2ae323142aabc10c690ba5c8fe35b2ee 100644
--- a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/AntisenseRnaRegionTest.java
+++ b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/AntisenseRnaRegionTest.java
@@ -113,7 +113,7 @@ public class AntisenseRnaRegionTest {
 		try {
 			AntisenseRnaRegion region = new AntisenseRnaRegion(new AntisenseRnaRegion());
 			int id = 91;
-			Species species = new Species();
+			AntisenseRna species = new AntisenseRna();
 			double pos = 4.6;
 			double size = 5.3;
 			AntisenseRnaRegionType type = AntisenseRnaRegionType.CODING_REGION;
diff --git a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/CompartmentComparatorTest.java b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/CompartmentComparatorTest.java
index 5e52e347f98eb96a467b4489d756457f70355d24..2bd397c337eb96379c0ab6469922ee7bceb50407 100644
--- a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/CompartmentComparatorTest.java
+++ b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/CompartmentComparatorTest.java
@@ -33,7 +33,7 @@ public class CompartmentComparatorTest {
 			assertEquals(0, comparator.compare(comp1, comp2));
 			assertEquals(0, comparator.compare(comp2, comp1));
 
-			comp1.setId(-1);
+			comp1.setElementId("AAA");
 			assertEquals(0, comparator.compare(comp1, comp2));
 			assertEquals(0, comparator.compare(comp2, comp1));
 
diff --git a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/ComplexSpeciesComparatorTest.java b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/ComplexSpeciesComparatorTest.java
index 8decad505fba5a013f54415fe5ce99bbe97f1e9e..0f9d38dd026f7163ea4866597041e8f53b3672ff 100644
--- a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/ComplexSpeciesComparatorTest.java
+++ b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/ComplexSpeciesComparatorTest.java
@@ -42,7 +42,7 @@ public class ComplexSpeciesComparatorTest {
 			assertEquals(0, comparator.compare(complex1, complex2));
 			assertEquals(0, comparator.compare(complex2, complex1));
 
-			complex1.setId(-1);
+			complex1.setElementId("AAA");
 			assertEquals(0, comparator.compare(complex1, complex2));
 			assertEquals(0, comparator.compare(complex2, complex1));
 
diff --git a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/DegradedComparatorTest.java b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/DegradedComparatorTest.java
index 0d15ec6b2a8c56fe6c2709dc3038aa40d1b20960..50364bb452a5c7265cfb85785a3ae89f96b42999 100644
--- a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/DegradedComparatorTest.java
+++ b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/DegradedComparatorTest.java
@@ -35,7 +35,7 @@ public class DegradedComparatorTest {
 			assertEquals(0, comparator.compare(degraded1, degraded2));
 			assertEquals(0, comparator.compare(degraded2, degraded1));
 
-			degraded1.setId(-1);
+			degraded1.setElementId("AAA");
 			assertEquals(0, comparator.compare(degraded1, degraded2));
 			assertEquals(0, comparator.compare(degraded2, degraded1));
 
diff --git a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/DrugComparatorTest.java b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/DrugComparatorTest.java
index 84c3de7bec661b1848ed2e0fb0a9c34447e7d0cc..c478814faa8939af8d2b956bd62f208e5b0626b6 100644
--- a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/DrugComparatorTest.java
+++ b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/DrugComparatorTest.java
@@ -35,7 +35,7 @@ public class DrugComparatorTest {
 			assertEquals(0, comparator.compare(drug1, drug2));
 			assertEquals(0, comparator.compare(drug2, drug1));
 
-			drug1.setId(-1);
+			drug1.setElementId("AAA");
 			assertEquals(0, comparator.compare(drug1, drug2));
 			assertEquals(0, comparator.compare(drug2, drug1));
 
diff --git a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/ElementTest.java b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/ElementTest.java
index b88371676a1a2211a6823693d87cba050e2bebee..7eac4d04d49cc69877b71d035f2adfeaa31113ce 100644
--- a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/ElementTest.java
+++ b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/ElementTest.java
@@ -104,21 +104,18 @@ public class ElementTest extends CellDesignerTestFunctions {
 	public void testGetters() {
 		try {
 			Element<?> element = Mockito.spy(Element.class);
-			int id = 4;
 			List<String> synonyms = new ArrayList<>();
 			List<String> formerSymbols = new ArrayList<>();
 			ComplexSpecies complex = new ComplexSpecies();
 			Model model = new ModelFullIndexed(null);
 			String formula = "str";
 
-			element.setId(id);
 			element.setSynonyms(synonyms);
 			element.setFormerSymbols(formerSymbols);
 			element.setComplex(complex);
 			element.setModel(model);
 			element.setFormula(formula);
 
-			assertEquals(id, element.getId());
 			assertEquals(synonyms, element.getSynonyms());
 			assertEquals(formerSymbols, element.getFormerSymbols());
 			assertEquals(complex, element.getComplex());
diff --git a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/GeneComparatorTest.java b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/GeneComparatorTest.java
index d93122574d7e709bcd7ed553b87281be3ba3817f..7e4ded16e3978c4d668878b48bb5f41f55c4c151 100644
--- a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/GeneComparatorTest.java
+++ b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/GeneComparatorTest.java
@@ -34,7 +34,7 @@ public class GeneComparatorTest {
 			assertEquals(0, comparator.compare(gene1, gene2));
 			assertEquals(0, comparator.compare(gene2, gene1));
 
-			gene1.setId(-1);
+			gene1.setElementId("AAA");
 			assertEquals(0, comparator.compare(gene1, gene2));
 			assertEquals(0, comparator.compare(gene2, gene1));
 
diff --git a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/IonComparatorTest.java b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/IonComparatorTest.java
index a55e4fb58c1c48589024511abdc014ceead2e48b..d30536e668e533993eb08488fad5bce9d32a5e06 100644
--- a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/IonComparatorTest.java
+++ b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/IonComparatorTest.java
@@ -35,7 +35,7 @@ public class IonComparatorTest {
 			assertEquals(0, comparator.compare(ion1, ion2));
 			assertEquals(0, comparator.compare(ion2, ion1));
 
-			ion1.setId(-1);
+			ion1.setElementId("AAA");
 			assertEquals(0, comparator.compare(ion1, ion2));
 			assertEquals(0, comparator.compare(ion2, ion1));
 
diff --git a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/ModificationResidueTest.java b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/ModificationResidueTest.java
index 1690e144ac1860c687600bc8ed6d70973197a770..9f3f99119e03fdc6a0fba75772875365ed2b74aa 100644
--- a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/ModificationResidueTest.java
+++ b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/ModificationResidueTest.java
@@ -88,7 +88,6 @@ public class ModificationResidueTest {
 			String nullStr = null;
 			Double angle = 2.0;
 			Species species = new Species();
-			int id = 5;
 
 			original.setAngle(doubleStr);
 			assertEquals(angle, original.getAngle(), Configuration.EPSILON);
@@ -111,9 +110,6 @@ public class ModificationResidueTest {
 			original.setSize(nullStr);
 			assertNull(original.getSize());
 
-			original.setId(id);
-			assertEquals(id, original.getId());
-
 			original.setSpecies(species);
 			assertEquals(species, original.getSpecies());
 
diff --git a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/PhenotypeComparatorTest.java b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/PhenotypeComparatorTest.java
index f734a146178ce5bd037ea577020df64e52b2850e..11e30dd99c502892763e7699171d426a8644f54a 100644
--- a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/PhenotypeComparatorTest.java
+++ b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/PhenotypeComparatorTest.java
@@ -33,7 +33,7 @@ public class PhenotypeComparatorTest {
 			assertEquals(0, comparator.compare(phenotype1, phenotype2));
 			assertEquals(0, comparator.compare(phenotype2, phenotype1));
 
-			phenotype1.setId(-1);
+			phenotype1.setElementId("AAA");
 			assertEquals(0, comparator.compare(phenotype1, phenotype2));
 			assertEquals(0, comparator.compare(phenotype2, phenotype1));
 
diff --git a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/ProteinComparatorTest.java b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/ProteinComparatorTest.java
index b9684ca5b2b1249abeb942172cd9b9670640deab..48bdfbb22eab417731297d65f907dbbd8eeae978 100644
--- a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/ProteinComparatorTest.java
+++ b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/ProteinComparatorTest.java
@@ -33,7 +33,7 @@ public class ProteinComparatorTest {
 			assertEquals(0, comparator.compare(aRna1, aRna2));
 			assertEquals(0, comparator.compare(aRna2, aRna1));
 
-			aRna1.setId(-1);
+			aRna1.setElementId("AAA");
 			assertEquals(0, comparator.compare(aRna1, aRna2));
 			assertEquals(0, comparator.compare(aRna2, aRna1));
 
diff --git a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/RnaComparatorTest.java b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/RnaComparatorTest.java
index 2b19c81e5c6c005109bb6ac7fd3d4cc64ba945b9..e2aca98f8eaaf48db98f8d17b77a600152bcf856 100644
--- a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/RnaComparatorTest.java
+++ b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/RnaComparatorTest.java
@@ -34,7 +34,7 @@ public class RnaComparatorTest {
 			assertEquals(0, comparator.compare(aRna1, aRna2));
 			assertEquals(0, comparator.compare(aRna2, aRna1));
 
-			aRna1.setId(-1);
+			aRna1.setElementId("AAA");
 			assertEquals(0, comparator.compare(aRna1, aRna2));
 			assertEquals(0, comparator.compare(aRna2, aRna1));
 
diff --git a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/RnaRegionTest.java b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/RnaRegionTest.java
index b40f127fe213d7b2127b3402e9c18db9bdfde9e0..fe45169fc08af8d07aab7135b84df9b5a1ef802b 100644
--- a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/RnaRegionTest.java
+++ b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/RnaRegionTest.java
@@ -116,13 +116,10 @@ public class RnaRegionTest {
 	public void testGetters() {
 		try {
 			RnaRegion region = new RnaRegion();
-			int id = 47;
 			double size = 2.5;
-			Species species = new GenericProtein();
-			region.setId(id);
+			Rna species = new Rna();
 			region.setSize(size);
 			region.setSpecies(species);
-			assertEquals(id, region.getId());
 			assertEquals(size, region.getSize(), Configuration.EPSILON);
 			assertEquals(species, region.getSpecies());
 		} catch (Exception e) {
diff --git a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/SimpleMoleculeComparatorTest.java b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/SimpleMoleculeComparatorTest.java
index 06e688cf76e925998efa705c91b77f12b8ba1ff6..05dbd82998c63203138abe63e1de972f312e69e0 100644
--- a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/SimpleMoleculeComparatorTest.java
+++ b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/SimpleMoleculeComparatorTest.java
@@ -35,7 +35,7 @@ public class SimpleMoleculeComparatorTest {
 			assertEquals(0, comparator.compare(simpleMolecule1, simpleMolecule2));
 			assertEquals(0, comparator.compare(simpleMolecule2, simpleMolecule1));
 
-			simpleMolecule1.setId(-1);
+			simpleMolecule1.setElementId("AAA");
 			assertEquals(0, comparator.compare(simpleMolecule1, simpleMolecule2));
 			assertEquals(0, comparator.compare(simpleMolecule2, simpleMolecule1));
 
diff --git a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/UnknownComparatorTest.java b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/UnknownComparatorTest.java
index 009dd1d89e550aa3b9e759a2f0ca95f14b08103c..f09907eb61b4cf259920df90efaaefc5847c1cf7 100644
--- a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/UnknownComparatorTest.java
+++ b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/UnknownComparatorTest.java
@@ -35,7 +35,7 @@ public class UnknownComparatorTest {
 			assertEquals(0, comparator.compare(aRna1, aRna2));
 			assertEquals(0, comparator.compare(aRna2, aRna1));
 
-			aRna1.setId(-1);
+			aRna1.setElementId("AAA");
 			assertEquals(0, comparator.compare(aRna1, aRna2));
 			assertEquals(0, comparator.compare(aRna2, aRna1));
 
diff --git a/reactome/src/main/java/lcsb/mapviewer/reactome/utils/comparators/DrugAndCatalystComparator.java b/reactome/src/main/java/lcsb/mapviewer/reactome/utils/comparators/DrugAndCatalystComparator.java
index fc0b0cc738464a0f5856989029672cf799ac18c3..b053e372fd22615ff29e04e538bb92e0e0342731 100644
--- a/reactome/src/main/java/lcsb/mapviewer/reactome/utils/comparators/DrugAndCatalystComparator.java
+++ b/reactome/src/main/java/lcsb/mapviewer/reactome/utils/comparators/DrugAndCatalystComparator.java
@@ -2,13 +2,12 @@ package lcsb.mapviewer.reactome.utils.comparators;
 
 import org.apache.log4j.Logger;
 
-import lcsb.mapviewer.converter.model.celldesigner.structure.Drug;
 import lcsb.mapviewer.model.map.layout.alias.DrugAlias;
 import lcsb.mapviewer.reactome.model.ReactomeCatalystActivity;
 
 /**
- * This class allows to compare {@link DrugAlias} element (internal representation)
- * and {@link ReactomeCatalystActivity} (reactome model).
+ * This class allows to compare {@link DrugAlias} element (internal
+ * representation) and {@link ReactomeCatalystActivity} (reactome model).
  * 
  * @author Piotr Gawron
  * 
diff --git a/reactome/src/main/java/lcsb/mapviewer/reactome/utils/comparators/GeneAndDefinedSetComparator.java b/reactome/src/main/java/lcsb/mapviewer/reactome/utils/comparators/GeneAndDefinedSetComparator.java
index 4807cee4ce09e44d24b7608011eee48a10c29b2e..e399fcca7e97688dba87e54b0247a64f6264de4b 100644
--- a/reactome/src/main/java/lcsb/mapviewer/reactome/utils/comparators/GeneAndDefinedSetComparator.java
+++ b/reactome/src/main/java/lcsb/mapviewer/reactome/utils/comparators/GeneAndDefinedSetComparator.java
@@ -2,13 +2,12 @@ package lcsb.mapviewer.reactome.utils.comparators;
 
 import org.apache.log4j.Logger;
 
-import lcsb.mapviewer.converter.model.celldesigner.structure.Gene;
 import lcsb.mapviewer.model.map.layout.alias.GeneAlias;
 import lcsb.mapviewer.reactome.model.ReactomeDefinedSet;
 
 /**
- * This class allows to compare {@link GeneAlias} element (internal representation)
- * and {@link ReactomeDefinedSet} (reactome model).
+ * This class allows to compare {@link GeneAlias} element (internal
+ * representation) and {@link ReactomeDefinedSet} (reactome model).
  * 
  * @author Piotr Gawron
  * 
diff --git a/reactome/src/main/java/lcsb/mapviewer/reactome/utils/comparators/GeneAndOtherEntityComparator.java b/reactome/src/main/java/lcsb/mapviewer/reactome/utils/comparators/GeneAndOtherEntityComparator.java
index d17cc13191903f55cd686b508e6358479907bd49..d43765ed4d893a9e94e361f6a2f732d2fa4a0ff5 100644
--- a/reactome/src/main/java/lcsb/mapviewer/reactome/utils/comparators/GeneAndOtherEntityComparator.java
+++ b/reactome/src/main/java/lcsb/mapviewer/reactome/utils/comparators/GeneAndOtherEntityComparator.java
@@ -1,14 +1,13 @@
 package lcsb.mapviewer.reactome.utils.comparators;
 
-import lcsb.mapviewer.converter.model.celldesigner.structure.Gene;
+import org.apache.log4j.Logger;
+
 import lcsb.mapviewer.model.map.layout.alias.GeneAlias;
 import lcsb.mapviewer.reactome.model.ReactomeOtherEntity;
 
-import org.apache.log4j.Logger;
-
 /**
- * This class allows to compare {@link GeneAlias} element (internal representation)
- * and {@link ReactomeOtherEntity} (reactome model).
+ * This class allows to compare {@link GeneAlias} element (internal
+ * representation) and {@link ReactomeOtherEntity} (reactome model).
  * 
  * @author Piotr Gawron
  * 
diff --git a/reactome/src/main/java/lcsb/mapviewer/reactome/utils/comparators/IonAndComplexComparator.java b/reactome/src/main/java/lcsb/mapviewer/reactome/utils/comparators/IonAndComplexComparator.java
index 526d85dec644d9799e6da8e3ac1720bee711040b..061b4ef15b5123905b653c4b42c7fb5eb8ecb766 100644
--- a/reactome/src/main/java/lcsb/mapviewer/reactome/utils/comparators/IonAndComplexComparator.java
+++ b/reactome/src/main/java/lcsb/mapviewer/reactome/utils/comparators/IonAndComplexComparator.java
@@ -4,7 +4,6 @@ import java.util.List;
 
 import lcsb.mapviewer.annotation.services.annotators.ChebiSearchException;
 import lcsb.mapviewer.common.exception.InvalidArgumentException;
-import lcsb.mapviewer.converter.model.celldesigner.structure.Ion;
 import lcsb.mapviewer.model.map.MiriamData;
 import lcsb.mapviewer.model.map.layout.alias.IonAlias;
 import lcsb.mapviewer.reactome.model.ReactomeComplex;
@@ -17,8 +16,8 @@ import lcsb.mapviewer.reactome.model.ReactomeSimpleEntity;
 import lcsb.mapviewer.reactome.utils.ComparatorException;
 
 /**
- * This class allows to compare {@link IonAlias} element (internal representation)
- * and {@link ReactomeComplex} (reactome model).
+ * This class allows to compare {@link IonAlias} element (internal
+ * representation) and {@link ReactomeComplex} (reactome model).
  * 
  * @author Piotr Gawron
  * 
diff --git a/reactome/src/main/java/lcsb/mapviewer/reactome/utils/comparators/IonAndDefinedSetComparator.java b/reactome/src/main/java/lcsb/mapviewer/reactome/utils/comparators/IonAndDefinedSetComparator.java
index f16d5afaa5b38e68ae7e1199393831d23c725a8e..104b0ddffc81656e4312505f507dbc67bd6f487b 100644
--- a/reactome/src/main/java/lcsb/mapviewer/reactome/utils/comparators/IonAndDefinedSetComparator.java
+++ b/reactome/src/main/java/lcsb/mapviewer/reactome/utils/comparators/IonAndDefinedSetComparator.java
@@ -1,7 +1,6 @@
 package lcsb.mapviewer.reactome.utils.comparators;
 
 import lcsb.mapviewer.common.exception.InvalidArgumentException;
-import lcsb.mapviewer.converter.model.celldesigner.structure.Ion;
 import lcsb.mapviewer.model.map.layout.alias.IonAlias;
 import lcsb.mapviewer.reactome.model.ReactomeComplex;
 import lcsb.mapviewer.reactome.model.ReactomeDefinedSet;
@@ -37,7 +36,8 @@ public class IonAndDefinedSetComparator extends ANodeComparator<IonAlias, Reacto
 			} else if (entity instanceof ReactomeEntityWithAccessionedSequence) {
 				result |= getGlobalComparator().compareNodes(species, (ReactomeEntityWithAccessionedSequence) entity);
 			} else {
-				throw new InvalidArgumentException("Cannot determine the way of comparison for provided class types: " + species.getClass() + ", " + entity.getClass());
+				throw new InvalidArgumentException(
+						"Cannot determine the way of comparison for provided class types: " + species.getClass() + ", " + entity.getClass());
 			}
 		}
 		return result;
diff --git a/reactome/src/main/java/lcsb/mapviewer/reactome/utils/comparators/IonAndEntityWithAccessionedSequenceComparator.java b/reactome/src/main/java/lcsb/mapviewer/reactome/utils/comparators/IonAndEntityWithAccessionedSequenceComparator.java
index e387838a8c7165bbd9177a52addc7ec7016d0422..9c6df33aa6aaeade95b425141b9f7b6558dfd9f4 100644
--- a/reactome/src/main/java/lcsb/mapviewer/reactome/utils/comparators/IonAndEntityWithAccessionedSequenceComparator.java
+++ b/reactome/src/main/java/lcsb/mapviewer/reactome/utils/comparators/IonAndEntityWithAccessionedSequenceComparator.java
@@ -1,12 +1,12 @@
 package lcsb.mapviewer.reactome.utils.comparators;
 
-import lcsb.mapviewer.converter.model.celldesigner.structure.Ion;
 import lcsb.mapviewer.model.map.layout.alias.IonAlias;
 import lcsb.mapviewer.reactome.model.ReactomeEntityWithAccessionedSequence;
 
 /**
- * This class allows to compare {@link IonAlias} element (internal representation)
- * and {@link ReactomeEntityWithAccessionedSequence} (reactome model).
+ * This class allows to compare {@link IonAlias} element (internal
+ * representation) and {@link ReactomeEntityWithAccessionedSequence} (reactome
+ * model).
  * 
  * @author Piotr Gawron
  * 
diff --git a/reactome/src/main/java/lcsb/mapviewer/reactome/utils/comparators/MoleculeAndCatalystComparator.java b/reactome/src/main/java/lcsb/mapviewer/reactome/utils/comparators/MoleculeAndCatalystComparator.java
index 53f3f62a1a922cfa2a20a6107908545cbb8fa4aa..dd64991b2651ffd7ba1b9ea302e4739b5595b10f 100644
--- a/reactome/src/main/java/lcsb/mapviewer/reactome/utils/comparators/MoleculeAndCatalystComparator.java
+++ b/reactome/src/main/java/lcsb/mapviewer/reactome/utils/comparators/MoleculeAndCatalystComparator.java
@@ -1,7 +1,6 @@
 package lcsb.mapviewer.reactome.utils.comparators;
 
 import lcsb.mapviewer.common.exception.InvalidArgumentException;
-import lcsb.mapviewer.converter.model.celldesigner.structure.SimpleMolecule;
 import lcsb.mapviewer.model.map.layout.alias.SimpleMoleculeAlias;
 import lcsb.mapviewer.reactome.model.ReactomeCatalystActivity;
 import lcsb.mapviewer.reactome.model.ReactomeComplex;
diff --git a/reactome/src/main/java/lcsb/mapviewer/reactome/utils/comparators/MoleculeAndComplexComparator.java b/reactome/src/main/java/lcsb/mapviewer/reactome/utils/comparators/MoleculeAndComplexComparator.java
index 483803281cecbc11b44b5b5a691a6010981f51bd..0221ea8f2108c223c5787863229ff8f1cb712062 100644
--- a/reactome/src/main/java/lcsb/mapviewer/reactome/utils/comparators/MoleculeAndComplexComparator.java
+++ b/reactome/src/main/java/lcsb/mapviewer/reactome/utils/comparators/MoleculeAndComplexComparator.java
@@ -2,7 +2,6 @@ package lcsb.mapviewer.reactome.utils.comparators;
 
 import lcsb.mapviewer.annotation.services.annotators.ChebiSearchException;
 import lcsb.mapviewer.common.exception.InvalidArgumentException;
-import lcsb.mapviewer.converter.model.celldesigner.structure.SimpleMolecule;
 import lcsb.mapviewer.model.map.MiriamData;
 import lcsb.mapviewer.model.map.layout.alias.SimpleMoleculeAlias;
 import lcsb.mapviewer.reactome.model.ReactomeComplex;
diff --git a/reactome/src/main/java/lcsb/mapviewer/reactome/utils/comparators/MoleculeAndDefinedSetComparator.java b/reactome/src/main/java/lcsb/mapviewer/reactome/utils/comparators/MoleculeAndDefinedSetComparator.java
index bce2b67b54087e759e8b2f7a923ab9cd3d7bdd62..3cbd349b761fb5d3270ca3921ac4d1082eee4296 100644
--- a/reactome/src/main/java/lcsb/mapviewer/reactome/utils/comparators/MoleculeAndDefinedSetComparator.java
+++ b/reactome/src/main/java/lcsb/mapviewer/reactome/utils/comparators/MoleculeAndDefinedSetComparator.java
@@ -1,7 +1,6 @@
 package lcsb.mapviewer.reactome.utils.comparators;
 
 import lcsb.mapviewer.common.exception.InvalidArgumentException;
-import lcsb.mapviewer.converter.model.celldesigner.structure.SimpleMolecule;
 import lcsb.mapviewer.model.map.layout.alias.SimpleMoleculeAlias;
 import lcsb.mapviewer.reactome.model.ReactomeComplex;
 import lcsb.mapviewer.reactome.model.ReactomeDefinedSet;
diff --git a/reactome/src/main/java/lcsb/mapviewer/reactome/utils/comparators/MoleculeAndEntityWithAccessionedSequenceComparator.java b/reactome/src/main/java/lcsb/mapviewer/reactome/utils/comparators/MoleculeAndEntityWithAccessionedSequenceComparator.java
index ad23aa7fd8885375f2329cc7f1966075ac75eee6..20d37fad3563a8bbe2216cf17c51c40b9d35e157 100644
--- a/reactome/src/main/java/lcsb/mapviewer/reactome/utils/comparators/MoleculeAndEntityWithAccessionedSequenceComparator.java
+++ b/reactome/src/main/java/lcsb/mapviewer/reactome/utils/comparators/MoleculeAndEntityWithAccessionedSequenceComparator.java
@@ -1,6 +1,5 @@
 package lcsb.mapviewer.reactome.utils.comparators;
 
-import lcsb.mapviewer.converter.model.celldesigner.structure.SimpleMolecule;
 import lcsb.mapviewer.model.map.layout.alias.SimpleMoleculeAlias;
 import lcsb.mapviewer.reactome.model.ReactomeEntityWithAccessionedSequence;
 
diff --git a/service/src/test/java/lcsb/mapviewer/services/impl/LayoutServiceTest2.java b/service/src/test/java/lcsb/mapviewer/services/impl/LayoutServiceTest2.java
index 478e70e64874de1083b3fb58e79a2b3d1c88a29b..222ab908dbf9f33f0415e51f53a2b543b277b064 100644
--- a/service/src/test/java/lcsb/mapviewer/services/impl/LayoutServiceTest2.java
+++ b/service/src/test/java/lcsb/mapviewer/services/impl/LayoutServiceTest2.java
@@ -20,7 +20,6 @@ import lcsb.mapviewer.common.Pair;
 import lcsb.mapviewer.common.TextFileUtils;
 import lcsb.mapviewer.converter.ConverterParams;
 import lcsb.mapviewer.converter.model.celldesigner.CellDesignerXmlParser;
-import lcsb.mapviewer.converter.model.celldesigner.structure.GenericProtein;
 import lcsb.mapviewer.model.map.MiriamData;
 import lcsb.mapviewer.model.map.MiriamType;
 import lcsb.mapviewer.model.map.layout.ColorSchema;
diff --git a/service/src/test/java/lcsb/mapviewer/services/impl/ProjectServiceTest.java b/service/src/test/java/lcsb/mapviewer/services/impl/ProjectServiceTest.java
index e445ef52df890b6f0cb48a6446c0e8016471d9b4..74b3894831c63aeb61ad99acd5481e9745eb56ac 100644
--- a/service/src/test/java/lcsb/mapviewer/services/impl/ProjectServiceTest.java
+++ b/service/src/test/java/lcsb/mapviewer/services/impl/ProjectServiceTest.java
@@ -29,7 +29,6 @@ import lcsb.mapviewer.commands.CopyCommand;
 import lcsb.mapviewer.converter.ComplexZipConverter;
 import lcsb.mapviewer.converter.ComplexZipConverterParams;
 import lcsb.mapviewer.converter.model.celldesigner.CellDesignerXmlParser;
-import lcsb.mapviewer.converter.model.celldesigner.structure.Protein;
 import lcsb.mapviewer.converter.zip.ModelZipEntryFile;
 import lcsb.mapviewer.converter.zip.ZipEntryFile;
 import lcsb.mapviewer.converter.zip.ZipEntryFileFactory;
diff --git a/service/src/test/java/lcsb/mapviewer/services/search/data/FullAliasViewFactoryTest.java b/service/src/test/java/lcsb/mapviewer/services/search/data/FullAliasViewFactoryTest.java
index b163c563012aa7191560aea5b586431a4226cbc6..69386a73bf5c9a5d2628d2f421ba1b6265d3eec4 100644
--- a/service/src/test/java/lcsb/mapviewer/services/search/data/FullAliasViewFactoryTest.java
+++ b/service/src/test/java/lcsb/mapviewer/services/search/data/FullAliasViewFactoryTest.java
@@ -21,7 +21,6 @@ import org.springframework.beans.factory.annotation.Autowired;
 
 import lcsb.mapviewer.annotation.data.Chebi;
 import lcsb.mapviewer.annotation.services.annotators.ChebiAnnotator;
-import lcsb.mapviewer.converter.model.celldesigner.structure.Compartment;
 import lcsb.mapviewer.model.graphics.PolylineData;
 import lcsb.mapviewer.model.map.MiriamData;
 import lcsb.mapviewer.model.map.MiriamRelationType;