diff --git a/pom.xml b/pom.xml
index 3870934ce911c5731b530ea4fff5af81741c8cf0..66393365d8277f5dd531cbfb651621d79e9137f2 100644
--- a/pom.xml
+++ b/pom.xml
@@ -80,8 +80,6 @@
 
 		<el.version>2.2.4</el.version>
 
-		<primafaces.version>6.2</primafaces.version>
-
 		<jsf.version>2.2.19</jsf.version>
 
 		<unboundid-ldapsdk.version>4.0.10</unboundid-ldapsdk.version>
@@ -126,11 +124,6 @@
 			<id>central</id>
 			<url>https://repo.maven.apache.org/maven2/</url>
 		</repository>
-		<repository>
-			<id>prime-repo</id>
-			<name>Prime Repo</name>
-			<url>https://repository.primefaces.org</url>
-		</repository>
 		<!-- Repository used for chebi -->
 		<repository>
 			<id>ebi-repo</id>
diff --git a/service/pom.xml b/service/pom.xml
index 32621827c2584f4f3d914175449d287cbbfb4e73..26fccc273e4482727cd3fb44ee2f2440398a1501 100644
--- a/service/pom.xml
+++ b/service/pom.xml
@@ -90,13 +90,6 @@
 			<version>${springframework.version}</version>
 		</dependency>
 
-		<!-- Primefaces, used for overlay objects that are passed to the client 
-			side -->
-		<dependency>
-			<groupId>org.primefaces</groupId>
-			<artifactId>primefaces</artifactId>
-			<version>${primafaces.version}</version>
-		</dependency>
 
 		<!-- Jsf, used for objects that are passed to the client side -->
 		<dependency>
diff --git a/service/src/main/java/lcsb/mapviewer/services/impl/ProjectService.java b/service/src/main/java/lcsb/mapviewer/services/impl/ProjectService.java
index 1a06e939ce48d52189efc42430add655f7c44c3d..c9f179281b75ea14b08db39dd7be095058e34af2 100644
--- a/service/src/main/java/lcsb/mapviewer/services/impl/ProjectService.java
+++ b/service/src/main/java/lcsb/mapviewer/services/impl/ProjectService.java
@@ -26,7 +26,6 @@ import org.apache.logging.log4j.LogManager;
 import org.apache.logging.log4j.Logger;
 import org.apache.logging.log4j.core.LogEvent;
 import org.hibernate.Hibernate;
-import org.primefaces.model.TreeNode;
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.stereotype.Service;
 
@@ -109,7 +108,6 @@ import lcsb.mapviewer.services.jobs.DeleteBackgroundMinervaJob;
 import lcsb.mapviewer.services.jobs.DeleteProjectMinervaJob;
 import lcsb.mapviewer.services.jobs.RefreshMiriamInfoMinervaJob;
 import lcsb.mapviewer.services.jobs.ReviveBackgroundsMinervaJob;
-import lcsb.mapviewer.services.overlay.AnnotatedObjectTreeRow;
 import lcsb.mapviewer.services.search.chemical.IChemicalService;
 import lcsb.mapviewer.services.search.drug.IDrugService;
 import lcsb.mapviewer.services.search.mirna.IMiRNAService;
@@ -511,33 +509,6 @@ public class ProjectService implements IProjectService {
     return new MinervaJob(MinervaJobType.REFRESH_MIRIAM_INFO, MinervaJobPriority.MEDIUM, params);
   }
 
-  @Override
-  public void updateClassAnnotatorTreeForUser(final User user, final TreeNode annotatorsTree, final boolean sbgnFormat,
-      final boolean networkBackgroundAsDefault) {
-    User dbUser = userDao.getById(user.getId());
-    if (dbUser.getAnnotationSchema() == null) {
-      dbUser.setAnnotationSchema(new UserAnnotationSchema());
-    }
-    UserAnnotationSchema annotationSchema = dbUser.getAnnotationSchema();
-
-    Queue<TreeNode> queue = new LinkedList<TreeNode>();
-    queue.add(annotatorsTree);
-    while (!queue.isEmpty()) {
-      TreeNode node = queue.poll();
-      queue.addAll(node.getChildren());
-      AnnotatedObjectTreeRow data = (AnnotatedObjectTreeRow) node.getData();
-      annotationSchema.addClassAnnotator(new UserClassAnnotators(data.getClazz(), data.getUsedAnnotators()));
-      annotationSchema.addClassRequiredAnnotations(
-          new UserClassRequiredAnnotations(data.getClazz(), data.getRequiredAnnotations()));
-      annotationSchema
-          .addClassValidAnnotations(new UserClassValidAnnotations(data.getClazz(), data.getValidAnnotations()));
-    }
-    annotationSchema.setSbgnFormat(sbgnFormat);
-    annotationSchema.setNetworkBackgroundAsDefault(networkBackgroundAsDefault);
-    userService.updateUser(dbUser);
-    user.setAnnotationSchema(annotationSchema);
-  }
-
   @Override
   public void updateProject(final Project project) {
     projectDao.update(project);
diff --git a/service/src/main/java/lcsb/mapviewer/services/interfaces/IProjectService.java b/service/src/main/java/lcsb/mapviewer/services/interfaces/IProjectService.java
index 6f4c657d5b202d70e3549fefa4da2300cf45a930..afdebf400c09dc79e5d7f6a0ce6ca151639dde5a 100644
--- a/service/src/main/java/lcsb/mapviewer/services/interfaces/IProjectService.java
+++ b/service/src/main/java/lcsb/mapviewer/services/interfaces/IProjectService.java
@@ -4,7 +4,6 @@ import java.io.IOException;
 import java.util.List;
 import java.util.Set;
 
-import org.primefaces.model.TreeNode;
 import org.springframework.transaction.annotation.Transactional;
 
 import lcsb.mapviewer.commands.CommandExecutionException;
@@ -92,26 +91,6 @@ public interface IProjectService extends MinervaJobExecutor {
   @Transactional
   Project createProject(final CreateProjectParams params) throws SecurityException;
 
-  /**
-   * Update default set of annotators, lists of required/valid annotations for a
-   * given user and default params used when creating project.
-   * 
-   * @param user
-   *          user for which we update information
-   * @param sbgnFormat
-   *          new
-   *          {@link lcsb.mapviewer.model.user.UserAnnotationSchema#sbgnFormat}
-   *          value
-   * @param networkBackgroundAsDefault
-   *          new networkBackgroundAsDefault value
-   * @param annotatorsTree
-   *          {@link TreeNode} that contains information about all classes that
-   *          can be annotated
-   */
-  @Transactional
-  void updateClassAnnotatorTreeForUser(final User user, final TreeNode annotatorsTree, final boolean sbgnFormat,
-      final boolean networkBackgroundAsDefault);
-
   /**
    * Method that updates information about raw {@link Project} object.
    *