diff --git a/annotation/src/main/java/lcsb/mapviewer/annotation/services/ChEMBLParser.java b/annotation/src/main/java/lcsb/mapviewer/annotation/services/ChEMBLParser.java
index 2029d14ff430ca6167b305fda54ff8b808130165..76aa0b70e6d139f4485a5259f95a6540eab744a4 100644
--- a/annotation/src/main/java/lcsb/mapviewer/annotation/services/ChEMBLParser.java
+++ b/annotation/src/main/java/lcsb/mapviewer/annotation/services/ChEMBLParser.java
@@ -215,6 +215,9 @@ public class ChEMBLParser extends DrugAnnotation implements IExternalService {
           } else if (node.getNodeName().equalsIgnoreCase("species_group_flag")) {
             // nothing to do here
             continue;
+          } else if (node.getNodeName().equalsIgnoreCase("cross_references")) {
+            // nothing to do here
+            continue;
           } else {
             logger.warn("Unknown node: " + node.getNodeName() + ";" + node.getTextContent());
           }
diff --git a/annotation/src/main/java/lcsb/mapviewer/annotation/services/DrugbankHTMLParser.java b/annotation/src/main/java/lcsb/mapviewer/annotation/services/DrugbankHTMLParser.java
index bfb4eb7ab87bf741be41f63801c9e3a1575f8010..155716d808c00880c3369cf3add17e0e2ea85134 100644
--- a/annotation/src/main/java/lcsb/mapviewer/annotation/services/DrugbankHTMLParser.java
+++ b/annotation/src/main/java/lcsb/mapviewer/annotation/services/DrugbankHTMLParser.java
@@ -327,6 +327,9 @@ public class DrugbankHTMLParser extends DrugAnnotation implements IExternalServi
 
       while (pageStart > 0 && pageStart < end) {
         int targetStart = page.indexOf("Details</a>", pageStart);
+        if (targetStart < 0) {
+          break;
+        }
         int nextTargetStart = page.indexOf("Details</a>", targetStart + 1);
         if (nextTargetStart < 0) {
           nextTargetStart = end;
@@ -715,7 +718,7 @@ public class DrugbankHTMLParser extends DrugAnnotation implements IExternalServi
 
       int organismPosition = page.indexOf("Organism</dt><dd class=\"col-md-10 col-sm-8\">");
       if (organismPosition >= 0) {
-        int organismStart = organismPosition+ "Organism</dt><dd class=\"col-md-10 col-sm-8\">".length();
+        int organismStart = organismPosition + "Organism</dt><dd class=\"col-md-10 col-sm-8\">".length();
         int organismEnd = page.indexOf("<", organismStart + 1);
         String organismName = page.substring(organismStart, organismEnd);
         if (!organismMatch(organismName, organisms)) {
@@ -765,4 +768,4 @@ public class DrugbankHTMLParser extends DrugAnnotation implements IExternalServi
     super.setWebPageDownloader(webPageDownloader);
   }
 
-}
\ No newline at end of file
+}
diff --git a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/annotation/RestAnnotationParserTest.java b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/annotation/RestAnnotationParserTest.java
index f9d45fd607a6ecc4e8bfb6c1ce9995de66c4f6b9..7c68b06fffef95131844d4fab59db4f57e8e847f 100644
--- a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/annotation/RestAnnotationParserTest.java
+++ b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/annotation/RestAnnotationParserTest.java
@@ -444,6 +444,12 @@ public class RestAnnotationParserTest extends CellDesignerTestFunctions {
 					// TODO Auto-generated method stub
 					
 				}
+
+        @Override
+        public String getElementId() {
+          // TODO Auto-generated method stub
+          return null;
+        }
 			});
 			fail("Exception expected");
 		} catch (NotImplementedException e) {
diff --git a/model-command/src/main/java/lcsb/mapviewer/commands/ColorModelCommand.java b/model-command/src/main/java/lcsb/mapviewer/commands/ColorModelCommand.java
index f7da34ff5dfc2d45ffe2881c0a8e5bd916aeb390..f6ff490e8d5364c39a14b0a0afe6d6c468e4be1f 100644
--- a/model-command/src/main/java/lcsb/mapviewer/commands/ColorModelCommand.java
+++ b/model-command/src/main/java/lcsb/mapviewer/commands/ColorModelCommand.java
@@ -11,6 +11,7 @@ import org.apache.log4j.Logger;
 
 import lcsb.mapviewer.common.Pair;
 import lcsb.mapviewer.common.comparator.StringComparator;
+import lcsb.mapviewer.common.exception.InvalidArgumentException;
 import lcsb.mapviewer.common.exception.NotImplementedException;
 import lcsb.mapviewer.model.graphics.ArrowTypeData;
 import lcsb.mapviewer.model.map.BioEntity;
@@ -133,10 +134,6 @@ public class ColorModelCommand extends ModelCommand {
       return false;
     }
 
-    if (schema.getReactionIdentifier() != null
-        && schema.getReactionIdentifier().equalsIgnoreCase(reaction.getIdReaction())) {
-      return true;
-    }
     if (schema.getGeneralIdentifier() != null && !schema.getGeneralIdentifier().equals("")) {
       MiriamData md = MiriamType.getMiriamDataFromIdentifier(schema.getGeneralIdentifier());
 
@@ -154,7 +151,7 @@ public class ColorModelCommand extends ModelCommand {
       }
     }
 
-    return false;
+    return true;
   }
 
   private boolean modelMatch(ModelData model, ColorSchema schema) {
@@ -189,6 +186,22 @@ public class ColorModelCommand extends ModelCommand {
     }
   }
 
+  protected boolean match(BioEntity element, ColorSchema schema) {
+    if (schema.getElementId() != null && !schema.getElementId().isEmpty()) {
+      if (!element.getElementId().equalsIgnoreCase(schema.getElementId())) {
+        return false;
+      }
+    }
+    if (element instanceof Element) {
+      return match((Element) element, schema);
+    } else if (element instanceof Reaction) {
+      return match((Reaction) element, schema);
+    } else {
+      throw new InvalidArgumentException("Don't know how to handle object: " + element);
+    }
+
+  }
+
   /**
    * Checks if the coloring schema should be used for the {@link Element}.
    * 
@@ -253,10 +266,6 @@ public class ColorModelCommand extends ModelCommand {
         }
       }
 
-      // if we have reaction id to match then reject
-      if (schema.getReactionIdentifier() != null) {
-        return false;
-      }
       return true;
     } else {
       return false;
@@ -272,16 +281,12 @@ public class ColorModelCommand extends ModelCommand {
     List<ColorSchema> result = new ArrayList<ColorSchema>();
     for (ColorSchema schema : schemas) {
       boolean found = false;
-      for (Element element : getModel().getElements()) {
+
+      for (BioEntity element : getModel().getBioEntities()) {
         if (match(element, schema)) {
           found = true;
         }
       }
-      for (Reaction reaction : getModel().getReactions()) {
-        if (match(reaction, schema)) {
-          found = true;
-        }
-      }
       if (!found) {
         result.add(schema);
       }
@@ -305,28 +310,18 @@ public class ColorModelCommand extends ModelCommand {
     List<Model> models = new ArrayList<>();
     models.add(getModel());
     models.addAll(getModel().getSubmodels());
-    for (Model model2 : models) {
+    for (Model model : models) {
       for (ColorSchema schema : schemas) {
-        for (Element element : model2.getElements()) {
+        for (BioEntity element : model.getBioEntities()) {
           if (match(element, schema)) {
             if (result.get(element) != null
                 && !colorExtractor.getNormalizedColor(result.get(element)).equals(Color.WHITE)) {
               throw new InvalidColorSchemaException(
-                  eu.getElementTag(element) + "Element is colored by more than one rule.");
+                  eu.getElementTag(element) + "BioEntity is colored by more than one rule.");
             }
             result.put(element, schema);
           }
         }
-        for (Reaction reaction : model2.getReactions()) {
-          if (match(reaction, schema)) {
-            if (result.get(reaction) != null
-                && !colorExtractor.getNormalizedColor(result.get(reaction)).equals(Color.WHITE)) {
-              throw new InvalidColorSchemaException(
-                  eu.getElementTag(reaction) + "Reaction is colored by more than one rule.");
-            }
-            result.put(reaction, schema);
-          }
-        }
       }
     }
     return result;
@@ -366,18 +361,12 @@ public class ColorModelCommand extends ModelCommand {
     }
 
     for (ColorSchema schema : schemas) {
-      for (Element element : result.getElements()) {
+      for (BioEntity element : result.getBioEntities()) {
         if (match(element, schema)) {
           schema.setMatches(schema.getMatches() + 1);
           applyColor(element, schema);
         }
       }
-      for (Reaction reaction : result.getReactions()) {
-        if (match(reaction, schema)) {
-          schema.setMatches(schema.getMatches() + 1);
-          applyColor(reaction, schema);
-        }
-      }
     }
 
     if (top) {
@@ -388,6 +377,16 @@ public class ColorModelCommand extends ModelCommand {
 
   }
 
+  private void applyColor(BioEntity element, ColorSchema schema) throws InvalidColorSchemaException {
+    if (element instanceof Element) {
+      applyColor((Element) element, schema);
+    } else if (element instanceof Reaction) {
+      applyColor((Reaction) element, schema);
+    } else {
+      throw new InvalidArgumentException("Don't know how to handle: " + element);
+    }
+  }
+
   @Override
   protected void executeImplementation() throws CommandExecutionException {
     try {
diff --git a/model-command/src/test/java/lcsb/mapviewer/commands/ColorModelCommandTest.java b/model-command/src/test/java/lcsb/mapviewer/commands/ColorModelCommandTest.java
index d523a7c938e27f7168f6e8048cbb3e44e804c92f..d240a93b7c25239f27c96d0db283afb02c1a5e30 100644
--- a/model-command/src/test/java/lcsb/mapviewer/commands/ColorModelCommandTest.java
+++ b/model-command/src/test/java/lcsb/mapviewer/commands/ColorModelCommandTest.java
@@ -16,6 +16,7 @@ import org.junit.Before;
 import org.junit.Test;
 
 import lcsb.mapviewer.common.Pair;
+import lcsb.mapviewer.model.map.BioEntity;
 import lcsb.mapviewer.model.map.MiriamType;
 import lcsb.mapviewer.model.map.layout.ColorSchema;
 import lcsb.mapviewer.model.map.layout.GenericColorSchema;
@@ -136,7 +137,7 @@ public class ColorModelCommandTest extends CommandTestFunctions {
       Reaction re1 = model.getReactionByReactionId("re1");
       Collection<ColorSchema> schemas = new ArrayList<ColorSchema>();
       ColorSchema schema = new GenericColorSchema();
-      schema.setReactionIdentifier("re1");
+      schema.setElementId("re1");
       schema.setColor(Color.RED);
       schemas.add(schema);
 
@@ -161,7 +162,7 @@ public class ColorModelCommandTest extends CommandTestFunctions {
       Reaction re2 = model.getReactionByReactionId("re2");
       Collection<ColorSchema> schemas = new ArrayList<ColorSchema>();
       ColorSchema schema = new GenericColorSchema();
-      schema.setReactionIdentifier("re2");
+      schema.setElementId("re2");
       schema.setValue(-1.0);
       schemas.add(schema);
 
@@ -267,7 +268,7 @@ public class ColorModelCommandTest extends CommandTestFunctions {
       Model model = getModelForFile("testFiles/sample.xml", false);
       Collection<ColorSchema> schemas = new ArrayList<>();
       ColorSchema schema = new GenericColorSchema();
-      schema.setReactionIdentifier("re1");
+      schema.setElementId("re1");
       schema.setLineWidth(3.0);
       schema.setColor(Color.BLUE);
       schema.setName("");
@@ -289,7 +290,7 @@ public class ColorModelCommandTest extends CommandTestFunctions {
       Model model = getModelForFile("testFiles/sample.xml", false);
       Collection<ColorSchema> schemas = new ArrayList<>();
       ColorSchema schema = new GenericColorSchema();
-      schema.setReactionIdentifier("re1");
+      schema.setElementId("re1");
       schema.setLineWidth(3.0);
       schema.setColor(Color.BLUE);
       schema.setName(null);
@@ -312,13 +313,13 @@ public class ColorModelCommandTest extends CommandTestFunctions {
   }
 
   @Test
-  public void testAliasMatchWithReactionId() throws Exception {
+  public void testAliasMatchWithInvalidElementId() throws Exception {
     try {
       GenericColorSchema colorSchema = new GenericColorSchema();
       colorSchema.setName(null);
-      colorSchema.setReactionIdentifier("1");
+      colorSchema.setElementId("1");
 
-      GenericProtein protein = new GenericProtein("id");
+      BioEntity protein = new GenericProtein("id");
       protein.setName("test");
 
       List<ColorSchema> schemas = new ArrayList<>();
@@ -328,7 +329,7 @@ public class ColorModelCommandTest extends CommandTestFunctions {
 
       assertFalse(factory.match(protein, colorSchema));
 
-      colorSchema.setReactionIdentifier(null);
+      colorSchema.setElementId(null);
       assertTrue(factory.match(protein, colorSchema));
 
     } catch (Exception e) {
@@ -368,7 +369,7 @@ public class ColorModelCommandTest extends CommandTestFunctions {
       Model model = getModelForFile("testFiles/reactions_to_color.xml", false);
 
       ColorSchema schema = new GenericColorSchema();
-      schema.setReactionIdentifier("re4");
+      schema.setElementId("re4");
       schema.setName(null);
       schema.setModelName(model.getName() + "XXX");
 
@@ -391,7 +392,7 @@ public class ColorModelCommandTest extends CommandTestFunctions {
       Model model = getModelForFile("testFiles/reactions_to_color.xml", false);
 
       ColorSchema schema = new GenericColorSchema();
-      schema.setReactionIdentifier("re4");
+      schema.setElementId("re4");
       schema.setName(null);
       schema.setModelName(model.getName());
 
@@ -452,4 +453,46 @@ public class ColorModelCommandTest extends CommandTestFunctions {
     }
   }
 
+
+  public void testAliasColoringWithUnknownElementSourceId() throws Exception {
+    try {
+      Model model = getModelForFile("testFiles/sample.xml", false);
+
+      ColorSchema schema = new GenericColorSchema();
+      schema.setElementId("xxx");
+
+      Collection<ColorSchema> schemas = new ArrayList<>();
+      schemas.add(schema);
+
+      ColorModelCommand factory = new ColorModelCommand(model, schemas, colorExtractor);
+      Map<Object, ColorSchema> map = factory.getModifiedElements();
+      assertEquals(0, map.values().size());
+
+    } catch (Exception e) {
+      e.printStackTrace();
+      throw e;
+    }
+  }
+
+  @Test
+  public void testAliasColoringWithElementIdMatch() throws Exception {
+    try {
+      Model model = getModelForFile("testFiles/sample.xml", false);
+
+      ColorSchema schema = new GenericColorSchema();
+      schema.setElementId(model.getElements().iterator().next().getElementId());
+
+      Collection<ColorSchema> schemas = new ArrayList<>();
+      schemas.add(schema);
+
+      ColorModelCommand factory = new ColorModelCommand(model, schemas, colorExtractor);
+      Map<Object, ColorSchema> map = factory.getModifiedElements();
+      assertEquals(1, map.values().size());
+
+    } catch (Exception e) {
+      e.printStackTrace();
+      throw e;
+    }
+  }
+
 }
diff --git a/model-command/testFiles/sample.xml b/model-command/testFiles/sample.xml
index 9bd01a8dbcb66032381ec959ff0ee965f319df67..8a0755ad0a623095df8241ef97c1f3ab3a917807 100644
--- a/model-command/testFiles/sample.xml
+++ b/model-command/testFiles/sample.xml
@@ -838,58 +838,9 @@ Synonyms: CNC, NCX1
 <rdf:Description rdf:about="#s15">
 <bqbiol:hasVersion>
 <rdf:Bag>
-<rdf:li rdf:resource="urn:miriam:refseq:NP_066920.1"/></rdf:Bag>
-</bqbiol:hasVersion>
-<bqbiol:hasVersion>
-<rdf:Bag>
 <rdf:li rdf:resource="urn:miriam:ncbigene:6546"/>
 </rdf:Bag>
 </bqbiol:hasVersion>
-<bqbiol:hasVersion>
-<rdf:Bag>
-<rdf:li rdf:resource="urn:miriam:refseq:NP_001106273.1"/>
-</rdf:Bag>
-</bqbiol:hasVersion>
-<bqbiol:hasVersion>
-<rdf:Bag>
-<rdf:li rdf:resource="urn:miriam:kegg.genes:hsa:6546"/>
-</rdf:Bag>
-</bqbiol:hasVersion>
-<bqbiol:hasVersion>
-<rdf:Bag>
-<rdf:li rdf:resource="urn:miriam:reactome:REACT_20130"/>
-</rdf:Bag>
-</bqbiol:hasVersion>
-<bqbiol:hasVersion>
-<rdf:Bag>
-<rdf:li rdf:resource="urn:miriam:pharmgkb.pathways:PA314"/>
-</rdf:Bag>
-</bqbiol:hasVersion>
-<bqbiol:hasVersion>
-<rdf:Bag>
-<rdf:li rdf:resource="urn:miriam:refseq:NP_001106272.1"/>
-</rdf:Bag>
-</bqbiol:hasVersion>
-<bqbiol:hasVersion>
-<rdf:Bag>
-<rdf:li rdf:resource="urn:miriam:kegg.genes:hsa%3A6546"/>
-</rdf:Bag>
-</bqbiol:hasVersion>
-<bqbiol:hasVersion>
-<rdf:Bag>
-<rdf:li rdf:resource="urn:miriam:refseq:NP_001239553.1"/>
-</rdf:Bag>
-</bqbiol:hasVersion>
-<bqbiol:hasVersion>
-<rdf:Bag>
-<rdf:li rdf:resource="urn:miriam:hgnc:2141"/>
-</rdf:Bag>
-</bqbiol:hasVersion>
-<bqbiol:hasVersion>
-<rdf:Bag>
-<rdf:li rdf:resource="urn:miriam:refseq:NP_001106271.1"/>
-</rdf:Bag>
-</bqbiol:hasVersion>
 </rdf:Description>
 </rdf:RDF>
 </body>
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/BioEntity.java b/model/src/main/java/lcsb/mapviewer/model/map/BioEntity.java
index b5aa17cc9bceed8fafc97fb1cf4b85203dc308f2..8361b25af4acdc6aa297309b900ab39db8b28a18 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/BioEntity.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/BioEntity.java
@@ -160,5 +160,7 @@ public interface BioEntity extends Serializable {
 	 * 
 	 * @return semantic zoom level visibility
 	 */
-	String getVisibilityLevel();
+    String getVisibilityLevel();
+    
+    String getElementId();
 }
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/layout/ColorSchema.java b/model/src/main/java/lcsb/mapviewer/model/map/layout/ColorSchema.java
index e4a4b1f2e2e1dcfecfcefd5151066e4b4e7850df..a8628a834534bf6818b6746332309f05188f12d2 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/layout/ColorSchema.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/layout/ColorSchema.java
@@ -7,6 +7,7 @@ import java.util.Collection;
 import java.util.List;
 
 import lcsb.mapviewer.common.Pair;
+import lcsb.mapviewer.model.map.BioEntity;
 import lcsb.mapviewer.model.map.MiriamType;
 import lcsb.mapviewer.model.map.model.Model;
 import lcsb.mapviewer.model.map.species.Element;
@@ -39,9 +40,9 @@ public abstract class ColorSchema implements Serializable {
   private String modelName = null;
 
   /**
-   * Identifier of the reaction to change the color.
+   * Original identifier of the {@link BioEntity} to change the color.
    */
-  private String reactionIdentifier = null;
+  private String elementId = null;
 
   /**
    * Should the direction of highlighted reaction be reversed.
@@ -110,7 +111,7 @@ public abstract class ColorSchema implements Serializable {
    */
   protected ColorSchema(ColorSchema original) {
     this.setName(original.getName());
-    this.setReactionIdentifier(original.getReactionIdentifier());
+    this.setElementId(original.getElementId());
     this.setReverseReaction(original.getReverseReaction());
     this.setLineWidth(original.getLineWidth());
     this.addCompartments(original.getCompartments());
@@ -364,23 +365,6 @@ public abstract class ColorSchema implements Serializable {
 
   }
 
-  /**
-   * @return the reactionIdentifier
-   * @see #reactionIdentifier
-   */
-  public String getReactionIdentifier() {
-    return reactionIdentifier;
-  }
-
-  /**
-   * @param reactionIdentifier
-   *          the reactionIdentifier to set
-   * @see #reactionIdentifier
-   */
-  public void setReactionIdentifier(String reactionIdentifier) {
-    this.reactionIdentifier = reactionIdentifier;
-  }
-
   /**
    * @return the lineWidth
    * @see #lineWidth
@@ -467,4 +451,12 @@ public abstract class ColorSchema implements Serializable {
     this.modelName = modelName;
   }
 
+  public String getElementId() {
+    return elementId;
+  }
+
+  public void setElementId(String elementId) {
+    this.elementId = elementId;
+  }
+
 }
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/reaction/Reaction.java b/model/src/main/java/lcsb/mapviewer/model/map/reaction/Reaction.java
index 18465317a8e3a5d458c54ce2b21937edbc924e67..96d295f430fc7d6d3a63542c12938d8b8f9bf3bb 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/reaction/Reaction.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/reaction/Reaction.java
@@ -879,4 +879,9 @@ public class Reaction implements BioEntity {
 
   }
 
+  @Override
+  public String getElementId() {
+    return getIdReaction();
+  }
+
 }
diff --git a/model/src/test/java/lcsb/mapviewer/model/map/layout/ColorSchemaTest.java b/model/src/test/java/lcsb/mapviewer/model/map/layout/ColorSchemaTest.java
index afeb53d81fd42d5d4e12e6d71dfe3e2891d8da3b..717ca331c5d130f0881272b2d6b2f3b0a3ab6b83 100644
--- a/model/src/test/java/lcsb/mapviewer/model/map/layout/ColorSchemaTest.java
+++ b/model/src/test/java/lcsb/mapviewer/model/map/layout/ColorSchemaTest.java
@@ -62,8 +62,8 @@ public class ColorSchemaTest {
 			cs.setLineWidth(lineWidth);
 			assertEquals(lineWidth, cs.getLineWidth());
 
-			cs.setReactionIdentifier(reactionIdentifier);
-			assertEquals(reactionIdentifier, cs.getReactionIdentifier());
+			cs.setElementId(reactionIdentifier);
+			assertEquals(reactionIdentifier, cs.getElementId());
 
 			cs.setReverseReaction(reverseReaction);
 			assertEquals(reverseReaction, cs.getReverseReaction());
diff --git a/service/src/main/java/lcsb/mapviewer/services/impl/LayoutService.java b/service/src/main/java/lcsb/mapviewer/services/impl/LayoutService.java
index 3e56dd04c2c760331cb683e5a3cbb1cb0bb3ad9a..990e348f5e63bef38210c4760b3baaa0ba4876d5 100644
--- a/service/src/main/java/lcsb/mapviewer/services/impl/LayoutService.java
+++ b/service/src/main/java/lcsb/mapviewer/services/impl/LayoutService.java
@@ -813,8 +813,8 @@ public class LayoutService implements ILayoutService {
         }
       }
       sb.append("\t");
-    } else if (column.equals(ColorSchemaColumn.REACTION_IDENTIFIER)) {
-      sb.append(schema.getReactionIdentifier() + "\t");
+    } else if (column.equals(ColorSchemaColumn.ELEMENT_IDENTIFIER)) {
+      sb.append(schema.getElementId() + "\t");
     } else if (column.equals(ColorSchemaColumn.LINE_WIDTH)) {
       sb.append(schema.getLineWidth() + "\t");
     } else if (column.equals(ColorSchemaColumn.REVERSE_REACTION)) {
@@ -870,8 +870,8 @@ public class LayoutService implements ILayoutService {
         }
       }
       sb.append("\t");
-    } else if (column.equals(ColorSchemaColumn.REACTION_IDENTIFIER)) {
-      sb.append(schema.getReactionIdentifier() + "\t");
+    } else if (column.equals(ColorSchemaColumn.ELEMENT_IDENTIFIER)) {
+      sb.append(schema.getElementId() + "\t");
     } else if (column.equals(ColorSchemaColumn.LINE_WIDTH)) {
       sb.append(schema.getLineWidth() + "\t");
     } else if (column.equals(ColorSchemaColumn.REVERSE_REACTION)) {
diff --git a/service/src/main/java/lcsb/mapviewer/services/utils/ColorSchemaReader.java b/service/src/main/java/lcsb/mapviewer/services/utils/ColorSchemaReader.java
index 0176a0da7e7e1832c80d4e7c0c93cde974ef9066..e2a41ccbe2666f1c9667ee54c84ea19f1c3b04a0 100644
--- a/service/src/main/java/lcsb/mapviewer/services/utils/ColorSchemaReader.java
+++ b/service/src/main/java/lcsb/mapviewer/services/utils/ColorSchemaReader.java
@@ -332,12 +332,12 @@ public class ColorSchemaReader {
       schema.setName(content);
     }
   }
+
   private void processModelNameColumn(ColorSchema schema, String content) {
     if (!content.isEmpty()) {
       schema.setModelName(content);
     }
   }
-  
 
   /**
    * Sets proper compartment names to {@link ColorSchema} from cell content.
@@ -466,8 +466,8 @@ public class ColorSchemaReader {
       }
       String[] columns = line.split("\t");
 
-      Map<ColorSchemaColumn, Integer> schemaColumns = new HashMap<ColorSchemaColumn, Integer>();
-      List<Pair<MiriamType, Integer>> customIdentifiers = new ArrayList<Pair<MiriamType, Integer>>();
+      Map<ColorSchemaColumn, Integer> schemaColumns = new HashMap<>();
+      List<Pair<MiriamType, Integer>> customIdentifiers = new ArrayList<>();
       parseColumns(columns, schemaColumns, customIdentifiers, ColorSchemaType.GENERIC);
 
       Integer valueColumn = schemaColumns.get(ColorSchemaColumn.VALUE);
@@ -475,7 +475,10 @@ public class ColorSchemaReader {
       Integer nameColumn = schemaColumns.get(ColorSchemaColumn.NAME);
       Integer modelNameColumn = schemaColumns.get(ColorSchemaColumn.MODEL_NAME);
       Integer identifierColumn = schemaColumns.get(ColorSchemaColumn.IDENTIFIER);
-      Integer reactionIdentifierColumn = schemaColumns.get(ColorSchemaColumn.REACTION_IDENTIFIER);
+      Integer elementIdentifierColumn = schemaColumns.get(ColorSchemaColumn.ELEMENT_IDENTIFIER);
+      if (elementIdentifierColumn == null) {
+        elementIdentifierColumn = schemaColumns.get(ColorSchemaColumn.REACTION_IDENTIFIER);
+      }
       Integer compartmentColumn = schemaColumns.get(ColorSchemaColumn.COMPARTMENT);
       Integer typeColumn = schemaColumns.get(ColorSchemaColumn.TYPE);
       Integer lineWidthColumn = schemaColumns.get(ColorSchemaColumn.LINE_WIDTH);
@@ -483,9 +486,10 @@ public class ColorSchemaReader {
       Integer descriptionColumn = schemaColumns.get(ColorSchemaColumn.DESCRIPTION);
 
       if (nameColumn == null && identifierColumn == null && customIdentifiers.size() == 0
-          && reactionIdentifierColumn == null) {
+          && elementIdentifierColumn == null) {
         throw new InvalidColorSchemaException(
-            "One of these columns is obligatory: name, identifier, reactionIdentifier");
+            "One of these columns is obligatory: " + ColorSchemaColumn.NAME.getTitle() + ","
+                + ColorSchemaColumn.IDENTIFIER.getTitle() + "," + ColorSchemaColumn.ELEMENT_IDENTIFIER.getTitle());
       }
 
       if (valueColumn == null && colorColumn == null) {
@@ -531,8 +535,8 @@ public class ColorSchemaReader {
         if (descriptionColumn != null) {
           schema.setDescription(values[descriptionColumn]);
         }
-        if (reactionIdentifierColumn != null) {
-          processReactionIdentifier(schema, values[reactionIdentifierColumn]);
+        if (elementIdentifierColumn != null) {
+          processReactionIdentifier(schema, values[elementIdentifierColumn]);
         }
         if (lineWidthColumn != null) {
           if (!values[lineWidthColumn].trim().equals("")) {
@@ -638,12 +642,12 @@ public class ColorSchemaReader {
    * @param schema
    *          {@link ColorSchema} where name should be set
    * @param content
-   *          content of the cell where reaction identifieris stored
+   *          content of the cell where reaction identifiers stored
    */
 
   private void processReactionIdentifier(ColorSchema schema, String content) {
     if (!content.isEmpty()) {
-      schema.setReactionIdentifier(content);
+      schema.setElementId(content);
     }
   }
 
@@ -746,8 +750,8 @@ public class ColorSchemaReader {
       if (schema.getModelName() != null) {
         result.add(ColorSchemaColumn.MODEL_NAME);
       }
-      if (schema.getReactionIdentifier() != null) {
-        result.add(ColorSchemaColumn.REACTION_IDENTIFIER);
+      if (schema.getElementId() != null) {
+        result.add(ColorSchemaColumn.ELEMENT_IDENTIFIER);
       }
       if (schema.getReverseReaction() != null) {
         result.add(ColorSchemaColumn.REVERSE_REACTION);
diff --git a/service/src/main/java/lcsb/mapviewer/services/utils/ColorSchemaXlsxReader.java b/service/src/main/java/lcsb/mapviewer/services/utils/ColorSchemaXlsxReader.java
index be39f1a333b1a6a9ec4e9834831ebf26574d978c..12a4f24bb406354047ab855482414801d0382d42 100644
--- a/service/src/main/java/lcsb/mapviewer/services/utils/ColorSchemaXlsxReader.java
+++ b/service/src/main/java/lcsb/mapviewer/services/utils/ColorSchemaXlsxReader.java
@@ -12,6 +12,7 @@ import java.util.Map;
 import java.util.Set;
 
 import org.apache.commons.io.FilenameUtils;
+import org.apache.commons.lang3.StringUtils;
 import org.apache.log4j.Logger;
 import org.apache.poi.hssf.usermodel.HSSFWorkbook;
 import org.apache.poi.ss.usermodel.Cell;
@@ -92,7 +93,7 @@ public class ColorSchemaXlsxReader {
       Integer nameColumn = null;
       Integer modelNameColumn = null;
       Integer identifierColumn = null;
-      Integer reactionIdentifierColumn = null;
+      Integer elementIdentifierColumn = null;
       Integer compartmentColumn = null;
       Integer typeColumn = null;
       Integer lineWidthColumn = null;
@@ -157,7 +158,10 @@ public class ColorSchemaXlsxReader {
           nameColumn = foundSchemaColumns.get(ColorSchemaColumn.NAME);
           modelNameColumn = foundSchemaColumns.get(ColorSchemaColumn.MODEL_NAME);
           identifierColumn = foundSchemaColumns.get(ColorSchemaColumn.IDENTIFIER);
-          reactionIdentifierColumn = foundSchemaColumns.get(ColorSchemaColumn.REACTION_IDENTIFIER);
+          elementIdentifierColumn = foundSchemaColumns.get(ColorSchemaColumn.ELEMENT_IDENTIFIER);
+          if (elementIdentifierColumn == null) {
+            elementIdentifierColumn = foundSchemaColumns.get(ColorSchemaColumn.REACTION_IDENTIFIER);
+          }
           compartmentColumn = foundSchemaColumns.get(ColorSchemaColumn.COMPARTMENT);
           typeColumn = foundSchemaColumns.get(ColorSchemaColumn.TYPE);
           lineWidthColumn = foundSchemaColumns.get(ColorSchemaColumn.LINE_WIDTH);
@@ -168,9 +172,10 @@ public class ColorSchemaXlsxReader {
           }
 
           if (nameColumn == null && identifierColumn == null && foundCustomIdentifiers.size() == 0
-              && reactionIdentifierColumn == null) {
+              && elementIdentifierColumn == null) {
             throw new InvalidColorSchemaException(
-                "One of these columns is obligatory: name, identifier, reactionIdentifier");
+                "One of these columns is obligatory: " + ColorSchemaColumn.NAME.getTitle() + ","
+                    + ColorSchemaColumn.IDENTIFIER.getTitle() + "," + ColorSchemaColumn.ELEMENT_IDENTIFIER.getTitle());
           }
 
           if (valueColumn == null && colorColumn == null) {
@@ -223,8 +228,8 @@ public class ColorSchemaXlsxReader {
           if (colorColumn != null) {
             schema.setColor(colorParser.parse(row.getCell(colorColumn).getStringCellValue()));
           }
-          if (reactionIdentifierColumn != null) {
-            schema.setReactionIdentifier(row.getCell(reactionIdentifierColumn).getStringCellValue());
+          if (elementIdentifierColumn != null) {
+            schema.setElementId(row.getCell(elementIdentifierColumn).getStringCellValue());
           }
           if (lineWidthColumn != null) {
             cell = row.getCell(lineWidthColumn);
@@ -271,7 +276,7 @@ public class ColorSchemaXlsxReader {
           }
 
           if (schema.getName() == null && schema.getGeneralIdentifier() == null && foundCustomIdentifiers.size() == 0
-              && schema.getReactionIdentifier() == null) {
+              && schema.getElementId() == null) {
             throw new InvalidColorSchemaException(
                 "One of these columns values is obligatory: name, identifier, reactionIdentifier");
           }
@@ -323,8 +328,8 @@ public class ColorSchemaXlsxReader {
       if (schema.getModelName() != null) {
         result.add(ColorSchemaColumn.MODEL_NAME);
       }
-      if (schema.getReactionIdentifier() != null) {
-        result.add(ColorSchemaColumn.REACTION_IDENTIFIER);
+      if (schema.getElementId() != null) {
+        result.add(ColorSchemaColumn.ELEMENT_IDENTIFIER);
       }
       if (schema.getReverseReaction() != null) {
         result.add(ColorSchemaColumn.REVERSE_REACTION);
diff --git a/service/src/main/java/lcsb/mapviewer/services/utils/data/ColorSchemaColumn.java b/service/src/main/java/lcsb/mapviewer/services/utils/data/ColorSchemaColumn.java
index a5a4025546064af5b3c53c2b64941f900d7408b5..0423331172c246d390a0c1742595c79aed8d19e0 100644
--- a/service/src/main/java/lcsb/mapviewer/services/utils/data/ColorSchemaColumn.java
+++ b/service/src/main/java/lcsb/mapviewer/services/utils/data/ColorSchemaColumn.java
@@ -53,8 +53,14 @@ public enum ColorSchemaColumn {
   IDENTIFIER("identifier", new ColorSchemaType[] { ColorSchemaType.GENERIC, ColorSchemaType.GENETIC_VARIANT }), //
 
   /**
-   * Reaction identifier.
+   * Element identifier.
    */
+  ELEMENT_IDENTIFIER("elementIdentifier", new ColorSchemaType[] { ColorSchemaType.GENERIC }), //
+  
+  /**
+   * Element identifier.
+   */
+  @Deprecated
   REACTION_IDENTIFIER("reactionIdentifier", new ColorSchemaType[] { ColorSchemaType.GENERIC }), //
 
   /**
diff --git a/service/src/test/java/lcsb/mapviewer/services/AllServicesTests.java b/service/src/test/java/lcsb/mapviewer/services/AllServicesTests.java
index 18f68071beadf1888077a5211b9bac7ab2f303e2..6b57e86398f844ab9e1f302e7b4d74e8f7fe5ed4 100644
--- a/service/src/test/java/lcsb/mapviewer/services/AllServicesTests.java
+++ b/service/src/test/java/lcsb/mapviewer/services/AllServicesTests.java
@@ -12,12 +12,11 @@ import lcsb.mapviewer.services.view.AllViewTests;
 
 @RunWith(Suite.class)
 @SuiteClasses({ AllImplServiceTests.class, //
-		AllOverlayTests.class, //
-		AllSearchTests.class, //
-		AllViewTests.class, //
-		AllUtilsTests.class, //
+    AllOverlayTests.class, //
+    AllSearchTests.class, //
+    AllViewTests.class, //
+    AllUtilsTests.class, //
 })
 public class AllServicesTests {
 
-}
-;
\ No newline at end of file
+};
\ No newline at end of file
diff --git a/service/src/test/java/lcsb/mapviewer/services/impl/LayoutServiceTest.java b/service/src/test/java/lcsb/mapviewer/services/impl/LayoutServiceTest.java
index cff85de5956a3db9ec4ad99d29bce1122ee1e3f8..ca85d27c3a208e4abbd7c949575e776baaa96e46 100644
--- a/service/src/test/java/lcsb/mapviewer/services/impl/LayoutServiceTest.java
+++ b/service/src/test/java/lcsb/mapviewer/services/impl/LayoutServiceTest.java
@@ -32,7 +32,6 @@ import lcsb.mapviewer.model.map.model.SubmodelType;
 import lcsb.mapviewer.model.user.BasicPrivilege;
 import lcsb.mapviewer.model.user.ObjectPrivilege;
 import lcsb.mapviewer.model.user.PrivilegeType;
-import lcsb.mapviewer.model.user.User;
 import lcsb.mapviewer.persist.dao.map.LayoutDao;
 import lcsb.mapviewer.services.ServiceTestFunctions;
 import lcsb.mapviewer.services.interfaces.ILayoutService;
@@ -214,20 +213,6 @@ public class LayoutServiceTest extends ServiceTestFunctions {
       layouts = layoutService.getCustomLayouts(model, user2, false, user2);
       assertEquals(0, layouts.size());
 
-      layoutService.addViewPrivilegeToLayout(row, user2);
-
-      layouts = layoutService.getCustomLayouts(model, user2, false, user);
-      assertEquals(1, layouts.size());
-
-      layoutService.dropViewPrivilegeFromLayout(row, user2);
-
-      layouts = layoutService.getCustomLayouts(model, user2, false, user);
-      assertEquals(0, layouts.size());
-
-      // null user shouldn't have access to custom layouts
-      layouts = layoutService.getCustomLayouts(model, (User) null, false, null);
-      assertEquals(0, layouts.size());
-
       layoutService.removeLayout(row, null);
 
     } catch (Exception e) {
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 0d39e9cb6d0e88baaf86092b6775bf51f84a09f7..1bf9bb3ab450e8e7dc75f0548927a9c75e6ee994 100644
--- a/service/src/test/java/lcsb/mapviewer/services/impl/LayoutServiceTest2.java
+++ b/service/src/test/java/lcsb/mapviewer/services/impl/LayoutServiceTest2.java
@@ -36,214 +36,215 @@ import lcsb.mapviewer.services.utils.data.ColorSchemaColumn;
 import lcsb.mapviewer.services.utils.data.ColorSchemaType;
 
 public class LayoutServiceTest2 {
-	Logger				 logger					= Logger.getLogger(LayoutServiceTest2.class);
-	ColorExtractor colorExtractor	= new ColorExtractor(Color.RED, Color.GREEN, Color.BLUE);
-
-	@Before
-	public void setUp() throws Exception {
-	}
-
-	@After
-	public void tearDown() throws Exception {
-	}
-
-	@Test
-	public void testValidPreprareTableResultForGeneric() throws Exception {
-		try {
-			class CSR extends ColorSchemaReader {
-				public Collection<ColorSchemaColumn> getSetColorSchemaColumns(Collection<ColorSchema> schemas) {
-					List<ColorSchemaColumn> result = new ArrayList<ColorSchemaColumn>();
-					for (ColorSchemaColumn csc : ColorSchemaColumn.values()) {
-						if (csc.getTypes().contains(ColorSchemaType.GENERIC)) {
-							result.add(csc);
-						}
-					}
-					return result;
-				}
-			}
-			;
-			List<ColorSchema> schemas = new ArrayList<ColorSchema>();
-			ColorSchema cs = new GenericColorSchema();
-			cs.setColor(Color.CYAN);
-			cs.addCompartment("BLA");
-			cs.addIdentifierColumn(new Pair<MiriamType, String>(MiriamType.CAS, "CAS_ID"));
-			cs.setLineWidth(3.3);
-			cs.setMatches(2);
-			cs.setName("UUU");
-			cs.setReactionIdentifier("RE ID");
-			cs.setReverseReaction(true);
-			cs.addType(GenericProtein.class);
-			cs.setValue(1111.1111);
-			schemas.add(cs);
-
-			LayoutService ls = new LayoutService();
-			String result = ls.prepareTableResult(schemas, new CSR());
-			assertNotNull(result);
-		} catch (Exception e) {
-			e.printStackTrace();
-			throw e;
-		}
-
-	}
-
-	@Test
-	public void testValidPreprareTableResultForGeneVariation() throws Exception {
-		try {
-			class CSR extends ColorSchemaReader {
-				public Collection<ColorSchemaColumn> getSetColorSchemaColumns(Collection<ColorSchema> schemas) {
-					List<ColorSchemaColumn> result = new ArrayList<ColorSchemaColumn>();
-					for (ColorSchemaColumn csc : ColorSchemaColumn.values()) {
-						if (csc.getTypes().contains(ColorSchemaType.GENETIC_VARIANT)) {
-							result.add(csc);
-						}
-					}
-					return result;
-				}
-			}
-			;
-			List<ColorSchema> schemas = new ArrayList<ColorSchema>();
-			GeneVariationColorSchema cs = new GeneVariationColorSchema();
-			cs.setColor(Color.CYAN);
-			cs.addCompartment("BLA");
-			cs.addIdentifierColumn(new Pair<MiriamType, String>(MiriamType.CAS, "CAS_ID"));
-			cs.setLineWidth(3.3);
-			cs.setMatches(2);
-			cs.setName("UUU");
-			cs.setReactionIdentifier("RE ID");
-			cs.setReverseReaction(true);
-			cs.addType(GenericProtein.class);
-			cs.setValue(1111.1111);
-			GeneVariation gv = new GeneVariation();
-			gv.setModifiedDna("C");
-			gv.setContig("chr1");
-			gv.setOriginalDna("T");
-			gv.setPosition(12);
-			gv.setReferenceGenomeType(ReferenceGenomeType.UCSC);
-			gv.setReferenceGenomeVersion("hg19");
-			cs.addGeneVariation(gv);
-			GeneVariation gv2 = new GeneVariation();
-			gv2.setModifiedDna("CC");
-			gv2.setContig("chr2");
-			gv2.setOriginalDna("TT");
-			gv2.setPosition(124);
-			gv2.setReferenceGenomeType(ReferenceGenomeType.UCSC);
-			gv2.setReferenceGenomeVersion("hg18");
-			gv2.addReference(new MiriamData(MiriamType.CHEBI, "XXX"));
-			cs.addGeneVariation(gv2);
-			schemas.add(cs);
-
-			LayoutService ls = new LayoutService();
-			String result = ls.prepareTableResult(schemas, new CSR());
-			assertNotNull(result);
-		} catch (Exception e) {
-			e.printStackTrace();
-			throw e;
-		}
-
-	}
-
-	@Test
-	public void testEmptyPreprareTableResultForGeneric() throws Exception {
-		try {
-			class CSR extends ColorSchemaReader {
-				public Collection<ColorSchemaColumn> getSetColorSchemaColumns(Collection<ColorSchema> schemas) {
-					List<ColorSchemaColumn> result = new ArrayList<ColorSchemaColumn>();
-					for (ColorSchemaColumn csc : ColorSchemaColumn.values()) {
-						if (csc.getTypes().contains(ColorSchemaType.GENERIC)) {
-							result.add(csc);
-						}
-					}
-					return result;
-				}
-			}
-			;
-			List<ColorSchema> schemas = new ArrayList<ColorSchema>();
-			ColorSchema cs = new GenericColorSchema();
-			schemas.add(cs);
-
-			LayoutService ls = new LayoutService();
-			String result = ls.prepareTableResult(schemas, new CSR());
-			assertNotNull(result);
-		} catch (Exception e) {
-			e.printStackTrace();
-			throw e;
-		}
-
-	}
-
-	@Test
-	public void testEmptyPreprareTableResultForGeneVariant() throws Exception {
-		try {
-			class CSR extends ColorSchemaReader {
-				public Collection<ColorSchemaColumn> getSetColorSchemaColumns(Collection<ColorSchema> schemas) {
-					List<ColorSchemaColumn> result = new ArrayList<ColorSchemaColumn>();
-					for (ColorSchemaColumn csc : ColorSchemaColumn.values()) {
-						if (csc.getTypes().contains(ColorSchemaType.GENETIC_VARIANT)) {
-							result.add(csc);
-						}
-					}
-					return result;
-				}
-			}
-			;
-			List<ColorSchema> schemas = new ArrayList<ColorSchema>();
-			ColorSchema cs = new GeneVariationColorSchema();
-			schemas.add(cs);
-
-			LayoutService ls = new LayoutService();
-			String result = ls.prepareTableResult(schemas, new CSR());
-			assertNotNull(result);
-		} catch (Exception e) {
-			e.printStackTrace();
-			throw e;
-		}
-
-	}
-
-	@Test
-	public void testGetLayoutAliasesForInvalidAlias() throws Exception {
-		try {
-
-			Model model = new CellDesignerXmlParser().createModel(new ConverterParams().filename("testFiles/coloring/problematicModel2.xml"));
-
-			FileInputStream fis = new FileInputStream("testFiles/coloring/problematicSchema2.txt");
-			CreateLayoutParams params = new CreateLayoutParams().name("Test").//
-					directory("testDir").//
-					model(model).//
-					colorInputStream(fis).//
-					async(false);
-			ColorSchemaReader reader = new ColorSchemaReader();
-			final Collection<ColorSchema> schemas = reader
-					.readColorSchema(params.getColorInputStream(), TextFileUtils.getHeaderParametersFromFile(params.getColorInputStream()));
-
-			ColorModelCommand command = new ColorModelCommand(model, schemas, colorExtractor);
-			command.execute();
-
-			command.getModifiedElements();
-
-		} catch (Exception e) {
-			e.printStackTrace();
-			throw e;
-		}
-	}
-
-	@Test
-	public void testSchemaWithCompartments() throws Exception {
-		try {
-			FileInputStream fis = new FileInputStream("testFiles/coloring/schemaWithCompartment.txt");
-			ColorSchemaReader reader = new ColorSchemaReader();
-			final Collection<ColorSchema> schemas = reader.readColorSchema(fis, new HashMap<>());
-			for (ColorSchema colorSchema : schemas) {
-				for (String string : colorSchema.getCompartments()) {
-					assertNotNull(string);
-					assertFalse(string.isEmpty());
-				}
-			}
-
-		} catch (Exception e) {
-			e.printStackTrace();
-			throw e;
-		}
-	}
+  Logger logger = Logger.getLogger(LayoutServiceTest2.class);
+  ColorExtractor colorExtractor = new ColorExtractor(Color.RED, Color.GREEN, Color.BLUE);
+
+  @Before
+  public void setUp() throws Exception {
+  }
+
+  @After
+  public void tearDown() throws Exception {
+  }
+
+  @Test
+  public void testValidPreprareTableResultForGeneric() throws Exception {
+    try {
+      class CSR extends ColorSchemaReader {
+        public Collection<ColorSchemaColumn> getSetColorSchemaColumns(Collection<ColorSchema> schemas) {
+          List<ColorSchemaColumn> result = new ArrayList<ColorSchemaColumn>();
+          for (ColorSchemaColumn csc : ColorSchemaColumn.values()) {
+            if (csc.getTypes().contains(ColorSchemaType.GENERIC)) {
+              result.add(csc);
+            }
+          }
+          return result;
+        }
+      }
+      ;
+      List<ColorSchema> schemas = new ArrayList<ColorSchema>();
+      ColorSchema cs = new GenericColorSchema();
+      cs.setColor(Color.CYAN);
+      cs.addCompartment("BLA");
+      cs.addIdentifierColumn(new Pair<MiriamType, String>(MiriamType.CAS, "CAS_ID"));
+      cs.setLineWidth(3.3);
+      cs.setMatches(2);
+      cs.setName("UUU");
+      cs.setElementId("RE ID");
+      cs.setReverseReaction(true);
+      cs.addType(GenericProtein.class);
+      cs.setValue(1111.1111);
+      schemas.add(cs);
+
+      LayoutService ls = new LayoutService();
+      String result = ls.prepareTableResult(schemas, new CSR());
+      assertNotNull(result);
+    } catch (Exception e) {
+      e.printStackTrace();
+      throw e;
+    }
+
+  }
+
+  @Test
+  public void testValidPreprareTableResultForGeneVariation() throws Exception {
+    try {
+      class CSR extends ColorSchemaReader {
+        public Collection<ColorSchemaColumn> getSetColorSchemaColumns(Collection<ColorSchema> schemas) {
+          List<ColorSchemaColumn> result = new ArrayList<ColorSchemaColumn>();
+          for (ColorSchemaColumn csc : ColorSchemaColumn.values()) {
+            if (csc.getTypes().contains(ColorSchemaType.GENETIC_VARIANT)) {
+              result.add(csc);
+            }
+          }
+          return result;
+        }
+      }
+      ;
+      List<ColorSchema> schemas = new ArrayList<ColorSchema>();
+      GeneVariationColorSchema cs = new GeneVariationColorSchema();
+      cs.setColor(Color.CYAN);
+      cs.addCompartment("BLA");
+      cs.addIdentifierColumn(new Pair<MiriamType, String>(MiriamType.CAS, "CAS_ID"));
+      cs.setLineWidth(3.3);
+      cs.setMatches(2);
+      cs.setName("UUU");
+      cs.setElementId("RE ID");
+      cs.setReverseReaction(true);
+      cs.addType(GenericProtein.class);
+      cs.setValue(1111.1111);
+      GeneVariation gv = new GeneVariation();
+      gv.setModifiedDna("C");
+      gv.setContig("chr1");
+      gv.setOriginalDna("T");
+      gv.setPosition(12);
+      gv.setReferenceGenomeType(ReferenceGenomeType.UCSC);
+      gv.setReferenceGenomeVersion("hg19");
+      cs.addGeneVariation(gv);
+      GeneVariation gv2 = new GeneVariation();
+      gv2.setModifiedDna("CC");
+      gv2.setContig("chr2");
+      gv2.setOriginalDna("TT");
+      gv2.setPosition(124);
+      gv2.setReferenceGenomeType(ReferenceGenomeType.UCSC);
+      gv2.setReferenceGenomeVersion("hg18");
+      gv2.addReference(new MiriamData(MiriamType.CHEBI, "XXX"));
+      cs.addGeneVariation(gv2);
+      schemas.add(cs);
+
+      LayoutService ls = new LayoutService();
+      String result = ls.prepareTableResult(schemas, new CSR());
+      assertNotNull(result);
+    } catch (Exception e) {
+      e.printStackTrace();
+      throw e;
+    }
+
+  }
+
+  @Test
+  public void testEmptyPreprareTableResultForGeneric() throws Exception {
+    try {
+      class CSR extends ColorSchemaReader {
+        public Collection<ColorSchemaColumn> getSetColorSchemaColumns(Collection<ColorSchema> schemas) {
+          List<ColorSchemaColumn> result = new ArrayList<ColorSchemaColumn>();
+          for (ColorSchemaColumn csc : ColorSchemaColumn.values()) {
+            if (csc.getTypes().contains(ColorSchemaType.GENERIC)) {
+              result.add(csc);
+            }
+          }
+          return result;
+        }
+      }
+      ;
+      List<ColorSchema> schemas = new ArrayList<ColorSchema>();
+      ColorSchema cs = new GenericColorSchema();
+      schemas.add(cs);
+
+      LayoutService ls = new LayoutService();
+      String result = ls.prepareTableResult(schemas, new CSR());
+      assertNotNull(result);
+    } catch (Exception e) {
+      e.printStackTrace();
+      throw e;
+    }
+
+  }
+
+  @Test
+  public void testEmptyPreprareTableResultForGeneVariant() throws Exception {
+    try {
+      class CSR extends ColorSchemaReader {
+        public Collection<ColorSchemaColumn> getSetColorSchemaColumns(Collection<ColorSchema> schemas) {
+          List<ColorSchemaColumn> result = new ArrayList<ColorSchemaColumn>();
+          for (ColorSchemaColumn csc : ColorSchemaColumn.values()) {
+            if (csc.getTypes().contains(ColorSchemaType.GENETIC_VARIANT)) {
+              result.add(csc);
+            }
+          }
+          return result;
+        }
+      }
+      ;
+      List<ColorSchema> schemas = new ArrayList<ColorSchema>();
+      ColorSchema cs = new GeneVariationColorSchema();
+      schemas.add(cs);
+
+      LayoutService ls = new LayoutService();
+      String result = ls.prepareTableResult(schemas, new CSR());
+      assertNotNull(result);
+    } catch (Exception e) {
+      e.printStackTrace();
+      throw e;
+    }
+
+  }
+
+  @Test
+  public void testGetLayoutAliasesForInvalidAlias() throws Exception {
+    try {
+
+      Model model = new CellDesignerXmlParser()
+          .createModel(new ConverterParams().filename("testFiles/coloring/problematicModel2.xml"));
+
+      FileInputStream fis = new FileInputStream("testFiles/coloring/problematicSchema2.txt");
+      CreateLayoutParams params = new CreateLayoutParams().name("Test").//
+          directory("testDir").//
+          model(model).//
+          colorInputStream(fis).//
+          async(false);
+      ColorSchemaReader reader = new ColorSchemaReader();
+      final Collection<ColorSchema> schemas = reader.readColorSchema(params.getColorInputStream(),
+          TextFileUtils.getHeaderParametersFromFile(params.getColorInputStream()));
+
+      ColorModelCommand command = new ColorModelCommand(model, schemas, colorExtractor);
+      command.execute();
+
+      command.getModifiedElements();
+
+    } catch (Exception e) {
+      e.printStackTrace();
+      throw e;
+    }
+  }
+
+  @Test
+  public void testSchemaWithCompartments() throws Exception {
+    try {
+      FileInputStream fis = new FileInputStream("testFiles/coloring/schemaWithCompartment.txt");
+      ColorSchemaReader reader = new ColorSchemaReader();
+      final Collection<ColorSchema> schemas = reader.readColorSchema(fis, new HashMap<>());
+      for (ColorSchema colorSchema : schemas) {
+        for (String string : colorSchema.getCompartments()) {
+          assertNotNull(string);
+          assertFalse(string.isEmpty());
+        }
+      }
+
+    } catch (Exception e) {
+      e.printStackTrace();
+      throw e;
+    }
+  }
 
 }
diff --git a/service/src/test/java/lcsb/mapviewer/services/utils/ColorSchemaReaderTest.java b/service/src/test/java/lcsb/mapviewer/services/utils/ColorSchemaReaderTest.java
index 6b904433256b636dd313f90cc6bcdd53f34aab85..d5cc32a2086bfb208dbd47976bbdb6caf77021cc 100644
--- a/service/src/test/java/lcsb/mapviewer/services/utils/ColorSchemaReaderTest.java
+++ b/service/src/test/java/lcsb/mapviewer/services/utils/ColorSchemaReaderTest.java
@@ -200,7 +200,7 @@ public class ColorSchemaReaderTest extends ServiceTestFunctions {
       Collection<ColorSchema> collection = reader.readColorSchema("testFiles/coloring/reactionSchema.txt");
       assertEquals(1, collection.size());
       ColorSchema schema = collection.iterator().next();
-      assertEquals("re1", schema.getReactionIdentifier());
+      assertEquals("re1", schema.getElementId());
       assertEquals(3.0, schema.getLineWidth(), EPSILON);
       assertEquals(Color.RED, schema.getColor());
     } catch (Exception e) {
diff --git a/service/src/test/java/lcsb/mapviewer/services/utils/ColorSchemaReaderXlsTest.java b/service/src/test/java/lcsb/mapviewer/services/utils/ColorSchemaReaderXlsTest.java
index 0c148914250f9010078c1e2c64130e9d20afdc54..bcca8eab38c691b33e0fc71424fb98b68ec6bedb 100644
--- a/service/src/test/java/lcsb/mapviewer/services/utils/ColorSchemaReaderXlsTest.java
+++ b/service/src/test/java/lcsb/mapviewer/services/utils/ColorSchemaReaderXlsTest.java
@@ -107,7 +107,7 @@ public class ColorSchemaReaderXlsTest extends ServiceTestFunctions {
 			Collection<ColorSchema> collection = reader.readColorSchema("testFiles/coloring/coloring.xls", "reactionSchema");
 			assertEquals(1, collection.size());
 			ColorSchema schema = collection.iterator().next();
-			assertEquals("re1", schema.getReactionIdentifier());
+			assertEquals("re1", schema.getElementId());
 			assertEquals(3.0, schema.getLineWidth(), EPSILON);
 			assertEquals(Color.RED, schema.getColor());
 		} catch (Exception e) {
diff --git a/service/src/test/java/lcsb/mapviewer/services/utils/ColorSchemaReaderXlsxTest.java b/service/src/test/java/lcsb/mapviewer/services/utils/ColorSchemaReaderXlsxTest.java
index 05bec4e13894aadda72459edf39a1407b508b6d6..e80d01d43bb4e369422659e57c924426aa5e4b12 100644
--- a/service/src/test/java/lcsb/mapviewer/services/utils/ColorSchemaReaderXlsxTest.java
+++ b/service/src/test/java/lcsb/mapviewer/services/utils/ColorSchemaReaderXlsxTest.java
@@ -107,7 +107,7 @@ public class ColorSchemaReaderXlsxTest extends ServiceTestFunctions {
 			Collection<ColorSchema> collection = reader.readColorSchema("testFiles/coloring/coloring.xlsx", "reactionSchema");
 			assertEquals(1, collection.size());
 			ColorSchema schema = collection.iterator().next();
-			assertEquals("re1", schema.getReactionIdentifier());
+			assertEquals("re1", schema.getElementId());
 			assertEquals(3.0, schema.getLineWidth(), EPSILON);
 			assertEquals(Color.RED, schema.getColor());
 		} catch (Exception e) {
diff --git a/service/testFiles/export_with_artifitial_comp.xml b/service/testFiles/export_with_artifitial_comp.xml
index 4f66b8045188b4d56bb9f9e1c889bb486534b914..72a9a9e799cb173b0ec55b71906563eb0a6879b3 100644
--- a/service/testFiles/export_with_artifitial_comp.xml
+++ b/service/testFiles/export_with_artifitial_comp.xml
@@ -3422,90 +3422,6 @@ Y
 <title/>
 </head>
 <body>
-<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#">
-<rdf:Description rdf:about="#s2616">
-<bqbiol:hasVersion>
-<rdf:Bag>
-<rdf:li rdf:resource="urn:miriam:refseq:NP_115903.1"/>
-</rdf:Bag>
-</bqbiol:hasVersion>
-<bqbiol:hasVersion>
-<rdf:Bag>
-<rdf:li rdf:resource="urn:miriam:panther.family:MAP1_LC3"/>
-</rdf:Bag>
-</bqbiol:hasVersion>
-<bqbiol:hasVersion>
-<rdf:Bag>
-<rdf:li rdf:resource="urn:miriam:panther.family:PTHR10969"/>
-</rdf:Bag>
-</bqbiol:hasVersion>
-<bqbiol:hasVersion>
-<rdf:Bag>
-<rdf:li rdf:resource="urn:miriam:ncbigene:84557"/>
-</rdf:Bag>
-</bqbiol:hasVersion>
-<bqbiol:hasVersion>
-<rdf:Bag>
-<rdf:li rdf:resource="urn:miriam:kegg.genes:hsa:84557"/>
-</rdf:Bag>
-</bqbiol:hasVersion>
-<bqbiol:isVersionOf>
-<rdf:Bag>
-<rdf:li rdf:resource="urn:miriam:pubmed:17580304"/>
-</rdf:Bag>
-</bqbiol:isVersionOf>
-<bqbiol:isDescribedBy>
-<rdf:Bag>
-<rdf:li rdf:resource="urn:miriam:pubmed:17580304"/>
-</rdf:Bag>
-</bqbiol:isDescribedBy>
-<bqbiol:isVersionOf>
-<rdf:Bag>
-<rdf:li rdf:resource="urn:miriam:pubmed:8833088"/>
-</rdf:Bag>
-</bqbiol:isVersionOf>
-<bqbiol:hasVersion>
-<rdf:Bag>
-<rdf:li rdf:resource="urn:miriam:refseq:NP_852610.1"/>
-</rdf:Bag>
-</bqbiol:hasVersion>
-<bqbiol:hasVersion>
-<rdf:Bag>
-<rdf:li rdf:resource="urn:miriam:entrez.gene:84557"/>
-</rdf:Bag>
-</bqbiol:hasVersion>
-<bqbiol:isDescribedBy>
-<rdf:Bag>
-<rdf:li rdf:resource="urn:miriam:pubmed:8833088"/>
-</rdf:Bag>
-</bqbiol:isDescribedBy>
-<bqbiol:hasVersion>
-<rdf:Bag>
-<rdf:li rdf:resource="urn:miriam:pharmgkb.pathways:PA30582"/>
-</rdf:Bag>
-</bqbiol:hasVersion>
-<bqbiol:hasVersion>
-<rdf:Bag>
-<rdf:li rdf:resource="urn:miriam:kegg.genes:hsa%3A84557"/>
-</rdf:Bag>
-</bqbiol:hasVersion>
-<bqbiol:hasVersion>
-<rdf:Bag>
-<rdf:li rdf:resource="urn:miriam:hgnc:6838"/>
-</rdf:Bag>
-</bqbiol:hasVersion>
-<bqbiol:hasVersion>
-<rdf:Bag>
-<rdf:li rdf:resource="urn:miriam:panther.family%3AMAP1_LC3"/>
-</rdf:Bag>
-</bqbiol:hasVersion>
-<bqbiol:hasVersion>
-<rdf:Bag>
-<rdf:li rdf:resource="urn:miriam:panther.family%3APTHR10969"/>
-</rdf:Bag>
-</bqbiol:hasVersion>
-</rdf:Description>
-</rdf:RDF>
 </body>
 </html>
 </notes>
@@ -3610,80 +3526,6 @@ Y
 <title/>
 </head>
 <body>
-<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#">
-<rdf:Description rdf:about="#s2612">
-<bqbiol:hasVersion>
-<rdf:Bag>
-<rdf:li rdf:resource="urn:miriam:panther.family:APG12"/>
-</rdf:Bag>
-</bqbiol:hasVersion>
-<bqbiol:hasVersion>
-<rdf:Bag>
-<rdf:li rdf:resource="urn:miriam:entrez.gene:9140"/>
-</rdf:Bag>
-</bqbiol:hasVersion>
-<bqbiol:isVersionOf>
-<rdf:Bag>
-<rdf:li rdf:resource="urn:miriam:pubmed:9852036"/>
-</rdf:Bag>
-</bqbiol:isVersionOf>
-<bqbiol:hasVersion>
-<rdf:Bag>
-<rdf:li rdf:resource="urn:miriam:panther.family:PTHR13385"/>
-</rdf:Bag>
-</bqbiol:hasVersion>
-<bqbiol:hasVersion>
-<rdf:Bag>
-<rdf:li rdf:resource="urn:miriam:reactome:REACT_25642"/>
-</rdf:Bag>
-</bqbiol:hasVersion>
-<bqbiol:hasVersion>
-<rdf:Bag>
-<rdf:li rdf:resource="urn:miriam:kegg.genes:hsa%3A9140"/>
-</rdf:Bag>
-</bqbiol:hasVersion>
-<bqbiol:hasVersion>
-<rdf:Bag>
-<rdf:li rdf:resource="urn:miriam:refseq:NP_004698.3"/>
-</rdf:Bag>
-</bqbiol:hasVersion>
-<bqbiol:hasVersion>
-<rdf:Bag>
-<rdf:li rdf:resource="urn:miriam:panther.family%3APTHR13385"/>
-</rdf:Bag>
-</bqbiol:hasVersion>
-<bqbiol:hasVersion>
-<rdf:Bag>
-<rdf:li rdf:resource="urn:miriam:pharmgkb.pathways:PA24879"/>
-</rdf:Bag>
-</bqbiol:hasVersion>
-<bqbiol:isDescribedBy>
-<rdf:Bag>
-<rdf:li rdf:resource="urn:miriam:pubmed:9852036"/>
-</rdf:Bag>
-</bqbiol:isDescribedBy>
-<bqbiol:hasVersion>
-<rdf:Bag>
-<rdf:li rdf:resource="urn:miriam:ncbigene:9140"/>
-</rdf:Bag>
-</bqbiol:hasVersion>
-<bqbiol:hasVersion>
-<rdf:Bag>
-<rdf:li rdf:resource="urn:miriam:panther.family%3AAPG12"/>
-</rdf:Bag>
-</bqbiol:hasVersion>
-<bqbiol:hasVersion>
-<rdf:Bag>
-<rdf:li rdf:resource="urn:miriam:kegg.genes:hsa:9140"/>
-</rdf:Bag>
-</bqbiol:hasVersion>
-<bqbiol:hasVersion>
-<rdf:Bag>
-<rdf:li rdf:resource="urn:miriam:hgnc:588"/>
-</rdf:Bag>
-</bqbiol:hasVersion>
-</rdf:Description>
-</rdf:RDF>
 </body>
 </html>
 </notes>
@@ -3778,85 +3620,6 @@ Y
 <title/>
 </head>
 <body>
-<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#">
-<rdf:Description rdf:about="#s1747">
-<bqbiol:hasVersion>
-<rdf:Bag>
-<rdf:li rdf:resource="urn:miriam:refseq:NP_115903.1"/>
-</rdf:Bag>
-</bqbiol:hasVersion>
-<bqbiol:hasVersion>
-<rdf:Bag>
-<rdf:li rdf:resource="urn:miriam:panther.family:MAP1_LC3"/>
-</rdf:Bag>
-</bqbiol:hasVersion>
-<bqbiol:hasVersion>
-<rdf:Bag>
-<rdf:li rdf:resource="urn:miriam:panther.family:PTHR10969"/>
-</rdf:Bag>
-</bqbiol:hasVersion>
-<bqbiol:hasVersion>
-<rdf:Bag>
-<rdf:li rdf:resource="urn:miriam:ncbigene:84557"/>
-</rdf:Bag>
-</bqbiol:hasVersion>
-<bqbiol:hasVersion>
-<rdf:Bag>
-<rdf:li rdf:resource="urn:miriam:kegg.genes:hsa:84557"/>
-</rdf:Bag>
-</bqbiol:hasVersion>
-<bqbiol:isVersionOf>
-<rdf:Bag>
-<rdf:li rdf:resource="urn:miriam:pubmed:17580304"/>
-</rdf:Bag>
-</bqbiol:isVersionOf>
-<bqbiol:isDescribedBy>
-<rdf:Bag>
-<rdf:li rdf:resource="urn:miriam:pubmed:17580304"/>
-</rdf:Bag>
-</bqbiol:isDescribedBy>
-<bqbiol:isVersionOf>
-<rdf:Bag>
-<rdf:li rdf:resource="urn:miriam:pubmed:8833088"/>
-</rdf:Bag>
-</bqbiol:isVersionOf>
-<bqbiol:hasVersion>
-<rdf:Bag>
-<rdf:li rdf:resource="urn:miriam:refseq:NP_852610.1"/>
-</rdf:Bag>
-</bqbiol:hasVersion>
-<bqbiol:isDescribedBy>
-<rdf:Bag>
-<rdf:li rdf:resource="urn:miriam:pubmed:8833088"/>
-</rdf:Bag>
-</bqbiol:isDescribedBy>
-<bqbiol:hasVersion>
-<rdf:Bag>
-<rdf:li rdf:resource="urn:miriam:pharmgkb.pathways:PA30582"/>
-</rdf:Bag>
-</bqbiol:hasVersion>
-<bqbiol:hasVersion>
-<rdf:Bag>
-<rdf:li rdf:resource="urn:miriam:kegg.genes:hsa%3A84557"/>
-</rdf:Bag>
-</bqbiol:hasVersion>
-<bqbiol:hasVersion>
-<rdf:Bag>
-<rdf:li rdf:resource="urn:miriam:hgnc:6838"/>
-</rdf:Bag>
-</bqbiol:hasVersion>
-<bqbiol:hasVersion>
-<rdf:Bag>
-<rdf:li rdf:resource="urn:miriam:panther.family%3AMAP1_LC3"/>
-</rdf:Bag>
-</bqbiol:hasVersion>
-<bqbiol:hasVersion>
-<rdf:Bag>
-<rdf:li rdf:resource="urn:miriam:panther.family%3APTHR10969"/>
-</rdf:Bag>
-</bqbiol:hasVersion>
-</rdf:Description>
-</rdf:RDF>
 </body>
 </html>
 </notes>
@@ -3976,8 +3739,19 @@ Y
 <title/>
 </head>
 <body>
-<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#">
-<rdf:Description rdf:about="#s2615">
+</body>
+</html>
+</notes>
+<annotation>
+<celldesigner:extension>
+<celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment>
+<celldesigner:speciesIdentity>
+<celldesigner:class>PROTEIN</celldesigner:class>
+<celldesigner:proteinReference>pr664</celldesigner:proteinReference>
+</celldesigner:speciesIdentity>
+</celldesigner:extension>
+<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
+<rdf:Description rdf:about="#s2481">
 <bqbiol:hasVersion>
 <rdf:Bag>
 <rdf:li rdf:resource="urn:miriam:refseq:NP_001177196.1"/>
@@ -3990,7 +3764,7 @@ Y
 </bqbiol:hasVersion>
 <bqbiol:hasVersion>
 <rdf:Bag>
-<rdf:li rdf:resource="urn:miriam:kegg.genes:hsa:55054"/>
+<rdf:li rdf:resource="urn:miriam:kegg.genes:hsa%3A55054"/>
 </rdf:Bag>
 </bqbiol:hasVersion>
 <bqbiol:hasVersion>
@@ -4030,139 +3804,15 @@ Y
 </bqbiol:hasVersion>
 </rdf:Description>
 </rdf:RDF>
-</body>
-</html>
-</notes>
-<annotation>
-<celldesigner:extension>
-<celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment>
-<celldesigner:speciesIdentity>
-<celldesigner:class>PROTEIN</celldesigner:class>
-<celldesigner:proteinReference>pr664</celldesigner:proteinReference>
-</celldesigner:speciesIdentity>
-</celldesigner:extension>
-<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
-<rdf:Description rdf:about="#s2481">
-<bqbiol:hasVersion>
-<rdf:Bag>
-<rdf:li rdf:resource="urn:miriam:refseq:NP_001177196.1"/>
-</rdf:Bag>
-</bqbiol:hasVersion>
-<bqbiol:hasVersion>
-<rdf:Bag>
-<rdf:li rdf:resource="urn:miriam:kegg.genes:hsa%3A55054"/>
-</rdf:Bag>
-</bqbiol:hasVersion>
-<bqbiol:hasVersion>
-<rdf:Bag>
-<rdf:li rdf:resource="urn:miriam:kegg.genes:hsa%3A55054"/>
-</rdf:Bag>
-</bqbiol:hasVersion>
-<bqbiol:hasVersion>
-<rdf:Bag>
-<rdf:li rdf:resource="urn:miriam:refseq:NP_110430.5"/>
-</rdf:Bag>
-</bqbiol:hasVersion>
-<bqbiol:hasVersion>
-<rdf:Bag>
-<rdf:li rdf:resource="urn:miriam:refseq:NP_001177195.1"/>
-</rdf:Bag>
-</bqbiol:hasVersion>
-<bqbiol:hasVersion>
-<rdf:Bag>
-<rdf:li rdf:resource="urn:miriam:refseq:NP_060444.3"/>
-</rdf:Bag>
-</bqbiol:hasVersion>
-<bqbiol:hasVersion>
-<rdf:Bag>
-<rdf:li rdf:resource="urn:miriam:refseq:NP_942593.2"/>
-</rdf:Bag>
-</bqbiol:hasVersion>
-<bqbiol:hasVersion>
-<rdf:Bag>
-<rdf:li rdf:resource="urn:miriam:ncbigene:55054"/>
-</rdf:Bag>
-</bqbiol:hasVersion>
-<bqbiol:isVersionOf>
-<rdf:Bag>
-<rdf:li rdf:resource="urn:miriam:entrez.gene:20959619"/>
-</rdf:Bag>
-</bqbiol:isVersionOf>
-<bqbiol:hasVersion>
-<rdf:Bag>
-<rdf:li rdf:resource="urn:miriam:hgnc:21498"/>
-</rdf:Bag>
-</bqbiol:hasVersion>
-</rdf:Description>
-</rdf:RDF>
-</annotation>
-</species>
-<species metaid="s2480" id="s2480" name="ATG5" compartment="c1" initialAmount="0" charge="0">
-<notes>
-<html xmlns="http://www.w3.org/1999/xhtml">
-<head>
-<title/>
-</head>
-<body>
-<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#">
-<rdf:Description rdf:about="#s2614">
-<bqbiol:hasVersion>
-<rdf:Bag>
-<rdf:li rdf:resource="urn:miriam:panther.family%3APTHR13040"/>
-</rdf:Bag>
-</bqbiol:hasVersion>
-<bqbiol:hasVersion>
-<rdf:Bag>
-<rdf:li rdf:resource="urn:miriam:ncbigene:9474"/>
-</rdf:Bag>
-</bqbiol:hasVersion>
-<bqbiol:hasVersion>
-<rdf:Bag>
-<rdf:li rdf:resource="urn:miriam:reactome:REACT_25578"/>
-</rdf:Bag>
-</bqbiol:hasVersion>
-<bqbiol:hasVersion>
-<rdf:Bag>
-<rdf:li rdf:resource="urn:miriam:kegg.genes:hsa%3A9474"/>
-</rdf:Bag>
-</bqbiol:hasVersion>
-<bqbiol:hasVersion>
-<rdf:Bag>
-<rdf:li rdf:resource="urn:miriam:kegg.genes:hsa:9474"/>
-</rdf:Bag>
-</bqbiol:hasVersion>
-<bqbiol:hasVersion>
-<rdf:Bag>
-<rdf:li rdf:resource="urn:miriam:panther.family%3AAPG5"/>
-</rdf:Bag>
-</bqbiol:hasVersion>
-<bqbiol:hasVersion>
-<rdf:Bag>
-<rdf:li rdf:resource="urn:miriam:refseq:NP_004840.1"/>
-</rdf:Bag>
-</bqbiol:hasVersion>
-<bqbiol:hasVersion>
-<rdf:Bag>
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-<rdf:Bag>
-<rdf:li rdf:resource="urn:miriam:panther.family:APG5"/>
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-<bqbiol:hasVersion>
-<rdf:Bag>
-<rdf:li rdf:resource="urn:miriam:hgnc:589"/>
-</rdf:Bag>
-</bqbiol:hasVersion>
-</rdf:Description>
-</rdf:RDF>
+</annotation>
+</species>
+<species metaid="s2480" id="s2480" name="ATG5" compartment="c1" initialAmount="0" charge="0">
+<notes>
+<html xmlns="http://www.w3.org/1999/xhtml">
+<head>
+<title/>
+</head>
+<body>
 </body>
 </html>
 </notes>
@@ -4242,45 +3892,6 @@ Y
 <title/>
 </head>
 <body>
-<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#">
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-<rdf:li rdf:resource="urn:miriam:ncbigene:10490"/>
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-</rdf:Bag>
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-<bqbiol:hasVersion>
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-</rdf:Bag>
-</bqbiol:hasVersion>
-<bqbiol:hasVersion>
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-<rdf:li rdf:resource="urn:miriam:hgnc:17793"/>
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-<bqbiol:hasVersion>
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-<rdf:li rdf:resource="urn:miriam:kegg.genes:hsa%3A10490"/>
-</rdf:Bag>
-</bqbiol:hasVersion>
-</rdf:Description>
-</rdf:RDF>
 </body>
 </html>
 </notes>
@@ -4343,70 +3954,6 @@ Y
 <title/>
 </head>
 <body>
-<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#">
-<rdf:Description rdf:about="#s2609">
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-<rdf:Bag>
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-<rdf:li rdf:resource="urn:miriam:reactome:REACT_20045"/>
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-<rdf:Bag>
-<rdf:li rdf:resource="urn:miriam:pubmed:9614193"/>
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-<bqbiol:hasVersion>
-<rdf:Bag>
-<rdf:li rdf:resource="urn:miriam:ncbigene:8673"/>
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-<bqbiol:hasVersion>
-<rdf:Bag>
-<rdf:li rdf:resource="urn:miriam:pharmgkb.pathways:PA37271"/>
-</rdf:Bag>
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-<rdf:Bag>
-<rdf:li rdf:resource="urn:miriam:pubmed:9878266"/>
-</rdf:Bag>
-</bqbiol:isDescribedBy>
-<bqbiol:hasVersion>
-<rdf:Bag>
-<rdf:li rdf:resource="urn:miriam:refseq:NP_003752.2"/>
-</rdf:Bag>
-</bqbiol:hasVersion>
-</rdf:Description>
-</rdf:RDF>
 </body>
 </html>
 </notes>
@@ -4527,8 +4074,22 @@ Y
 <title/>
 </head>
 <body>
-<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#">
-<rdf:Description rdf:about="#s2190">
+</body>
+</html>
+</notes>
+<annotation>
+<celldesigner:extension>
+<celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment>
+<celldesigner:speciesIdentity>
+<celldesigner:class>PROTEIN</celldesigner:class>
+<celldesigner:proteinReference>pr1029</celldesigner:proteinReference>
+</celldesigner:speciesIdentity>
+<celldesigner:listOfCatalyzedReactions>
+<celldesigner:catalyzed reaction="re17"/>
+</celldesigner:listOfCatalyzedReactions>
+</celldesigner:extension>
+<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
+<rdf:Description rdf:about="#s2217">
 <bqbiol:hasVersion>
 <rdf:Bag>
 <rdf:li rdf:resource="urn:miriam:pharmgkb.pathways:PA134898340"/>
@@ -4571,7 +4132,7 @@ Y
 </bqbiol:hasVersion>
 <bqbiol:hasVersion>
 <rdf:Bag>
-<rdf:li rdf:resource="urn:miriam:kegg.genes:hsa:23192"/>
+<rdf:li rdf:resource="urn:miriam:kegg.genes:hsa%3A23192"/>
 </rdf:Bag>
 </bqbiol:hasVersion>
 <bqbiol:hasVersion>
@@ -4601,103 +4162,15 @@ Y
 </bqbiol:hasVersion>
 </rdf:Description>
 </rdf:RDF>
-</body>
-</html>
-</notes>
+</annotation>
+</species>
+<species metaid="s1819" id="s1819" name="amino acids" compartment="c1" initialAmount="0" charge="0">
 <annotation>
 <celldesigner:extension>
 <celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment>
 <celldesigner:speciesIdentity>
-<celldesigner:class>PROTEIN</celldesigner:class>
-<celldesigner:proteinReference>pr1029</celldesigner:proteinReference>
-</celldesigner:speciesIdentity>
-<celldesigner:listOfCatalyzedReactions>
-<celldesigner:catalyzed reaction="re17"/>
-</celldesigner:listOfCatalyzedReactions>
-</celldesigner:extension>
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-<rdf:Description rdf:about="#s2217">
-<bqbiol:hasVersion>
-<rdf:Bag>
-<rdf:li rdf:resource="urn:miriam:pharmgkb.pathways:PA134898340"/>
-</rdf:Bag>
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-<rdf:Bag>
-<rdf:li rdf:resource="urn:miriam:refseq:NP_847896.1"/>
-</rdf:Bag>
-</bqbiol:hasVersion>
-<bqbiol:hasVersion>
-<rdf:Bag>
-<rdf:li rdf:resource="urn:miriam:panther.family:Peptidase_C54"/>
-</rdf:Bag>
-</bqbiol:hasVersion>
-<bqbiol:hasVersion>
-<rdf:Bag>
-<rdf:li rdf:resource="urn:miriam:entrez.gene:23192"/>
-</rdf:Bag>
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-<rdf:li rdf:resource="urn:miriam:kegg.genes:hsa%3A23192"/>
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-<rdf:Bag>
-<rdf:li rdf:resource="urn:miriam:panther.family%3APeptidase_C54"/>
-</rdf:Bag>
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-<bqbiol:isDescribedBy>
-<rdf:Bag>
-<rdf:li rdf:resource="urn:miriam:pubmed:12446702"/>
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-</bqbiol:isDescribedBy>
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-<rdf:Bag>
-<rdf:li rdf:resource="urn:miriam:ncbigene:23192"/>
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-<rdf:li rdf:resource="urn:miriam:kegg.genes:hsa%3A23192"/>
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-</bqbiol:isVersionOf>
-<bqbiol:hasVersion>
-<rdf:Bag>
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-</rdf:Bag>
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-<bqbiol:hasVersion>
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-<rdf:li rdf:resource="urn:miriam:panther.family%3APTHR22624"/>
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-<rdf:li rdf:resource="urn:miriam:panther.family:PTHR22624"/>
-</rdf:Bag>
-</bqbiol:hasVersion>
-</rdf:Description>
-</rdf:RDF>
-</annotation>
-</species>
-<species metaid="s1819" id="s1819" name="amino acids" compartment="c1" initialAmount="0" charge="0">
-<annotation>
-<celldesigner:extension>
-<celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment>
-<celldesigner:speciesIdentity>
-<celldesigner:class>SIMPLE_MOLECULE</celldesigner:class>
-<celldesigner:name>amino acids</celldesigner:name>
+<celldesigner:class>SIMPLE_MOLECULE</celldesigner:class>
+<celldesigner:name>amino acids</celldesigner:name>
 </celldesigner:speciesIdentity>
 </celldesigner:extension>
 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
@@ -4723,75 +4196,6 @@ Y
 <title/>
 </head>
 <body>
-<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#">
-<rdf:Description rdf:about="#s2608">
-<bqbiol:hasVersion>
-<rdf:Bag>
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-<rdf:Bag>
-<rdf:li rdf:resource="urn:miriam:kegg.genes:hsa:55626"/>
-</rdf:Bag>
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-</rdf:Bag>
-</bqbiol:isVersionOf>
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-<rdf:Bag>
-<rdf:li rdf:resource="urn:miriam:kegg.genes:hsa%3A55626"/>
-</rdf:Bag>
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-<rdf:li rdf:resource="urn:miriam:pubmed:17589504"/>
-</rdf:Bag>
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-<rdf:li rdf:resource="urn:miriam:pharmgkb.pathways:PA162376307"/>
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-<rdf:Bag>
-<rdf:li rdf:resource="urn:miriam:pubmed:17603510"/>
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-<bqbiol:isVersionOf>
-<rdf:Bag>
-<rdf:li rdf:resource="urn:miriam:entrez.gene:55626"/>
-</rdf:Bag>
-</bqbiol:isVersionOf>
-<bqbiol:isDescribedBy>
-<rdf:Bag>
-<rdf:li rdf:resource="urn:miriam:pubmed:17622796"/>
-</rdf:Bag>
-</bqbiol:isDescribedBy>
-<bqbiol:hasVersion>
-<rdf:Bag>
-<rdf:li rdf:resource="urn:miriam:ncbigene:55626"/>
-</rdf:Bag>
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-<rdf:Bag>
-<rdf:li rdf:resource="urn:miriam:pubmed:17622796"/>
-</rdf:Bag>
-</bqbiol:isVersionOf>
-</rdf:Description>
-</rdf:RDF>
 </body>
 </html>
 </notes>
@@ -4881,60 +4285,6 @@ Y
 <title/>
 </head>
 <body>
-<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#">
-<rdf:Description rdf:about="#s2607">
-<bqbiol:isVersionOf>
-<rdf:Bag>
-<rdf:li rdf:resource="urn:miriam:pubmed:18843052"/>
-</rdf:Bag>
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-<bqbiol:hasVersion>
-<rdf:Bag>
-<rdf:li rdf:resource="urn:miriam:refseq:NP_055739.2"/>
-</rdf:Bag>
-</bqbiol:hasVersion>
-<bqbiol:hasVersion>
-<rdf:Bag>
-<rdf:li rdf:resource="urn:miriam:hgnc:19962"/>
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-<bqbiol:hasVersion>
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-<rdf:li rdf:resource="urn:miriam:pharmgkb.pathways:PA165478560"/>
-</rdf:Bag>
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-<bqbiol:hasVersion>
-<rdf:Bag>
-<rdf:li rdf:resource="urn:miriam:entrez.gene:22863"/>
-</rdf:Bag>
-</bqbiol:hasVersion>
-<bqbiol:hasVersion>
-<rdf:Bag>
-<rdf:li rdf:resource="urn:miriam:kegg.genes:hsa%3A22863"/>
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-<rdf:Bag>
-<rdf:li rdf:resource="urn:miriam:ncbigene:22863"/>
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-<bqbiol:isDescribedBy>
-<rdf:Bag>
-<rdf:li rdf:resource="urn:miriam:pubmed:18843052"/>
-</rdf:Bag>
-</bqbiol:isDescribedBy>
-<bqbiol:hasVersion>
-<rdf:Bag>
-<rdf:li rdf:resource="urn:miriam:pharmgkb.pathways:PA134921789"/>
-</rdf:Bag>
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-<rdf:Bag>
-<rdf:li rdf:resource="urn:miriam:kegg.genes:hsa:22863"/>
-</rdf:Bag>
-</bqbiol:hasVersion>
-</rdf:Description>
-</rdf:RDF>
 </body>
 </html>
 </notes>
@@ -5009,8 +4359,19 @@ Y
 <title/>
 </head>
 <body>
-<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#">
-<rdf:Description rdf:about="#s1743">
+</body>
+</html>
+</notes>
+<annotation>
+<celldesigner:extension>
+<celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment>
+<celldesigner:speciesIdentity>
+<celldesigner:class>PROTEIN</celldesigner:class>
+<celldesigner:proteinReference>pr649</celldesigner:proteinReference>
+</celldesigner:speciesIdentity>
+</celldesigner:extension>
+<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
+<rdf:Description rdf:about="#s1785">
 <bqbiol:isVersionOf>
 <rdf:Bag>
 <rdf:li rdf:resource="urn:miriam:pubmed:9765397"/>
@@ -5043,7 +4404,7 @@ Y
 </bqbiol:hasVersion>
 <bqbiol:hasVersion>
 <rdf:Bag>
-<rdf:li rdf:resource="urn:miriam:kegg.genes:hsa:8678"/>
+<rdf:li rdf:resource="urn:miriam:kegg.genes:hsa%3A8678"/>
 </rdf:Bag>
 </bqbiol:hasVersion>
 <bqbiol:hasVersion>
@@ -5078,6 +4439,15 @@ Y
 </bqbiol:hasVersion>
 </rdf:Description>
 </rdf:RDF>
+</annotation>
+</species>
+<species metaid="s1639" id="s1639" name="BCL2" compartment="default" initialAmount="0" charge="0">
+<notes>
+<html xmlns="http://www.w3.org/1999/xhtml">
+<head>
+<title/>
+</head>
+<body>
 </body>
 </html>
 </notes>
@@ -5086,167 +4456,39 @@ Y
 <celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment>
 <celldesigner:speciesIdentity>
 <celldesigner:class>PROTEIN</celldesigner:class>
-<celldesigner:proteinReference>pr649</celldesigner:proteinReference>
+<celldesigner:proteinReference>pr292</celldesigner:proteinReference>
 </celldesigner:speciesIdentity>
 </celldesigner:extension>
 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
-<rdf:Description rdf:about="#s1785">
-<bqbiol:isVersionOf>
-<rdf:Bag>
-<rdf:li rdf:resource="urn:miriam:pubmed:9765397"/>
-</rdf:Bag>
-</bqbiol:isVersionOf>
+<rdf:Description rdf:about="#s1639">
 <bqbiol:hasVersion>
 <rdf:Bag>
-<rdf:li rdf:resource="urn:miriam:pharmgkb.pathways:PA25337"/>
+<rdf:li rdf:resource="urn:miriam:hgnc:990"/>
 </rdf:Bag>
 </bqbiol:hasVersion>
-<bqbiol:isDescribedBy>
-<rdf:Bag>
-<rdf:li rdf:resource="urn:miriam:pubmed:9765397"/>
-</rdf:Bag>
-</bqbiol:isDescribedBy>
 <bqbiol:hasVersion>
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@@ -5391,40 +4584,6 @@ Y
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@@ -5484,8 +4643,19 @@ Y
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-<rdf:Description rdf:about="#s1745">
+</body>
+</html>
+</notes>
+<annotation>
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+<celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment>
+<celldesigner:speciesIdentity>
+<celldesigner:class>PROTEIN</celldesigner:class>
+<celldesigner:proteinReference>pr652</celldesigner:proteinReference>
+</celldesigner:speciesIdentity>
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@@ -5518,7 +4688,7 @@ Y
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@@ -5538,6 +4708,15 @@ Y
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@@ -5546,222 +4725,74 @@ Y
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@@ -5791,45 +4822,6 @@ Y
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@@ -5889,50 +4881,6 @@ Y
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@@ -5997,55 +4945,6 @@ Y
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@@ -6086,272 +4985,104 @@ Y
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+<title/>
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@@ -6506,206 +5237,42 @@ Y
 </annotation>
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@@ -7388,110 +5738,6 @@ Y
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@@ -7886,40 +6038,6 @@ Y
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