diff --git a/vcell-client/pom.xml b/vcell-client/pom.xml
index a822a73b6b..090f51abb0 100644
--- a/vcell-client/pom.xml
+++ b/vcell-client/pom.xml
@@ -2,8 +2,20 @@
 <project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
 	xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
 	<modelVersion>4.0.0</modelVersion>
-
-	<parent>
+    <build>
+        <plugins>
+            <plugin>
+                <groupId>org.apache.maven.plugins</groupId>
+                <artifactId>maven-compiler-plugin</artifactId>
+                <configuration>
+                    <source>11</source>
+                    <target>11</target>
+                </configuration>
+            </plugin>
+        </plugins>
+    </build>
+
+    <parent>
 		<groupId>org.vcell</groupId>
 		<artifactId>vcell-pom</artifactId>
 		<version>0.0.1-SNAPSHOT</version>
diff --git a/vcell-admin/src/main/java/cbit/vcell/server/manage/ServerConfiguration.java b/vcell-client/src/main/java/cbit/image/gui/manage/ServerConfiguration.java
similarity index 96%
rename from vcell-admin/src/main/java/cbit/vcell/server/manage/ServerConfiguration.java
rename to vcell-client/src/main/java/cbit/image/gui/manage/ServerConfiguration.java
index f4333c9d0b..79b245569c 100644
--- a/vcell-admin/src/main/java/cbit/vcell/server/manage/ServerConfiguration.java
+++ b/vcell-client/src/main/java/cbit/image/gui/manage/ServerConfiguration.java
@@ -1,129 +1,129 @@
-/*
- * Copyright (C) 1999-2011 University of Connecticut Health Center
- *
- * Licensed under the MIT License (the "License").
- * You may not use this file except in compliance with the License.
- * You may obtain a copy of the License at:
- *
- *  http://www.opensource.org/licenses/mit-license.php
- */
-
-package cbit.vcell.server.manage;
-
-import java.io.File;
-import java.io.FileNotFoundException;
-import java.io.FileReader;
-import java.io.IOException;
-import java.io.LineNumberReader;
-import java.util.Vector;/**
- * Insert the type's description here.
- * Creation date: (10/24/2001 2:25:13 PM)
- * @author: Ion Moraru
- */
-public class ServerConfiguration {
-	private VCellHost[] allHosts = new VCellHost[0];
-/**
- * Insert the method's description here.
- * Creation date: (10/24/2001 3:29:24 PM)
- * @param configurationFile java.io.File
- * @exception java.io.IOException The exception description.
- * @exception java.io.FileNotFoundException The exception description.
- */
-public ServerConfiguration(File configurationFile) throws IOException, FileNotFoundException {
-	LineNumberReader reader = new LineNumberReader(new FileReader(configurationFile));
-	Vector hosts = new Vector();
-	VCellHost host = null;
-	String line = reader.readLine();
-	while (line != null) {
-		if (!line.startsWith("#")) {
-			if(line.startsWith("hosttype=")) {
-				if (host != null) hosts.add(host);
-				String type = line.substring(line.indexOf("=") + 1);
-				if (type.equals("vcell")) {
-					host = new VCellHost(VCellHost.VCELL_SERVER);
-				} else if (type.equals("data")) {
-					host = new VCellHost(VCellHost.DATA_SERVER);
-				} else if (type.equals("database")) {
-					host = new VCellHost(VCellHost.DATABASE_SERVER);
-				} else if (type.equals("compute")) {
-					host = new VCellHost(VCellHost.COMPUTE_SERVER);
-				} else {
-					host = null;
-				}
-			} else if (line.startsWith("name=")) {
-				if (host != null) host.setName(line.substring(line.indexOf("=") + 1));
-			} else if (line.startsWith("port=")) {
-				if (host != null) host.setPort(Integer.parseInt(line.substring(line.indexOf("=") + 1)));
-			} else if (line.startsWith("startcmd=")) {
-				if (host != null) host.setStartCommand(line.substring(line.indexOf("=") + 1));
-			} else if (line.startsWith("stopcmd=")) {
-				if (host != null) host.setStopCommand(line.substring(line.indexOf("=") + 1));
-			} else if (line.startsWith("logfile=")) {
-				if (host != null) host.setLogFile(new File(line.substring(line.indexOf("=") + 1)));
-			} else if (line.startsWith("restart=")) {
-				if (host != null) host.setRestartIfDead(Boolean.valueOf(line.substring(line.indexOf("=") + 1)).booleanValue());
-			}
-		}
-		line = reader.readLine();
-	}
-	if (host != null) hosts.add(host);
-	allHosts = ((VCellHost[])org.vcell.util.BeanUtils.getArray(hosts, VCellHost.class));
-}
-/**
- * Insert the method's description here.
- * Creation date: (10/24/2001 7:04:58 PM)
- * @return cbit.vcell.server.manage.VCellHost[]
- */
-public VCellHost[] getComputeServerHosts() {
-	return getHosts(VCellHost.COMPUTE_SERVER);
-}
-/**
- * Insert the method's description here.
- * Creation date: (10/24/2001 7:04:58 PM)
- * @return cbit.vcell.server.manage.VCellHost[]
- */
-public VCellHost[] getDatabaseServerHosts() {
-	return getHosts(VCellHost.DATABASE_SERVER);
-}
-/**
- * Insert the method's description here.
- * Creation date: (10/24/2001 7:04:58 PM)
- * @return cbit.vcell.server.manage.VCellHost[]
- */
-public VCellHost[] getDataServerHosts() {
-	return getHosts(VCellHost.DATA_SERVER);
-}
-/**
- * Insert the method's description here.
- * Creation date: (10/24/2001 7:13:10 PM)
- * @return cbit.vcell.server.manage.VCellHost[]
- * @param hostType int
- */
-public VCellHost[] getHosts(int hostType) {
-	synchronized (allHosts) {
-		int n = 0;
-		for (int i=0;i<allHosts.length;i++) {
-			if (allHosts[i].getType() == hostType) {
-				n++;
-			}
-		}
-		VCellHost[] hosts = new VCellHost[n];
-		n = 0;
-		for (int i=0;i<allHosts.length;i++) {
-			if (allHosts[i].getType() == hostType) {
-				hosts[n] = allHosts[i];
-				n++;
-			}
-		}
-		return hosts;
-	}
-}
-/**
- * Insert the method's description here.
- * Creation date: (10/24/2001 7:04:58 PM)
- * @return cbit.vcell.server.manage.VCellHost[]
- */
-public VCellHost[] getVCellServerHosts() {
-	return getHosts(VCellHost.VCELL_SERVER);
-}
-}
+/*
+ * Copyright (C) 1999-2011 University of Connecticut Health Center
+ *
+ * Licensed under the MIT License (the "License").
+ * You may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at:
+ *
+ *  http://www.opensource.org/licenses/mit-license.php
+ */
+
+package cbit.image.gui.manage;
+
+import java.io.File;
+import java.io.FileNotFoundException;
+import java.io.FileReader;
+import java.io.IOException;
+import java.io.LineNumberReader;
+import java.util.Vector;/**
+ * Insert the type's description here.
+ * Creation date: (10/24/2001 2:25:13 PM)
+ * @author: Ion Moraru
+ */
+public class ServerConfiguration {
+	private VCellHost[] allHosts = new VCellHost[0];
+/**
+ * Insert the method's description here.
+ * Creation date: (10/24/2001 3:29:24 PM)
+ * @param configurationFile java.io.File
+ * @exception java.io.IOException The exception description.
+ * @exception java.io.FileNotFoundException The exception description.
+ */
+public ServerConfiguration(File configurationFile) throws IOException, FileNotFoundException {
+	LineNumberReader reader = new LineNumberReader(new FileReader(configurationFile));
+	Vector hosts = new Vector();
+	VCellHost host = null;
+	String line = reader.readLine();
+	while (line != null) {
+		if (!line.startsWith("#")) {
+			if(line.startsWith("hosttype=")) {
+				if (host != null) hosts.add(host);
+				String type = line.substring(line.indexOf("=") + 1);
+				if (type.equals("vcell")) {
+					host = new VCellHost(VCellHost.VCELL_SERVER);
+				} else if (type.equals("data")) {
+					host = new VCellHost(VCellHost.DATA_SERVER);
+				} else if (type.equals("database")) {
+					host = new VCellHost(VCellHost.DATABASE_SERVER);
+				} else if (type.equals("compute")) {
+					host = new VCellHost(VCellHost.COMPUTE_SERVER);
+				} else {
+					host = null;
+				}
+			} else if (line.startsWith("name=")) {
+				if (host != null) host.setName(line.substring(line.indexOf("=") + 1));
+			} else if (line.startsWith("port=")) {
+				if (host != null) host.setPort(Integer.parseInt(line.substring(line.indexOf("=") + 1)));
+			} else if (line.startsWith("startcmd=")) {
+				if (host != null) host.setStartCommand(line.substring(line.indexOf("=") + 1));
+			} else if (line.startsWith("stopcmd=")) {
+				if (host != null) host.setStopCommand(line.substring(line.indexOf("=") + 1));
+			} else if (line.startsWith("logfile=")) {
+				if (host != null) host.setLogFile(new File(line.substring(line.indexOf("=") + 1)));
+			} else if (line.startsWith("restart=")) {
+				if (host != null) host.setRestartIfDead(Boolean.valueOf(line.substring(line.indexOf("=") + 1)).booleanValue());
+			}
+		}
+		line = reader.readLine();
+	}
+	if (host != null) hosts.add(host);
+	allHosts = ((VCellHost[])org.vcell.util.BeanUtils.getArray(hosts, VCellHost.class));
+}
+/**
+ * Insert the method's description here.
+ * Creation date: (10/24/2001 7:04:58 PM)
+ * @return cbit.vcell.server.manage.VCellHost[]
+ */
+public VCellHost[] getComputeServerHosts() {
+	return getHosts(VCellHost.COMPUTE_SERVER);
+}
+/**
+ * Insert the method's description here.
+ * Creation date: (10/24/2001 7:04:58 PM)
+ * @return cbit.vcell.server.manage.VCellHost[]
+ */
+public VCellHost[] getDatabaseServerHosts() {
+	return getHosts(VCellHost.DATABASE_SERVER);
+}
+/**
+ * Insert the method's description here.
+ * Creation date: (10/24/2001 7:04:58 PM)
+ * @return cbit.vcell.server.manage.VCellHost[]
+ */
+public VCellHost[] getDataServerHosts() {
+	return getHosts(VCellHost.DATA_SERVER);
+}
+/**
+ * Insert the method's description here.
+ * Creation date: (10/24/2001 7:13:10 PM)
+ * @return cbit.vcell.server.manage.VCellHost[]
+ * @param hostType int
+ */
+public VCellHost[] getHosts(int hostType) {
+	synchronized (allHosts) {
+		int n = 0;
+		for (int i=0;i<allHosts.length;i++) {
+			if (allHosts[i].getType() == hostType) {
+				n++;
+			}
+		}
+		VCellHost[] hosts = new VCellHost[n];
+		n = 0;
+		for (int i=0;i<allHosts.length;i++) {
+			if (allHosts[i].getType() == hostType) {
+				hosts[n] = allHosts[i];
+				n++;
+			}
+		}
+		return hosts;
+	}
+}
+/**
+ * Insert the method's description here.
+ * Creation date: (10/24/2001 7:04:58 PM)
+ * @return cbit.vcell.server.manage.VCellHost[]
+ */
+public VCellHost[] getVCellServerHosts() {
+	return getHosts(VCellHost.VCELL_SERVER);
+}
+}
diff --git a/vcell-admin/src/main/java/cbit/vcell/server/manage/VCellHost.java b/vcell-client/src/main/java/cbit/image/gui/manage/VCellHost.java
similarity index 95%
rename from vcell-admin/src/main/java/cbit/vcell/server/manage/VCellHost.java
rename to vcell-client/src/main/java/cbit/image/gui/manage/VCellHost.java
index db8844a4c7..b499776469 100644
--- a/vcell-admin/src/main/java/cbit/vcell/server/manage/VCellHost.java
+++ b/vcell-client/src/main/java/cbit/image/gui/manage/VCellHost.java
@@ -1,144 +1,144 @@
-/*
- * Copyright (C) 1999-2011 University of Connecticut Health Center
- *
- * Licensed under the MIT License (the "License").
- * You may not use this file except in compliance with the License.
- * You may obtain a copy of the License at:
- *
- *  http://www.opensource.org/licenses/mit-license.php
- */
-
-package cbit.vcell.server.manage;
-
-import java.io.File;
-/**
- * Insert the type's description here.
- * Creation date: (10/24/2001 6:46:47 PM)
- * @author: Ion Moraru
- */
-public class VCellHost {
-	public final static int UNKNOWN_SERVER = -1;
-	public final static int VCELL_SERVER = 1000;
-	public final static int DATA_SERVER = 1001;
-	public final static int COMPUTE_SERVER = 1002;
-	public final static int DATABASE_SERVER = 1003;
-	private int type = 0;
-	private String name = null;
-	private int port = 0;
-	private String startCommand = null;
-	private String stopCommand = null;
-	private File logFile = null;
-	private boolean restartIfDead = false;
-/**
- * Insert the method's description here.
- * Creation date: (10/24/2001 7:00:22 PM)
- * @param type int
- */
-public VCellHost(int type) {
-	this.type=type;
-}
-/**
- * Insert the method's description here.
- * Creation date: (10/26/2001 7:14:37 PM)
- * @return java.io.File
- */
-public java.io.File getLogFile() {
-	return logFile;
-}
-/**
- * Insert the method's description here.
- * Creation date: (10/24/2001 6:48:51 PM)
- * @return java.lang.String
- */
-public java.lang.String getName() {
-	return name;
-}
-/**
- * Insert the method's description here.
- * Creation date: (10/24/2001 6:48:51 PM)
- * @return int
- */
-public int getPort() {
-	return port;
-}
-/**
- * Insert the method's description here.
- * Creation date: (10/24/2001 6:48:51 PM)
- * @return java.lang.String
- */
-public java.lang.String getStartCommand() {
-	return startCommand;
-}
-/**
- * Insert the method's description here.
- * Creation date: (10/24/2001 6:48:51 PM)
- * @return java.lang.String
- */
-public java.lang.String getStopCommand() {
-	return stopCommand;
-}
-/**
- * Insert the method's description here.
- * Creation date: (10/24/2001 6:57:37 PM)
- * @return int
- */
-public int getType() {
-	return type;
-}
-/**
- * Insert the method's description here.
- * Creation date: (10/24/2001 6:48:51 PM)
- * @return boolean
- */
-public boolean isRestartIfDead() {
-	return restartIfDead;
-}
-/**
- * Insert the method's description here.
- * Creation date: (10/26/2001 7:14:37 PM)
- * @param newLogFile java.io.File
- */
-void setLogFile(java.io.File newLogFile) {
-	logFile = newLogFile;
-}
-/**
- * Insert the method's description here.
- * Creation date: (10/24/2001 6:54:52 PM)
- * @param newName java.lang.String
- */
-void setName(java.lang.String newName) {
-	name = newName;
-}
-/**
- * Insert the method's description here.
- * Creation date: (10/24/2001 6:54:52 PM)
- * @param newPort int
- */
-void setPort(int newPort) {
-	port = newPort;
-}
-/**
- * Insert the method's description here.
- * Creation date: (10/24/2001 6:54:52 PM)
- * @param newRestartIfDead boolean
- */
-void setRestartIfDead(boolean newRestartIfDead) {
-	restartIfDead = newRestartIfDead;
-}
-/**
- * Insert the method's description here.
- * Creation date: (10/24/2001 6:54:52 PM)
- * @param newStartCommand java.lang.String
- */
-void setStartCommand(java.lang.String newStartCommand) {
-	startCommand = newStartCommand;
-}
-/**
- * Insert the method's description here.
- * Creation date: (10/24/2001 6:54:52 PM)
- * @param newStopCommand java.lang.String
- */
-void setStopCommand(java.lang.String newStopCommand) {
-	stopCommand = newStopCommand;
-}
-}
+/*
+ * Copyright (C) 1999-2011 University of Connecticut Health Center
+ *
+ * Licensed under the MIT License (the "License").
+ * You may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at:
+ *
+ *  http://www.opensource.org/licenses/mit-license.php
+ */
+
+package cbit.image.gui.manage;
+
+import java.io.File;
+/**
+ * Insert the type's description here.
+ * Creation date: (10/24/2001 6:46:47 PM)
+ * @author: Ion Moraru
+ */
+public class VCellHost {
+	public final static int UNKNOWN_SERVER = -1;
+	public final static int VCELL_SERVER = 1000;
+	public final static int DATA_SERVER = 1001;
+	public final static int COMPUTE_SERVER = 1002;
+	public final static int DATABASE_SERVER = 1003;
+	private int type = 0;
+	private String name = null;
+	private int port = 0;
+	private String startCommand = null;
+	private String stopCommand = null;
+	private File logFile = null;
+	private boolean restartIfDead = false;
+/**
+ * Insert the method's description here.
+ * Creation date: (10/24/2001 7:00:22 PM)
+ * @param type int
+ */
+public VCellHost(int type) {
+	this.type=type;
+}
+/**
+ * Insert the method's description here.
+ * Creation date: (10/26/2001 7:14:37 PM)
+ * @return java.io.File
+ */
+public java.io.File getLogFile() {
+	return logFile;
+}
+/**
+ * Insert the method's description here.
+ * Creation date: (10/24/2001 6:48:51 PM)
+ * @return java.lang.String
+ */
+public java.lang.String getName() {
+	return name;
+}
+/**
+ * Insert the method's description here.
+ * Creation date: (10/24/2001 6:48:51 PM)
+ * @return int
+ */
+public int getPort() {
+	return port;
+}
+/**
+ * Insert the method's description here.
+ * Creation date: (10/24/2001 6:48:51 PM)
+ * @return java.lang.String
+ */
+public java.lang.String getStartCommand() {
+	return startCommand;
+}
+/**
+ * Insert the method's description here.
+ * Creation date: (10/24/2001 6:48:51 PM)
+ * @return java.lang.String
+ */
+public java.lang.String getStopCommand() {
+	return stopCommand;
+}
+/**
+ * Insert the method's description here.
+ * Creation date: (10/24/2001 6:57:37 PM)
+ * @return int
+ */
+public int getType() {
+	return type;
+}
+/**
+ * Insert the method's description here.
+ * Creation date: (10/24/2001 6:48:51 PM)
+ * @return boolean
+ */
+public boolean isRestartIfDead() {
+	return restartIfDead;
+}
+/**
+ * Insert the method's description here.
+ * Creation date: (10/26/2001 7:14:37 PM)
+ * @param newLogFile java.io.File
+ */
+void setLogFile(java.io.File newLogFile) {
+	logFile = newLogFile;
+}
+/**
+ * Insert the method's description here.
+ * Creation date: (10/24/2001 6:54:52 PM)
+ * @param newName java.lang.String
+ */
+void setName(java.lang.String newName) {
+	name = newName;
+}
+/**
+ * Insert the method's description here.
+ * Creation date: (10/24/2001 6:54:52 PM)
+ * @param newPort int
+ */
+void setPort(int newPort) {
+	port = newPort;
+}
+/**
+ * Insert the method's description here.
+ * Creation date: (10/24/2001 6:54:52 PM)
+ * @param newRestartIfDead boolean
+ */
+void setRestartIfDead(boolean newRestartIfDead) {
+	restartIfDead = newRestartIfDead;
+}
+/**
+ * Insert the method's description here.
+ * Creation date: (10/24/2001 6:54:52 PM)
+ * @param newStartCommand java.lang.String
+ */
+void setStartCommand(java.lang.String newStartCommand) {
+	startCommand = newStartCommand;
+}
+/**
+ * Insert the method's description here.
+ * Creation date: (10/24/2001 6:54:52 PM)
+ * @param newStopCommand java.lang.String
+ */
+void setStopCommand(java.lang.String newStopCommand) {
+	stopCommand = newStopCommand;
+}
+}
diff --git a/vcell-client/src/main/java/cbit/vcell/client/desktop/biomodel/AnnotationsPanel.java b/vcell-client/src/main/java/cbit/vcell/client/desktop/biomodel/AnnotationsPanel.java
deleted file mode 100644
index 500f8985a2..0000000000
--- a/vcell-client/src/main/java/cbit/vcell/client/desktop/biomodel/AnnotationsPanel.java
+++ /dev/null
@@ -1,1145 +0,0 @@
-/*
- * Copyright (C) 1999-2011 University of Connecticut Health Center
- *
- * Licensed under the MIT License (the "License").
- * You may not use this file except in compliance with the License.
- * You may obtain a copy of the License at:
- *
- *  http://www.opensource.org/licenses/mit-license.php
- */
-
-package cbit.vcell.client.desktop.biomodel;
-
-import java.awt.BorderLayout;
-import java.awt.Color;
-import java.awt.Component;
-import java.awt.Dimension;
-import java.awt.GridBagConstraints;
-import java.awt.GridBagLayout;
-import java.awt.Insets;
-import java.awt.SystemColor;
-import java.awt.event.ActionEvent;
-import java.awt.event.ActionListener;
-import java.awt.event.FocusEvent;
-import java.awt.event.FocusListener;
-import java.awt.event.KeyEvent;
-import java.awt.event.KeyListener;
-import java.awt.event.MouseAdapter;
-import java.awt.event.MouseEvent;
-import java.awt.event.MouseListener;
-import java.beans.PropertyChangeEvent;
-import java.beans.PropertyChangeListener;
-import java.util.ArrayList;
-import java.util.Collections;
-import java.util.HashSet;
-import java.util.List;
-import java.util.Map;
-import java.util.StringTokenizer;
-
-import javax.swing.BorderFactory;
-import javax.swing.DefaultComboBoxModel;
-import javax.swing.DefaultListCellRenderer;
-import javax.swing.JButton;
-import javax.swing.JComboBox;
-import javax.swing.JLabel;
-import javax.swing.JList;
-import javax.swing.JOptionPane;
-import javax.swing.JPanel;
-import javax.swing.JScrollPane;
-import javax.swing.JSplitPane;
-import javax.swing.JTextField;
-import javax.swing.JTextPane;
-import javax.swing.JTree;
-import javax.swing.event.TreeSelectionEvent;
-import javax.swing.event.TreeSelectionListener;
-import javax.swing.tree.DefaultMutableTreeNode;
-import javax.swing.tree.DefaultTreeCellRenderer;
-import javax.swing.tree.DefaultTreeSelectionModel;
-import javax.swing.tree.TreePath;
-
-import org.vcell.model.rbm.MolecularType;
-import org.vcell.pathway.BioPaxObject;
-import org.vcell.sybil.models.AnnotationQualifiers;
-import org.vcell.sybil.models.miriam.MIRIAMQualifier;
-import org.vcell.sybil.models.miriam.MIRIAMRef.URNParseFailureException;
-import org.vcell.util.Compare;
-import org.vcell.util.Displayable;
-import org.vcell.util.document.BioModelInfo;
-import org.vcell.util.document.Identifiable;
-import org.vcell.util.document.MathModelInfo;
-import org.vcell.util.gui.DialogUtils;
-
-import cbit.vcell.biomodel.BioModel;
-import cbit.vcell.biomodel.meta.MiriamManager;
-import cbit.vcell.biomodel.meta.VCMetaData;
-import cbit.vcell.biomodel.meta.VCMetaDataMiriamManager;
-import cbit.vcell.biomodel.meta.VCMetaDataMiriamManager.VCMetaDataDataType;
-import cbit.vcell.biomodel.meta.MiriamManager.DataType;
-import cbit.vcell.biomodel.meta.MiriamManager.MiriamRefGroup;
-import cbit.vcell.biomodel.meta.MiriamManager.MiriamResource;
-import cbit.vcell.client.PopupGenerator;
-import cbit.vcell.desktop.BioModelCellRenderer;
-import cbit.vcell.mapping.ReactionSpec;
-import cbit.vcell.mapping.SimulationContext;
-import cbit.vcell.mapping.SpeciesContextSpec;
-import cbit.vcell.model.Model;
-import cbit.vcell.model.RbmObservable;
-import cbit.vcell.model.ReactionRule;
-import cbit.vcell.model.ReactionStep;
-import cbit.vcell.model.Species;
-import cbit.vcell.model.SpeciesContext;
-import cbit.vcell.model.Structure;
-import cbit.vcell.solver.Simulation;
-import cbit.vcell.xml.gui.MiriamTreeModel;
-import cbit.vcell.xml.gui.MiriamTreeModel.LinkNode;
-/**
- * Superclass for all the Annotation panels
- * Creation date: (11/6/2018 3:44:00 PM)
- * @author: Dan Vasilescu
- */
-@SuppressWarnings("serial")
-public class AnnotationsPanel extends DocumentEditorSubPanel {
-	private BioModel bioModel = null;
-	private VCMetaData vcMetaData = null;
-	MiriamTreeModel miriamTreeModel = null;
-	
-	private Identifiable selectedObject = null;
-	
-	public static final String ACTION_ADD ="Add...";
-	public static final String ACTION_DELETE ="Delete";
-	public static final String ACTION_REMOVE_TEXT = "Delete";
-	public static final String ACTION_GOTO ="Go";
-	public static final int COMBO_QUALIFIER_WIDTH = 140;
-	public static final int MAX_DESCRIPTION_LENGTH = 145;
-	public static final int MAX_URI_LENGTH = 130;
-	
-	private EventHandler eventHandler = new EventHandler();
-	
-	private JTree jTreeMIRIAM = null;
-
-	private JPanel jPanelNewIdentifier = null;			// add new identity dialog
-	private JPanel jPanelIdentifierManager = null;		// upper panel with the identity provider combobox, Navigate and Add buttons
-	private JPanel jPanelLowerLeft = null;				// lower left panel with the  Delete buttons
-	private JPanel jBottomPanel = null;
-	private JSplitPane splitPane = null;
-	private JScrollPane jScrollPane = null;			// will show the MIRIAM JTree
-	
-	private JComboBox jComboBoxURI = null;			// identity provider combo
-	private DefaultComboBoxModel defaultComboBoxModelURI = null;
-	private JComboBox jComboBoxQualifier = null;	// annotation qualifier combo (isDescribedBy, etc)
-	private DefaultComboBoxModel defaultComboBoxModelQualifier = new DefaultComboBoxModel();
-	
-	private JTextField jTextFieldFormalID = null;	// immortal ID text
-	private JButton jButtonAddRef = null;			// add a cross-reference
-	private JButton jButtonDeleteRef = null;		// delete selected cross-reference
-	private JButton jButtonRemoveText = null;		// remove text annotation
-
-	private JTextPane annotationTextArea = null;
-	private String emptyHtmlText = null;	// content of annotationTextArea after initialization with null
-						// will contain an empty html object "<html><header></header><body><p style="margin-top: 0"></p></body></html>"
-	private static String emptyHtmlText2 = "<html><header></header><body></body></html>";	// really empty
-	
-
-	private class EventHandler extends MouseAdapter implements ActionListener, FocusListener, PropertyChangeListener, KeyListener {
-		public void focusGained(FocusEvent e) {
-		}
-		public void focusLost(FocusEvent e) {
-			if (e.getSource() == annotationTextArea) {
-				changeTextAnnotation();
-			}
-		}
-		@Override
-		public void mouseExited(MouseEvent e) {
-			super.mouseExited(e);
-			if(e.getSource() == annotationTextArea) {
-				changeTextAnnotation();
-			}
-		}
-		@Override
-		public void propertyChange(PropertyChangeEvent evt) {
-			if (evt.getSource() instanceof SpeciesContext
-					|| evt.getSource() instanceof MolecularType
-					|| evt.getSource() instanceof ReactionRule
-					|| evt.getSource() instanceof ReactionStep
-					|| evt.getSource() instanceof RbmObservable
-					|| evt.getSource() instanceof BioModel
-					|| evt.getSource() instanceof Structure
-					|| evt.getSource() instanceof Model.ModelParameter
-					|| evt.getSource() instanceof BioPaxObject
-					
-					|| evt.getSource() instanceof SimulationContext
-//					|| evt.getSource() instanceof Simulation			// TODO: check why is not saving
-//					|| evt.getSource() instanceof SpeciesContextSpec	// TODO: can't use species name for spec too, need some hack
-//					|| evt.getSource() instanceof ReactionSpec
-					) {
-				initializeComboBoxURI();
-				updateInterface();
-			}
-		}
-		@Override
-		public void actionPerformed(ActionEvent evt) {
-			if (evt.getSource() == getJButtonAddRef()) {
-				addIdentifier();
-			} else if(evt.getSource() == getJButtonDeleteRef()) {
-				removeIdentifier();
-			} else if(evt.getSource() == getJButtonRemoveText()) {
-				removeText();
-			}
-		}
-		@Override
-		public void keyPressed(KeyEvent e) {
-		}
-		@Override
-		public void keyReleased(KeyEvent e) {
-			// too expensive to parse it at each keystroke
-//			System.out.println("key released");
-//			if (e.getSource() == annotationTextArea) {
-//				String text = annotationTextArea.getText();
-//				text = text.replaceAll("(\n\r|\n|\r)", "");
-//				text = text.replaceAll(" ", "");
-//				System.out.println(text);
-//			}
-		}
-		@Override
-		public void keyTyped(KeyEvent e) {
-		}
-	}
-	
-	public class ComboboxToolTipRenderer extends DefaultListCellRenderer {
-		List<String> tooltips;
-		@SuppressWarnings("rawtypes")
-		@Override
-		public Component getListCellRendererComponent(JList list, Object value, int index, boolean isSelected, boolean cellHasFocus) {
-			Component comp;
-			if(value == null) {
-				comp = super.getListCellRendererComponent(list, value, index, isSelected, cellHasFocus);
-			} else if(value instanceof DataType) {
-				DataType dt = (DataType)value;
-				comp = super.getListCellRendererComponent(list,dt.getDataTypeName(),index,isSelected,cellHasFocus);
-			} else if(value instanceof MIRIAMQualifier) {
-				MIRIAMQualifier mc = (MIRIAMQualifier)value;
-				comp = super.getListCellRendererComponent(list,mc.getDescription(),index,isSelected,cellHasFocus);
-			} else {
-				comp = super.getListCellRendererComponent(list, value, index, isSelected, cellHasFocus);
-			}
-			if (-1 < index && null != value && null != tooltips) {
-				list.setToolTipText(tooltips.get(index));
-			}
-		return comp;
-		}
-		public void setTooltips(List<String> tooltips) {
-			this.tooltips = tooltips;
-		}
-	}
-
-
-public AnnotationsPanel() {
-	super();
-	initialize();
-}
-
-private void handleException(java.lang.Throwable exception) {
-	System.out.println("--------- UNCAUGHT EXCEPTION ---------");
-	exception.printStackTrace(System.out);
-}
-
-private JPanel getJPanelNewIdentifier() {
-	jPanelNewIdentifier = new JPanel();
-	jPanelNewIdentifier.setLayout(new GridBagLayout());
-//	jPanelNewIdentifier.setPreferredSize(new Dimension(725, 37));
-//	jPanelNewIdentifier.setBorder(BorderFactory.createLineBorder(SystemColor.windowBorder, 2));
-		
-	VCMetaDataDataType mdt = (VCMetaDataDataType)getJComboBoxURI().getSelectedItem();
-	int gridx = 0;
-	int gridy = 0;
-	GridBagConstraints gbc = new GridBagConstraints();
-	gbc.insets = new Insets(3, 15, 3, 0);		// top left bottom right
-	gbc.gridx = gridx;
-	gbc.gridy = gridy;
-	gbc.anchor = GridBagConstraints.WEST;
-	jPanelNewIdentifier.add(new JLabel("Provider: "), gbc);
-	
-	gridx++;
-	gbc = new GridBagConstraints();
-	gbc.insets = new Insets(3, 5, 3, 4);
-	gbc.gridx = gridx;
-	gbc.gridy = gridy;
-	gbc.anchor = GridBagConstraints.WEST;
-	jPanelNewIdentifier.add(new JLabel("<html><b>" + mdt.getDataTypeName() + "</b></html>"), gbc);
-
-	// ------------------------------------- Qualifier combobox  -----------------------------
-	
-	gridx++;
-	gbc = new GridBagConstraints();
-	gbc.insets = new Insets(3, 15, 3, 0);		// top left bottom right
-	gbc.gridx = gridx;
-	gbc.gridy = gridy;
-	jPanelNewIdentifier.add(new JLabel("Qualifier"), gbc);
-	
-	gridx++;
-	gbc = new GridBagConstraints();
-	gbc.insets = new Insets(3, 5, 3, 4);
-	gbc.gridx = gridx;
-	gbc.gridy = gridy;
-	jPanelNewIdentifier.add(getJComboBoxQualifier(), gbc);
-
-	// -------------------------------------------------------------------------------
-	gridx++;
-	gbc = new GridBagConstraints();
-	gbc.insets = new Insets(3, 15, 3, 0);
-	gbc.gridx = gridx;
-	gbc.gridy = gridy;
-	gbc.anchor = GridBagConstraints.WEST;
-	jPanelNewIdentifier.add(new JLabel("Identifier ID"), gbc);
-		
-	gridx++;
-	gbc = new GridBagConstraints();
-	gbc.insets = new Insets(3, 5, 3, 4);
-	gbc.gridx = gridx;
-	gbc.gridy = gridy;
-	gbc.anchor = GridBagConstraints.WEST;
-	jPanelNewIdentifier.add(getJTextFieldFormalID(), gbc);
-	getJTextFieldFormalID().setText("NewID");
-
-	gridx++;
-	gbc = new GridBagConstraints();
-	gbc.insets = new Insets(3, 15, 3, 0);
-	gbc.gridx = gridx;
-	gbc.gridy = gridy;
-	gbc.anchor = GridBagConstraints.WEST;
-	jPanelNewIdentifier.add(new JLabel("<html>Example: <b>" + mdt.getExample() +"</b></html>"), gbc);
-	
-	gridx++;
-	gbc = new GridBagConstraints();
-	gbc.insets = new Insets(3, 15, 3, 0);
-	gbc.gridx = gridx;
-	gbc.gridy = gridy;
-	gbc.weightx = 1.0;
-	gbc.anchor = GridBagConstraints.EAST;
-	jPanelNewIdentifier.add(new JLabel(), gbc);
-
-	// ---------------------------------------------------------------------
-	gridx = 0;
-	gridy++;
-	
-	JLabel linkLabel = new JLabel();
-	String s = "<html>" + "Navigate to" + "&nbsp;<font color=\"" + "blue" + "\"><a href=" + mdt.getDataTypeURL() + ">" + mdt.getDataTypeURL() + "</a></font>&nbsp;&nbsp;";
-	s += "and find the identifier ID, then paste it in the box above." + "</html>";
-	linkLabel.setToolTipText("Double-click to open link");
-	linkLabel.setText(s);
-	linkLabel.addMouseListener(new MouseAdapter() {
-		public void mousePressed(MouseEvent e) {
-			if(e.getClickCount() == 2) {
-				showBrowseToLink(mdt);
-			}
-		} 
-	});
-	
-	gbc = new GridBagConstraints();
-	gbc.insets = new Insets(3, 15, 3, 0);
-	gbc.gridx = gridx;
-	gbc.gridy = gridy;
-	gbc.gridwidth = 8;
-	gbc.anchor = GridBagConstraints.WEST;
-	jPanelNewIdentifier.add(linkLabel, gbc);
-	
-	// ---------------------------------------------------------------------
-	List <String> rows = new ArrayList<> ();
-	String value = mdt.getDescription();
-	StringTokenizer tokenizer = new StringTokenizer(value, " ");
-	String row = "";
-	while(tokenizer.hasMoreTokens()) {
-		String word = tokenizer.nextToken();
-		if((row.length() + word.length()) > MAX_DESCRIPTION_LENGTH) {
-			rows.add(row);
-			row = word + " ";
-		} else {
-			row += word + " ";
-		}
-	}
-	if(!row.isEmpty()) {
-		rows.add(row);
-	}
-	for(String currentRow : rows) {
-		gridx = 0;
-		gridy++;
-		gbc = new GridBagConstraints();
-		gbc.insets = new Insets(3, 15, 3, 0);
-		gbc.gridx = gridx;
-		gbc.gridy = gridy;
-		gbc.gridwidth = 8;
-		gbc.fill = GridBagConstraints.HORIZONTAL;
-		gbc.weightx = 1.0;
-		jPanelNewIdentifier.add(new JLabel(currentRow), gbc);
-
-	}
-	return jPanelNewIdentifier;
-}
-private JPanel getJPanelLeftTitle() {
-	JPanel jPanelLeftTitle = new JPanel();
-	jPanelLeftTitle.setLayout(new GridBagLayout());
-	jPanelLeftTitle.setPreferredSize(new Dimension(260, 37));
-	jPanelLeftTitle.setBorder(BorderFactory.createLineBorder(SystemColor.windowBorder, 1));
-	int gridx = 0;
-	GridBagConstraints gbc = new GridBagConstraints();
-	gbc.insets = new Insets(3, 15, 3, 0);		// top left bottom right
-	gbc.gridx = gridx;
-	gbc.gridy = 0;
-	gbc.fill = GridBagConstraints.HORIZONTAL;
-	gbc.weightx = 1.0;
-	jPanelLeftTitle.add(new JLabel("User defined cross-references."), gbc);
-	return jPanelLeftTitle;
-}
-private JPanel getJPanelRightTitle() {
-	JPanel jPanelRightTitle = new JPanel();
-	jPanelRightTitle.setLayout(new GridBagLayout());
-	jPanelRightTitle.setBorder(BorderFactory.createLineBorder(SystemColor.windowBorder, 1));
-	
-	int gridx = 0;
-	GridBagConstraints gbc = new GridBagConstraints();
-	gbc.gridx = gridx;
-	gbc.gridy = 0;
-	gbc.insets = new Insets(6, 8, 0, 0);		// top left bottom right
-	gbc.anchor = GridBagConstraints.NORTHWEST;
-	jPanelRightTitle.add(new JLabel("Text Annotations"), gbc);
-	
-	gridx++;
-	gbc = new java.awt.GridBagConstraints();
-	gbc.gridx = gridx; 
-	gbc.gridy = 0;
-	gbc.weightx = 1.0;
-	gbc.weighty = 1.0;
-	gbc.fill = java.awt.GridBagConstraints.BOTH;
-	jPanelRightTitle.add(new JLabel(), gbc);
-	
-	gridx++;
-	gbc = new java.awt.GridBagConstraints();
-	gbc.gridx = gridx; 
-	gbc.gridy = 0;
-	gbc.insets = new Insets(3, 0, 3, 3);
-	gbc.anchor = GridBagConstraints.NORTHEAST;
-	jPanelRightTitle.add(getJButtonRemoveText(), gbc);
-	
-	getJButtonRemoveText().addActionListener(eventHandler);
-	return jPanelRightTitle;
-}
-private JPanel getJPanelIdentifierManager() {
-	if (jPanelIdentifierManager == null) {
-		jPanelIdentifierManager = new JPanel();
-		jPanelIdentifierManager.setLayout(new GridBagLayout());
-		jPanelIdentifierManager.setPreferredSize(new Dimension(260, 37));
-		jPanelIdentifierManager.setBorder(BorderFactory.createLineBorder(SystemColor.windowBorder, 1));
-		
-		int gridx = 0;
-		GridBagConstraints gbc = new GridBagConstraints();
-		gbc.insets = new Insets(3, 15, 3, 0);		// top left bottom right
-		gbc.gridx = gridx;
-		gbc.gridy = 0;
-		jPanelIdentifierManager.add(new JLabel("Provider"), gbc);
-		
-		gridx++;
-		gbc = new GridBagConstraints();
-		gbc.insets = new Insets(3, 5, 3, 4);
-		gbc.gridx = gridx;
-		gbc.gridy = 0;
-		jPanelIdentifierManager.add(getJComboBoxURI(), gbc);
-		
-		gridx++;
-		gbc = new GridBagConstraints();
-		gbc.insets = new Insets(3, 5, 3, 5);
-		gbc.gridx = gridx;
-		gbc.gridy = 0;
-		jPanelIdentifierManager.add(getJButtonAddRef(), gbc);
-
-		gridx++;
-		gbc = new GridBagConstraints();
-		gbc.insets = new Insets(3, 0, 3, 0);
-		gbc.gridx = gridx;
-		gbc.gridy = 0;
-		gbc.fill = GridBagConstraints.HORIZONTAL;
-		gbc.weightx = 1.0;
-		jPanelIdentifierManager.add(new JLabel(""), gbc);
-		
-		getJButtonAddRef().addActionListener(eventHandler);
-	}
-	return jPanelIdentifierManager;
-}
-private JPanel getJPanelLowerLeft() {
-	if (jPanelLowerLeft == null) {
-		jPanelLowerLeft = new JPanel();
-		jPanelLowerLeft.setLayout(new GridBagLayout());
-		jPanelLowerLeft.setPreferredSize(new Dimension(300, 37));
-		jPanelLowerLeft.setBorder(BorderFactory.createLineBorder(SystemColor.windowBorder, 1));
-		
-		int gridx = 0;
-		GridBagConstraints gbc = new GridBagConstraints();
-		gbc.insets = new Insets(3, 3, 3, 3);
-		gbc.gridx = gridx;
-		gbc.gridy = 0;
-		jPanelLowerLeft.add(getJButtonDeleteRef(), gbc);
-		
-		gridx++;
-		gbc = new GridBagConstraints();
-		gbc.insets = new Insets(3, 0, 3, 0);
-		gbc.gridx = gridx;
-		gbc.gridy = 0;
-		gbc.fill = GridBagConstraints.HORIZONTAL;
-		gbc.weightx = 1.0;
-		jPanelLowerLeft.add(new JLabel(""), gbc);
-		
-		getJButtonDeleteRef().setEnabled(false);
-		getJButtonDeleteRef().addActionListener(eventHandler);
-	}
-	return jPanelLowerLeft;
-}
-
-private JComboBox getJComboBoxQualifier() {
-	if (jComboBoxQualifier == null) {
-		jComboBoxQualifier = new JComboBox();
-//		defaultComboBoxModelQualifier = new DefaultComboBoxModel();	// already allocated
-		jComboBoxQualifier.setModel(defaultComboBoxModelQualifier);
-		Dimension d = jComboBoxQualifier.getPreferredSize();
-		jComboBoxQualifier.setMinimumSize(new Dimension(COMBO_QUALIFIER_WIDTH, d.height));
-		jComboBoxQualifier.setPreferredSize(new Dimension(COMBO_QUALIFIER_WIDTH, d.height));
-		ComboboxToolTipRenderer renderer = new ComboboxToolTipRenderer();
-		jComboBoxQualifier.setRenderer(renderer);
-	}
-	return jComboBoxQualifier;
-}
-private JTextField getJTextFieldFormalID() {
-	if (jTextFieldFormalID == null) {
-		jTextFieldFormalID = new JTextField();
-		jTextFieldFormalID.setText("NewID");
-		Dimension d = jTextFieldFormalID.getPreferredSize();
-		jTextFieldFormalID.setMinimumSize(new Dimension(100, d.height));
-		jTextFieldFormalID.setPreferredSize(new Dimension(100, d.height));
-	}
-	return jTextFieldFormalID;
-}
-
-@SuppressWarnings({ "rawtypes", "unchecked" })
-private JComboBox getJComboBoxURI() {
-	if (jComboBoxURI == null) {
-		jComboBoxURI = new JComboBox();
-		defaultComboBoxModelURI = new DefaultComboBoxModel();
-		jComboBoxURI.setModel(defaultComboBoxModelURI);
-		Dimension d = jComboBoxURI.getPreferredSize();
-		jComboBoxURI.setMinimumSize(new Dimension(MAX_URI_LENGTH, d.height));
-		jComboBoxURI.setPreferredSize(new Dimension(MAX_URI_LENGTH, d.height));
-		ComboboxToolTipRenderer renderer = new ComboboxToolTipRenderer();
-		jComboBoxURI.setRenderer(renderer);
-//		jComboBoxURI.setRenderer(new DefaultListCellRenderer() {
-//			public Component getListCellRendererComponent(JList list, Object value, int index, boolean isSelected, boolean cellHasFocus) {
-//				if(value == null) {
-//					return super.getListCellRendererComponent(list, value, index, isSelected, cellHasFocus);
-//				} else {
-//					DataType dt = (DataType)value;
-//					Component comp = super.getListCellRendererComponent(list,dt.getDataTypeName(),index,isSelected,cellHasFocus);
-//					return comp;
-//				}
-//			}
-//		});
-	}
-	return jComboBoxURI;
-}
-
-private JPanel getBottomPanel() {
-	if (jBottomPanel == null) {
-		
-		jBottomPanel = new JPanel();
-		jBottomPanel.setLayout(new BorderLayout());
-		jBottomPanel.add(getSplitPane(), BorderLayout.CENTER);
-	}
-	return jBottomPanel;
-
-}
-private JSplitPane getSplitPane() {
-	if (splitPane == null) {
-		
-		JPanel leftPanel = new JPanel();
-		leftPanel.setLayout(new GridBagLayout());
-		leftPanel.setBackground(Color.white);
-		
-		int gridy = 0;
-		GridBagConstraints gbc = new java.awt.GridBagConstraints();
-		gbc.gridx = 0; 
-		gbc.gridy = gridy;
-		gbc.weightx = 1.0;
-		gbc.weighty = 0;
-		gbc.insets = new Insets(3, 3, 1, 3);
-		gbc.fill = java.awt.GridBagConstraints.HORIZONTAL;
-		gbc.anchor = GridBagConstraints.NORTHWEST;
-		leftPanel.add(getJPanelLeftTitle(), gbc);
-
-		gridy++;
-		gbc = new java.awt.GridBagConstraints();
-		gbc.gridx = 0; 
-		gbc.gridy = gridy;
-		gbc.weightx = 1.0;
-		gbc.weighty = 0;
-		gbc.insets = new Insets(2, 3, 1, 3);
-		gbc.fill = java.awt.GridBagConstraints.HORIZONTAL;
-		gbc.anchor = GridBagConstraints.NORTHWEST;
-		leftPanel.add(getJPanelIdentifierManager(), gbc);
-
-		gridy++;
-		gbc = new java.awt.GridBagConstraints();
-		gbc.gridx = 0; 
-		gbc.gridy = gridy;
-		gbc.weightx = 1.0;
-		gbc.weighty = 1.0;
-		gbc.insets = new Insets(2, 3, 1, 3);
-		gbc.fill = java.awt.GridBagConstraints.BOTH;
-		gbc.anchor = GridBagConstraints.SOUTHWEST;
-		leftPanel.add(getJScrollPane(), gbc);
-		
-		gridy++;
-		gbc = new java.awt.GridBagConstraints();
-		gbc.gridx = 0; 
-		gbc.gridy = gridy;
-		gbc.weightx = 1.0;
-		gbc.weighty = 0;
-		gbc.insets = new Insets(2, 3, 3, 3);
-		gbc.fill = java.awt.GridBagConstraints.BOTH;
-		gbc.anchor = GridBagConstraints.SOUTHWEST;
-		leftPanel.add(getJPanelLowerLeft(), gbc);
-		// -----------------------------------------------------------------------
-		
-		JPanel rightPanel = new JPanel();
-		rightPanel.setLayout(new GridBagLayout());
-		rightPanel.setBackground(Color.white);
-
-		gridy = 0;
-		gbc = new java.awt.GridBagConstraints();
-		gbc.gridx = 0; 
-		gbc.gridy = gridy;
-		gbc.insets = new Insets(3, 3, 2, 2);
-		gbc.fill = java.awt.GridBagConstraints.HORIZONTAL;
-		gbc.anchor = GridBagConstraints.NORTHWEST;
-		rightPanel.add(getJPanelRightTitle(), gbc);
-
-		annotationTextArea = new JTextPane();
-		annotationTextArea.setContentType("text/html");
-		annotationTextArea.setEditable(false);
-		annotationTextArea.addFocusListener(eventHandler);
-		annotationTextArea.addMouseListener(eventHandler);
-		JScrollPane annotationPanel = new JScrollPane(annotationTextArea);
-
-		gridy++;
-		gbc = new java.awt.GridBagConstraints();
-		gbc.gridx = 0; 
-		gbc.gridy = gridy;
-		gbc.weightx = 1.0;
-		gbc.weighty = 1.0;
-		gbc.insets = new Insets(1, 3, 1, 2);
-		gbc.fill = java.awt.GridBagConstraints.BOTH;
-		gbc.anchor = GridBagConstraints.NORTHWEST;
-		rightPanel.add(annotationPanel, gbc);
-		// ----------------------------------------------------------------------------------
-				
-		splitPane = new JSplitPane(JSplitPane.HORIZONTAL_SPLIT);
-		splitPane.setOneTouchExpandable(true);
-		splitPane.setLeftComponent(leftPanel);
-		splitPane.setRightComponent(rightPanel);
-		splitPane.setResizeWeight(0.1);
-		splitPane.setDividerLocation(0.3);
-		
-		annotationTextArea.addKeyListener(eventHandler);
-	}
-	return splitPane;
-}
-	
-private JScrollPane getJScrollPane() {
-	if (jScrollPane == null) {
-		jScrollPane = new JScrollPane();
-		jScrollPane.setViewportView(getJTreeMIRIAM());
-	}
-	return jScrollPane;
-}
-private JTree getJTreeMIRIAM() {
-	if (jTreeMIRIAM == null) {
-		try {
-			DefaultTreeSelectionModel ivjLocalSelectionModel;
-			ivjLocalSelectionModel = new DefaultTreeSelectionModel();
-			ivjLocalSelectionModel.setSelectionMode(1);
-			jTreeMIRIAM = new JTree();
-			jTreeMIRIAM.setName("JTree1");
-			jTreeMIRIAM.setToolTipText("");
-			jTreeMIRIAM.setBounds(0, 0, 357, 405);
-			jTreeMIRIAM.setMinimumSize(new java.awt.Dimension(100, 72));
-			jTreeMIRIAM.setSelectionModel(ivjLocalSelectionModel);
-			jTreeMIRIAM.setRowHeight(0);
-			jTreeMIRIAM.setRootVisible(false);
-			
-			// Add cellRenderer
-			DefaultTreeCellRenderer dtcr = new BioModelCellRenderer(null) {
-				@Override
-				public Component getTreeCellRendererComponent(JTree tree, Object value, boolean sel, boolean expanded, boolean leaf, int row, boolean hasFocus) {
-					// default for LinkNode is in BioModelCellRenderer.java
-					JLabel component = (JLabel)super.getTreeCellRendererComponent(tree, value, sel, expanded, leaf, row, hasFocus);
-					// TODO: here
-					component.setIcon(null);
-					return component;
-				}
-			};
-			jTreeMIRIAM.setCellRenderer(dtcr);
-			
-			MouseListener mouseListener = new MouseAdapter() {
-				@Override
-				public void mouseClicked(MouseEvent e) {
-					super.mouseClicked(e);
-//					TreePath closestMousePath =jTreeMIRIAM.getClosestPathForLocation(e.getPoint().x, e.getPoint().y);
-//					showPopup(e, closestMousePath);
-				}
-
-				@Override
-				public void mouseReleased(MouseEvent e) {
-					super.mouseReleased(e);
-//					TreePath closestMousePath =jTreeMIRIAM.getClosestPathForLocation(e.getPoint().x, e.getPoint().y);
-//					showPopup(e,closestMousePath);
-				}
-
-				public void mousePressed(MouseEvent e) {
-					TreePath closestMousePath =jTreeMIRIAM.getClosestPathForLocation(e.getPoint().x, e.getPoint().y);
-					jTreeMIRIAM.setSelectionPath(closestMousePath);
-//					showPopup(e,closestMousePath);
-					if(e.getClickCount() == 2) {
-						DefaultMutableTreeNode node = (DefaultMutableTreeNode)jTreeMIRIAM.getLastSelectedPathComponent();
-						if (node instanceof LinkNode) {
-							showBrowseToLink((LinkNode)node);
-						}
-					}
-				} 
-			};
-			jTreeMIRIAM.addMouseListener(mouseListener);
-
-		} catch (java.lang.Throwable ivjExc) {
-			ivjExc.printStackTrace(System.out);
-		}
-	}
-	return jTreeMIRIAM;
-}
-private void showBrowseToLink(LinkNode linkNode) {
-	String link = linkNode.getLink();
-	if (link != null) {
-		DialogUtils.browserLauncher(jTreeMIRIAM, link, "failed to launch");
-	}else{
-		DialogUtils.showWarningDialog(this, "No Web-site link available");
-	}
-}
-private void showBrowseToLink(VCMetaDataDataType md) {
-	String link = md.getDataTypeURL();
-	if (link != null) {
-		DialogUtils.browserLauncher(getJComboBoxURI(), link, "Failed to launch");
-	} else {
-		DialogUtils.showWarningDialog(this, "No Web-site link available");
-	}
-}
-
-private void initialize() {
-	try {
-		setLayout(new GridBagLayout());
-		setBackground(Color.white);
-		
-		int gridy = 0;
-		GridBagConstraints gbc = new java.awt.GridBagConstraints();
-		gbc.gridx = 0; 
-		gbc.gridy = gridy;
-		gbc.weightx = 1.0;
-		gbc.weighty = 1.0;
-		gbc.insets = new Insets(4, 4, 4, 4);
-		gbc.fill = java.awt.GridBagConstraints.BOTH;
-		gbc.anchor = GridBagConstraints.SOUTHWEST;
-		add(getBottomPanel(), gbc);
-		
-		JTextPane tenpTextPane = new JTextPane();	// used just to initialize emptyText once
-		tenpTextPane.setContentType("text/html");
-		tenpTextPane.setText(null);
-		emptyHtmlText = tenpTextPane.getText();
-		
-		initializeComboBoxQualifier();
-
-        getJTreeMIRIAM().addTreeSelectionListener(new TreeSelectionListener() {
-			public void valueChanged(TreeSelectionEvent e) {
-				TreePath tp = ((JTree)e.getSource()).getSelectionPath();
-				if(tp == null) {
-					getJButtonDeleteRef().setEnabled(false);
-				} else {
-					Object lastPathComponent = tp.getLastPathComponent();
-					getJButtonDeleteRef().setEnabled(tp != null && lastPathComponent instanceof LinkNode);
-				}
-			}
-		});
-
-	} catch (java.lang.Throwable ivjExc) {
-		handleException(ivjExc);
-	}
-}
-
-private void changeTextAnnotation() {
-	try{
-		if (bioModel == null || selectedObject == null) {
-			return;
-		}
-		Identifiable entity = getIdentifiable(selectedObject);
-		String textAreaStr = (annotationTextArea.getText() == null || annotationTextArea.getText().length()==0?null:annotationTextArea.getText());
-		String oldText = bioModel.getVCMetaData().getFreeTextAnnotation(entity);
-
-		if(textAreaStr == null || textAreaStr.isEmpty() || emptyHtmlText.equals(textAreaStr)) {	// no annotation now, the field is empty
-			bioModel.getVCMetaData().deleteFreeTextAnnotation(entity);	// delete, if there's something previously saved
-			if(selectedObject instanceof ReactionStep) {
-				// we tell ReactionPropertiesPanel to refresh the annotation icon
-				((ReactionStep) selectedObject).firePropertyChange("addIdentifier", false, true);
-			}
-		} else if(!Compare.isEqualOrNull(oldText,textAreaStr)) {		// some text annotation different from what's already saved
-			bioModel.getVCMetaData().setFreeTextAnnotation(entity, textAreaStr);	// overwrite
-			if(selectedObject instanceof ReactionStep) {
-				// we tell ReactionPropertiesPanel to refresh the text annotation icon
-				((ReactionStep) selectedObject).firePropertyChange("addIdentifier", false, true);
-			}
-		}
-	} catch(Exception e) {
-		e.printStackTrace(System.out);
-		PopupGenerator.showErrorDialog(this,"Annotation Error\n"+e.getMessage(), e);
-	}
-}
-private void removeText() {
-	if (bioModel == null || selectedObject == null) {
-		return;
-	}
-	Identifiable entity = getIdentifiable(selectedObject);
-	annotationTextArea.setText(null);
-	bioModel.getVCMetaData().deleteFreeTextAnnotation(entity);	// delete, if there's something previously saved
-	if(selectedObject instanceof ReactionStep) {
-		((ReactionStep) selectedObject).firePropertyChange("addIdentifier", false, true);
-	}
-}
-
-public void setBioModel(BioModel newValue) {
-	if (newValue == bioModel) {
-		return;
-	}
-	bioModel = newValue;
-	vcMetaData = bioModel.getVCMetaData();
-
-	// set tree model on jTableMIRIAM here, since we have access to miriamDescrHeir here
-	miriamTreeModel = new MiriamTreeModel(new DefaultMutableTreeNode("Object Annotations",true), vcMetaData, false);
-	jTreeMIRIAM.setModel(miriamTreeModel);
-
-	initializeComboBoxURI();
-	getJTextFieldFormalID().setText("NewID");
-	updateInterface();
-}
-
-private void updateInterface() {
-	if (bioModel == null) {
-		return;
-	}
-	Identifiable entity = getIdentifiable(selectedObject);
-	if(selectedObject != null && entity != null) {
-		getJComboBoxURI().setEnabled(true);
-		getJTextFieldFormalID().setEnabled(true);
-		getJButtonAddRef().setEnabled(true);
-		getJButtonRemoveText().setEnabled(true);
-		VCMetaDataDataType mdt = (VCMetaDataDataType)getJComboBoxURI().getSelectedItem();
-		miriamTreeModel.createTree(entity);
-		
-		String freeText = bioModel.getVCMetaData().getFreeTextAnnotation(entity);
-		if(freeText == null || freeText.isEmpty()) {
-			annotationTextArea.setText(null);
-		} else {
-			annotationTextArea.setText(freeText);
-		}
-		annotationTextArea.setEditable(true);
-		annotationTextArea.setCaretPosition(0);
-	} else {
-		getJComboBoxURI().setEnabled(false);
-		getJTextFieldFormalID().setEnabled(false);
-		getJButtonAddRef().setEnabled(false);
-		getJButtonRemoveText().setEnabled(false);
-		miriamTreeModel.createTree(null);
-
-		annotationTextArea.setText(null);
-		annotationTextArea.setEditable(false);
-	}
-}
-public static Identifiable getIdentifiable(Identifiable selectedObject) {
-	//
-	// for SpeciesContext objects:
-	//		MIRIAM tree needs the Species				!!!
-	//		text Annotation needs the SpeciesContext
-	//
-	// !!!	use this only for the tree !!!
-	//
-	if(selectedObject == null) {
-		return null;
-	}
-	if(selectedObject instanceof SpeciesContext) {
-		return (Species)((SpeciesContext)selectedObject).getSpecies();
-	} else if(selectedObject instanceof MolecularType) {
-		return (MolecularType)selectedObject;
-	} else if(selectedObject instanceof ReactionRule) {
-		return (ReactionRule)selectedObject;
-	} else if(selectedObject instanceof ReactionStep) {
-		return (ReactionStep)selectedObject;
-	} else if(selectedObject instanceof RbmObservable) {
-		return (RbmObservable)selectedObject;
-	} else if(selectedObject instanceof BioModel) {
-		return (BioModel)selectedObject;
-	} else if(selectedObject instanceof Structure) {
-		return (Structure)selectedObject;
-	} else if(selectedObject instanceof BioPaxObject) {
-		return null;
-	} else if(selectedObject instanceof Model.ModelParameter) {
-		return (Model.ModelParameter)selectedObject;
-	} else if(selectedObject instanceof SimulationContext) {
-		return (SimulationContext)selectedObject;
-//	} else if(selectedObject instanceof Simulation) {
-//		return (Simulation)selectedObject;
-//	} else if(selectedObject instanceof SpeciesContextSpec) {
-//		return (SpeciesContextSpec)selectedObject;
-//	} else if(selectedObject instanceof ReactionSpec) {
-//		return (ReactionSpec)selectedObject;
-	} else {
-		return null;
-	}
-}
-
-@Override
-protected void onSelectedObjectsChange(Object[] selectedObjects) {
-	if (selectedObjects != null && selectedObjects.length == 1) {
-		if(selectedObjects[0] instanceof BioModelInfo || selectedObjects[0] instanceof MathModelInfo) {
-			return;
-		}
-		if(selectedObjects[0] instanceof Identifiable && selectedObjects[0] instanceof Displayable) {
-			selectedObject = (Identifiable)selectedObjects[0];
-			System.out.println("AnnotationsPanel: class: " + selectedObject.getClass().getSimpleName() + ", selected object: " + ((Displayable)selectedObject).getDisplayName());
-		} else {
-			selectedObject = null;
-			System.out.println("Unsupported or null entity");
-		}
-		initializeComboBoxURI();		// if selectedObject or entity are null we just empty the combobox
-		getJButtonDeleteRef().setEnabled(false);
-		getJTextFieldFormalID().setText("NewID");
-		updateInterface();
-	}
-}
-	
-// -------------------------------------------------------------------------------------------------------
-
-private void addIdentifier() {
-	if(PopupGenerator.showComponentOKCancelDialog(AnnotationsPanel.this, getJPanelNewIdentifier(), "Define New Formal Identifier") != JOptionPane.OK_OPTION) {
-		return;
-	}
-	MIRIAMQualifier qualifier = (MIRIAMQualifier)getJComboBoxQualifier().getSelectedItem();
-	MiriamManager.DataType objectNamespace = (MiriamManager.DataType)getJComboBoxURI().getSelectedItem();
-	String objectID = getJTextFieldFormalID().getText();
-	if(objectID.compareTo("NewID") == 0) {
-		return;
-	}
-	MiriamManager miriamManager = vcMetaData.getMiriamManager();
-	HashSet<MiriamResource> miriamResources = new HashSet<MiriamResource>();
-	try {
-		Identifiable entity = getIdentifiable(selectedObject);
-		MiriamResource mr = miriamManager.createMiriamResource(objectNamespace.getBaseURN()+":"+objectID);
-		miriamResources.add(mr);
-		miriamManager.addMiriamRefGroup(entity, qualifier, miriamResources);
-//		System.out.println(vcMetaData.printRdfStatements());
-		updateInterface();
-		if(selectedObject instanceof ReactionStep) {
-			// we tell ReactionPropertiesPanel to refresh the annotation icon
-			((ReactionStep) selectedObject).firePropertyChange("addIdentifier", false, true);
-		}
-	} catch (Exception e) {
-		e.printStackTrace();
-		DialogUtils.showErrorDialog(this,"Add Identifier failed:\n"+e.getMessage(), e);
-	}
-}
-private void removeIdentifier() {
-	Object treeNode = jTreeMIRIAM.getLastSelectedPathComponent();
-	if (treeNode instanceof LinkNode) {
-		LinkNode linkNode = (LinkNode)treeNode;
-		MiriamResource resourceToDelete = linkNode.getMiriamResource();
-		Identifiable entity = getIdentifiable(selectedObject);
-		//Map<MiriamRefGroup, MIRIAMQualifier> refGroupsToRemove = vcMetaData.getMiriamManager().getAllMiriamRefGroups(entity);
-		MiriamManager mm = vcMetaData.getMiriamManager();
-		Map<MiriamRefGroup,MIRIAMQualifier> refGroupsToRemove = mm.getMiriamTreeMap().get(entity);
-		
-		boolean found = false;
-		for (MiriamRefGroup refGroup : refGroupsToRemove.keySet()){
-			MIRIAMQualifier qualifier = refGroupsToRemove.get(refGroup);
-			for (MiriamResource miriamResource : refGroup.getMiriamRefs()) {
-				
-				if(!isEqual(miriamResource, resourceToDelete)) {
-					continue;
-				}
-				try {
-					mm.remove2(entity, qualifier, refGroup);	// remove the ref group for this resource
-					System.out.println(vcMetaData.printRdfStatements());
-
-					found = true;
-					break;
-				} catch (URNParseFailureException e) {
-					e.printStackTrace(System.out);
-				}
-			}
-			if(found == true) {
-				updateInterface();
-				if(selectedObject instanceof ReactionStep) {
-					((ReactionStep) selectedObject).firePropertyChange("addIdentifier", true, false);
-				}
-				break;
-			}
-		}
-	}
-}
-
-private boolean isEqual(MiriamResource aThis, MiriamResource aThat) {
-	if (aThis == aThat) {
-		return true;
-	}
-	if (!(aThis instanceof MiriamResource)) {
-		return false;
-	}
-	if (!(aThat instanceof MiriamResource)) {
-		return false;
-	}
-	MiriamResource athis = (MiriamResource)aThis;
-	MiriamResource athat = (MiriamResource)aThat;
-	
-	if (athis.getDataType() != null && athat.getDataType() != null && !athis.getDataType().equals(athat.getDataType())) {
-		return false;
-	}
-	if (!Compare.isEqual(athis.getMiriamURN(), athat.getMiriamURN())) {
-		return false;
-	}
-	if (!Compare.isEqual(athis.getIdentifier(), athat.getIdentifier())) {
-		return false;
-	}
-	return true;
-}
-
-@SuppressWarnings("unchecked")
-private void initializeComboBoxURI() {
-	Identifiable entity = getIdentifiable(selectedObject);
-	defaultComboBoxModelURI.removeAllElements();
-	List<String> tooltips = new ArrayList<String> ();
-	List<DataType> dataTypeList = new ArrayList<>();
-	if(entity == null) {
-		for (DataType dt : vcMetaData.getMiriamManager().getAllDataTypes().values()) {
-			dataTypeList.add(dt);
-		}
-	} else {	
-		for (DataType dt : VCMetaDataMiriamManager.getSpecificDataTypes(entity)) {
-			dataTypeList.add(dt);
-		}
-	}
-	Collections.sort(dataTypeList);
-	for(DataType dt : dataTypeList) {
-		tooltips.add(dt.getDescription());
-		defaultComboBoxModelURI.addElement(dt);
-	}
-	((ComboboxToolTipRenderer)getJComboBoxURI().getRenderer()).setTooltips(tooltips);
-}
-private void initializeComboBoxQualifier() {
-	//Set<MIRIAMQualifier> MIRIAM_all;
-	//AnnotationQualifiers.MIRIAM_all;
-	List<MIRIAMQualifier> qualifierList = new ArrayList<>();
-	for(MIRIAMQualifier qualifier : AnnotationQualifiers.MIRIAM_all) {
-		qualifierList.add(qualifier);
-	}
-	Collections.sort(qualifierList);
-	for(MIRIAMQualifier qualifier : qualifierList) {
-		defaultComboBoxModelQualifier.addElement(qualifier);
-	}
-}
-
-private JButton getJButtonAddRef() {
-	if (jButtonAddRef == null) {
-		jButtonAddRef = new JButton();
-		jButtonAddRef.setText(ACTION_ADD);
-		jButtonAddRef.setToolTipText("Add a new reference with this provider");
-	}
-	return jButtonAddRef;
-}
-private JButton getJButtonDeleteRef() {
-	if (jButtonDeleteRef == null) {
-		jButtonDeleteRef = new JButton();
-		jButtonDeleteRef.setText(ACTION_DELETE);
-		jButtonDeleteRef.setToolTipText("Delete the selected cross-reference");
-
-	}
-	return jButtonDeleteRef;
-}
-private JButton getJButtonRemoveText() {
-	if (jButtonRemoveText == null) {
-		jButtonRemoveText = new JButton();
-		jButtonRemoveText.setText(ACTION_REMOVE_TEXT);
-		jButtonRemoveText.setToolTipText("Remove the entire text annotation");
-	}
-	return jButtonRemoveText;
-}
-	/*
-
-Universal (goes in all types of annotations):
-PubMed ID https://www.ncbi.nlm.nih.gov/pubmed
-DOI: https://www.doi.org/
-
-Model
-BioModels Database https://www.ebi.ac.uk/biomodels/
-Reactome: https://reactome.org/
-Grey: NeuronDB: https://senselab.med.yale.edu/neurondb/
-Grey: https://senselab.med.yale.edu/modeldb/
-Grey: CellML Model Repository: https://models.cellml.org/cellml
-
-Species/Molecules/Observables:
-CheBI: https://www.ebi.ac.uk/chebi/
-Kegg Compound: https://www.genome.jp/kegg/compound/
-Uniprot: https://www.uniprot.org/
-Enzyme Nomenclature: http://www.sbcs.qmul.ac.uk/iubmb/enzyme/
-Gene Ontology: http://www.geneontology.org/
-Reactome: https://reactome.org/
-
-Reactions
-Kegg Reaction: https://www.genome.jp/kegg/reaction/
-Kegg Pathway: https://www.genome.jp/kegg/pathway.html
-Reactome: https://reactome.org/
-Grey: BRENDA: https://www.brenda-enzymes.org/
-Grey: BIND  https://www.bindingdb.org/bind/index.jsp
-
-Parameters (all grey for now)
-Grey:BIND https://www.bindingdb.org/bind/index.jsp
-
-Structures
-Grey: BRENDA: https://www.brenda-enzymes.org/
-Grey: Gene Ontology  http://geneontology.org/
-
-
-DataType DataType_PIR 			"PIRSF"
-DataType DataType_DOI 			"DOI"
-DataType DataType_BIOMODELS 	"BioModels Database"
-DataType DataType_Chebi 		"ChEBI"
-DataType DataType_IntAct 		"IntAct"
-DataType DataType_InterPro 		"InterPro"
-DataType DataType_ECCODE 		"Enzyme Nomenclature"
-DataType DataType_ENSEMBLE 		"Ensembl"
-DataType DataType_GO 			"Gene Ontology"
-DataType DataType_KEGGCOMPOUND 	"KEGG Compound"
-DataType DataType_KEGGPATHWAY 	"KEGG Pathway"
-DataType DataType_KEGGREACTION 	"KEGG Reaction"
-DataType DataType_PUBMED 		"PubMed"
-DataType DataType_TAXONOMY 		"Taxonomy"
-DataType DataType_REACTOME 		"Reactome"
-DataType DataType_UNIPROT 		"UniProt"
-DataType DataType_ICD 			"ICD"
-
-
-
-
-*/
-
-
-
-
-
-}
diff --git a/vcell-client/src/main/java/cbit/vcell/client/desktop/biomodel/BioModelEditor.java b/vcell-client/src/main/java/cbit/vcell/client/desktop/biomodel/BioModelEditor.java
index 1eaa09851c..b084fd93cc 100644
--- a/vcell-client/src/main/java/cbit/vcell/client/desktop/biomodel/BioModelEditor.java
+++ b/vcell-client/src/main/java/cbit/vcell/client/desktop/biomodel/BioModelEditor.java
@@ -24,6 +24,7 @@
 import javax.swing.JComponent;
 import javax.swing.ListSelectionModel;
 
+import cbit.vcell.client.desktop.biomodel.annotations.AnnotationsPanel;
 import org.vcell.model.rbm.MolecularType;
 import org.vcell.model.rbm.SpeciesPattern;
 import org.vcell.pathway.BioPaxObject;
@@ -53,7 +54,6 @@
 import cbit.vcell.clientdb.DocumentManager;
 import cbit.vcell.data.DataSymbol;
 import cbit.vcell.desktop.BioModelNode;
-import cbit.vcell.desktop.BioModelNode.PublicationInfoNode;
 import cbit.vcell.geometry.CSGObject;
 import cbit.vcell.geometry.GeometryInfo;
 import cbit.vcell.geometry.gui.CSGObjectPropertiesPanel;
diff --git a/vcell-client/src/main/java/cbit/vcell/client/desktop/biomodel/BioModelEditorModelPanel.java b/vcell-client/src/main/java/cbit/vcell/client/desktop/biomodel/BioModelEditorModelPanel.java
index 1047e7a5f6..bb3bd61dc2 100644
--- a/vcell-client/src/main/java/cbit/vcell/client/desktop/biomodel/BioModelEditorModelPanel.java
+++ b/vcell-client/src/main/java/cbit/vcell/client/desktop/biomodel/BioModelEditorModelPanel.java
@@ -61,6 +61,7 @@
 import javax.swing.event.ListSelectionEvent;
 import javax.swing.event.ListSelectionListener;
 
+import cbit.vcell.client.desktop.biomodel.annotations.AnnotationsPanel;
 import org.vcell.model.rbm.MolecularType;
 import org.vcell.model.rbm.RbmNetworkGenerator.CompartmentMode;
 import org.vcell.model.rbm.RbmUtils;
diff --git a/vcell-client/src/main/java/cbit/vcell/client/desktop/biomodel/ReactionPropertiesPanel.java b/vcell-client/src/main/java/cbit/vcell/client/desktop/biomodel/ReactionPropertiesPanel.java
index 3bd7be0d1e..8da9e0b8e5 100644
--- a/vcell-client/src/main/java/cbit/vcell/client/desktop/biomodel/ReactionPropertiesPanel.java
+++ b/vcell-client/src/main/java/cbit/vcell/client/desktop/biomodel/ReactionPropertiesPanel.java
@@ -13,7 +13,6 @@
 import java.awt.Color;
 import java.awt.Component;
 import java.awt.Dimension;
-import java.awt.Font;
 import java.awt.GridBagConstraints;
 import java.awt.GridBagLayout;
 import java.awt.Insets;
@@ -22,7 +21,6 @@
 import java.awt.event.FocusListener;
 import java.awt.event.MouseAdapter;
 import java.awt.event.MouseEvent;
-import java.awt.event.MouseListener;
 import java.beans.PropertyChangeEvent;
 import java.beans.PropertyChangeListener;
 import java.beans.PropertyVetoException;
@@ -39,10 +37,10 @@
 import javax.swing.JList;
 import javax.swing.JPanel;
 import javax.swing.JScrollPane;
-import javax.swing.JTextArea;
 import javax.swing.JTextField;
 import javax.swing.ListSelectionModel;
 
+import cbit.vcell.client.desktop.biomodel.annotations.AnnotationsPanel;
 import org.vcell.pathway.BioPaxObject;
 import org.vcell.pathway.Entity;
 import org.vcell.relationship.RelationshipEvent;
@@ -50,18 +48,14 @@
 import org.vcell.relationship.RelationshipObject;
 import org.vcell.sybil.models.miriam.MIRIAMQualifier;
 import org.vcell.util.BeanUtils;
-import org.vcell.util.Compare;
 import org.vcell.util.document.Identifiable;
-import org.vcell.util.gui.CollapsiblePanel;
 import org.vcell.util.gui.DialogUtils;
 import org.vcell.util.gui.ScrollTable;
 import org.vcell.util.gui.VCellIcons;
 
 import cbit.vcell.biomodel.BioModel;
 import cbit.vcell.biomodel.meta.MiriamManager;
-import cbit.vcell.biomodel.meta.VCMetaData;
 import cbit.vcell.biomodel.meta.MiriamManager.MiriamRefGroup;
-import cbit.vcell.client.PopupGenerator;
 import cbit.vcell.client.desktop.biomodel.DocumentEditorTreeModel.DocumentEditorTreeFolderClass;
 import cbit.vcell.client.desktop.biomodel.SelectionManager.ActiveView;
 import cbit.vcell.client.desktop.biomodel.SelectionManager.ActiveViewID;
diff --git a/vcell-client/src/main/java/cbit/vcell/client/desktop/biomodel/annotations/AddAnnotationsPanel.java b/vcell-client/src/main/java/cbit/vcell/client/desktop/biomodel/annotations/AddAnnotationsPanel.java
new file mode 100644
index 0000000000..621df12f44
--- /dev/null
+++ b/vcell-client/src/main/java/cbit/vcell/client/desktop/biomodel/annotations/AddAnnotationsPanel.java
@@ -0,0 +1,362 @@
+package cbit.vcell.client.desktop.biomodel.annotations;
+
+import cbit.vcell.biomodel.meta.VCMetaDataMiriamManager;
+import org.vcell.util.document.Identifiable;
+import org.xml.sax.SAXException;
+
+import javax.swing.*;
+import javax.swing.event.ListSelectionEvent;
+import javax.swing.event.ListSelectionListener;
+import javax.xml.parsers.ParserConfigurationException;
+import java.awt.*;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.io.IOException;
+import java.net.URISyntaxException;
+import java.util.List;
+import java.util.Objects;
+
+public class AddAnnotationsPanel extends JFrame implements ActionListener {
+
+    private JButton searchButton;
+    private JTextField searchBar;
+    private JList<String> list;
+    private JComboBox<String> ontologiesBox;
+    private JComboBox<String> containsBox;
+    private JComboBox<String> limitBox;
+    private JTextArea descriptionArea;
+    private List<SearchElement> SearchElements;
+    private final JButton addButton, oKButton;
+    private final AnnotationsPanel annotationsPanel; //to connect AnnotationsPanel with AddAnnotationsPanel
+    private String annotDescription;
+    private JComboBox jComboBoxURI, jComboBoxQualifier;			// identity provider combo
+    DefaultComboBoxModel defaultComboBoxModelURI = null;
+    public static final int MAX_URI_LENGTH = 130;
+    private Identifiable selectedObject = null;
+
+    public AddAnnotationsPanel (AnnotationsPanel annotationsPanel, JComboBox JComboBoxURI, JComboBox JComboBoxQualifier) {
+        this.annotationsPanel = annotationsPanel;
+        this.jComboBoxURI = (JComboBoxURI==null) ? new JComboBox<>(): JComboBoxURI;
+        this.jComboBoxQualifier = (JComboBoxQualifier==null) ? new JComboBox<>(): JComboBoxQualifier;
+
+        setTitle("Add Annotations");
+        setResizable(false);
+        setLocationRelativeTo(null);
+
+        GridBagLayout gbl = new GridBagLayout();
+        JPanel mainPanel = new JPanel(gbl);
+
+
+        GridBagConstraints gbc = new GridBagConstraints();
+        gbc.weightx = 1;
+        gbc.weighty = 1;
+        gbc.fill = GridBagConstraints.BOTH;
+        gbc.insets = new Insets(15,0,0,0);
+
+        //Add left panel for searching annotations
+        gbc.gridy = 0;
+        JPanel searchPanel = new JPanel();
+        addSearchPanelComponents(searchPanel);
+        mainPanel.add(searchPanel, gbc);
+
+        //Add right panel for descriptions
+        gbc.gridx = 1;
+        gbc.gridwidth = 2;
+        gbc.insets = new Insets(0,15,0,0);
+        JPanel descriptionPanel = new JPanel();
+        addDescriptionPanelComponents(descriptionPanel);
+        mainPanel.add(descriptionPanel,gbc);
+
+        //Add JComboBox for qualifier
+        gbc.gridy = 1;
+        gbc.gridx = 0;
+        gbc.fill = GridBagConstraints.VERTICAL;
+        gbc.anchor = GridBagConstraints.EAST;
+        gbc.insets = new Insets(0,0,12,10);
+        mainPanel.add(jComboBoxQualifier,gbc);
+
+        //Add "add" button to main panel
+        gbc.gridy = 1;
+        gbc.gridx = 1;
+        gbc.fill = GridBagConstraints.NONE;
+        gbc.anchor = GridBagConstraints.WEST;
+        gbc.insets = new Insets(0,0,12,0);
+        addButton = new JButton("Add");
+        addButton.addActionListener(this);
+        mainPanel.add(addButton, gbc);
+
+        //Add OK button to main panel
+        gbc.gridy = 1;
+        gbc.gridx = 2;
+        gbc.fill = GridBagConstraints.NONE;
+        gbc.anchor = GridBagConstraints.EAST;
+        gbc.insets = new Insets(0,0,12,15);
+        oKButton = new JButton("OK");
+        oKButton.setSize(10,20);
+        oKButton.setMinimumSize(oKButton.getPreferredSize());
+        oKButton.addActionListener(this);
+        mainPanel.add(oKButton, gbc);
+
+        this.getContentPane().add(mainPanel);
+        this.pack();
+        this.setDefaultCloseOperation(DISPOSE_ON_CLOSE);
+        this.setVisible(true);
+    }
+
+    public JButton getOkButton() {
+        return oKButton;
+    }
+
+    private void addSearchPanelComponents(JPanel leftPanel) {
+        GridBagLayout sGbl = new GridBagLayout();
+        GridBagConstraints sGbc = new GridBagConstraints();
+        leftPanel.setLayout(sGbl);
+
+        sGbc.weightx = 1;
+        sGbc.weighty = 1;
+        sGbc.fill = GridBagConstraints.NONE;
+
+        //adding select ontology Label
+        sGbc.gridy = 0;
+        sGbc.gridx = 0;
+        sGbc.insets = new Insets(0,10,0,0);
+        JLabel selectOntologyLabel = new JLabel("Select Ontology:");
+        leftPanel.add(selectOntologyLabel, sGbc);
+
+        //adding ontologies combobox
+        sGbc.gridy = 0;
+        sGbc.gridx = 1;
+        sGbc.insets = new Insets(0,10,0,0);
+
+//        ontologiesBox = new JComboBox<>();
+//        ontologiesBox.addItem("All Selected");
+//        ontologiesBox.addItem("GO");
+//        ontologiesBox.addItem("NCIT");
+//        ontologiesBox.addItem("CHEBI");
+//        ontologiesBox.addItem("FMA");
+//        ontologiesBox.addItem("BTO");
+//        leftPanel.add(ontologiesBox, sGbc);
+//        leftPanel.add(annotationsPanel.getJComboBoxURI(), sGbc);
+        leftPanel.add(jComboBoxURI, sGbc);
+
+        //adding search label
+        sGbc.gridy = 1;
+        sGbc.gridx = 0;
+        sGbc.anchor = GridBagConstraints.EAST;
+        sGbc.insets = new Insets(15,0,0,0);
+        JLabel searchLabel = new JLabel("Search term:");
+        leftPanel.add(searchLabel, sGbc);
+
+        //adding contains/exaxt Jcombobox
+        sGbc.gridy = 1;
+        sGbc.gridx = 1;
+        sGbc.anchor = GridBagConstraints.CENTER;
+        sGbc.insets = new Insets(15,0,0,5);
+
+        containsBox = new JComboBox<>();
+        containsBox.addItem("contains");
+        containsBox.addItem("exact");
+        leftPanel.add(containsBox, sGbc);
+
+        //adding search bar
+        sGbc.gridy = 1;
+        sGbc.fill = GridBagConstraints.HORIZONTAL;
+        sGbc.gridx = 2;
+        sGbc.gridwidth = 2;
+        sGbc.anchor = GridBagConstraints.CENTER;
+        sGbc.insets = new Insets(15,0,0,10);
+        searchBar = new JTextField(25);
+        leftPanel.add(searchBar, sGbc);
+
+        //adding limit label
+        sGbc.fill = GridBagConstraints.NONE;
+        sGbc.anchor = GridBagConstraints.EAST;
+        sGbc.gridwidth = 1;
+        sGbc.gridy = 2;
+        sGbc.gridx = 0;
+        sGbc.insets = new Insets(8,0,0,3);
+        JLabel limitLabel = new JLabel("Limit to");
+        leftPanel.add(limitLabel, sGbc);
+
+        //adding limit JComboBox
+        sGbc.fill = GridBagConstraints.HORIZONTAL;
+        sGbc.anchor = GridBagConstraints.CENTER;
+        sGbc.gridy = 2;
+        sGbc.gridx = 1;
+        sGbc.insets = new Insets(8,0,0,2);
+        limitBox = new JComboBox<>();
+        limitBox.addItem("50");
+        limitBox.addItem("100");
+        limitBox.addItem("500");
+
+        leftPanel.add(limitBox, sGbc);
+
+        //adding limit term label
+        sGbc.fill = GridBagConstraints.NONE;
+        sGbc.anchor = GridBagConstraints.WEST;
+        sGbc.gridy = 2;
+        sGbc.gridx = 2;
+        sGbc.insets = new Insets(8,0,0,3);
+        JLabel elementLabel = new JLabel("elements");
+        leftPanel.add(elementLabel, sGbc);
+
+        //adding search button
+        sGbc.anchor = GridBagConstraints.EAST;
+        sGbc.gridy = 2;
+        sGbc.gridx = 3;
+//        sGbc.insets = new Insets(8,0,0,0);
+        searchButton = new JButton("Search");
+        searchButton.addActionListener(this);
+        leftPanel.add(searchButton, sGbc);
+
+
+        //adding results label
+        sGbc.fill = GridBagConstraints.HORIZONTAL;
+        sGbc.gridy = 3;
+        sGbc.gridx = 0;
+        sGbc.gridwidth = 4;
+        sGbc.insets = new Insets(8,10,0,0);
+        JLabel resultLabel = new JLabel("Search Results:");
+        leftPanel.add(resultLabel, sGbc);
+
+        //adding term list
+        sGbc.gridy = 4;
+        sGbc.gridx = 0;
+        sGbc.insets = new Insets(0,10,15,0);
+        sGbc.ipady = 80;
+        list = new JList<>();
+        list.setSelectionMode(ListSelectionModel.SINGLE_SELECTION);
+        list.addListSelectionListener(new ListSelectionListener() {
+            @Override
+            public void valueChanged(ListSelectionEvent listSelectionEvent) {
+                if (!listSelectionEvent.getValueIsAdjusting()) {
+                    getDescription();
+                }
+            }
+        });
+        leftPanel.add(new JScrollPane(list), sGbc);
+    }
+
+    private void addDescriptionPanelComponents(JPanel rightPanel) {
+        GridBagLayout dGbl = new GridBagLayout();
+        GridBagConstraints dGbc = new GridBagConstraints();
+        rightPanel.setLayout(dGbl);
+
+        dGbc.weightx = 1;
+        dGbc.weighty = 0.5;
+        dGbc.fill = GridBagConstraints.HORIZONTAL;
+
+        //adding label
+        dGbc.gridy = 0;
+        dGbc.anchor = GridBagConstraints.SOUTH;
+        dGbc.insets = new Insets(0,0,5,0);
+        JLabel descLabel = new JLabel("Description:");
+        rightPanel.add(descLabel, dGbc);
+
+        //adding text area
+        dGbc.weighty = 1;
+        dGbc.gridy = 1;
+        dGbc.ipady = 30;
+        dGbc.anchor = GridBagConstraints.NORTH;
+        dGbc.fill = GridBagConstraints.BOTH;
+        dGbc.insets = new Insets(0,0,20,15);
+        descriptionArea = new JTextArea();
+        descriptionArea.setLineWrap(true);
+        descriptionArea.setWrapStyleWord(true);
+        descriptionArea.setColumns(35);
+        descriptionArea.setEditable(false);
+//        descriptionArea.setMaximumSize(new Dimension(10,10));
+        rightPanel.add(new JScrollPane(descriptionArea),dGbc);
+    }
+
+
+    @Override
+    public void actionPerformed(ActionEvent evt) {
+        if (evt.getSource() == searchButton) {
+            getSearchResults();
+        } else if (evt.getSource() == addButton) {
+            setAnnotationDescAndIdentifier();
+        } else if (evt.getSource() == oKButton) {
+            this.dispose();
+        }
+    }
+
+    private void getSearchResults() {
+        //clear description area and search list before new
+        descriptionArea.setText(null);
+//        list.removeAll();
+        DefaultListModel<String> dlm = new DefaultListModel<>();
+        String searchTerm = searchBar.getText();
+        BioPortalSearch bioPortalSearch = new BioPortalSearch();
+
+//        String bioPortalDatabases = Objects.equals(ontologiesBox.getSelectedItem(), "All Selected") ?
+//                "GO,NCIT,CHEBI,FMA,BTO" : Objects.requireNonNull(ontologiesBox.getSelectedItem()).toString();
+        //MiriamManager.DataType dataType = (MiriamManager.DataType) annotationsPanel.getJComboBoxURI().getSelectedItem();
+        VCMetaDataMiriamManager.VCMetaDataDataType mdt = (VCMetaDataMiriamManager.VCMetaDataDataType)jComboBoxURI.getSelectedItem();
+//        String bioPortalDatabases = dataType.getDataTypeName();
+        String bioPortalDatabases = mdt.getDataTypeName();
+
+        boolean exactMatch = Objects.equals(containsBox.getSelectedItem(), "exact");
+
+        int pageSize = Integer.parseInt(Objects.requireNonNull(limitBox.getSelectedItem()).toString());
+
+        try {
+            SearchElements = bioPortalSearch.search(searchTerm,pageSize,bioPortalDatabases,exactMatch);
+            if (!SearchElements.isEmpty()) {
+                list.setEnabled(true);
+                list.setFont(new Font("TimesRoman",Font.PLAIN,13));
+                for (SearchElement element: SearchElements) {
+                    dlm.addElement(element.getEntityName());
+                }
+            } else {
+                list.setFont(new Font("Arial", Font.BOLD, 14));
+                dlm.addElement("No matches found");
+                list.setEnabled(false);
+            }
+            list.setModel(dlm);
+        } catch (IOException | SAXException | URISyntaxException | ParserConfigurationException |
+                 InterruptedException ex) {
+            throw new RuntimeException(ex);
+        }
+    }
+
+    private void getDescription() {
+        if (!list.isSelectionEmpty()) {
+            annotDescription = SearchElements.get(list.getSelectedIndex()).toString();
+            descriptionArea.setText(annotDescription);
+            descriptionArea.setCaretPosition(0);
+        }
+    }
+
+    private void setAnnotationDescAndIdentifier() {
+        if (!list.isSelectionEmpty()) {
+            annotationsPanel.addToAnnotationTextArea(annotDescription);
+        }
+        annotationsPanel.addIdentifier(SearchElements.get(list.getSelectedIndex()));
+    }
+
+    //getter and setter for JComboBoxURI
+    public JComboBox getjComboBoxURI() {
+        return jComboBoxURI;
+    }
+
+    public void setjComboBoxURI(JComboBox jComboBoxURI) {
+        this.jComboBoxURI = jComboBoxURI;
+    }
+
+
+//    JComboBox getJComboBoxURI() {
+//        if (jComboBoxURI == null) {
+//            jComboBoxURI = new JComboBox();
+//            defaultComboBoxModelURI = new DefaultComboBoxModel();
+//            jComboBoxURI.setModel(defaultComboBoxModelURI);
+//            Dimension d = jComboBoxURI.getPreferredSize();
+//            jComboBoxURI.setMinimumSize(new Dimension(MAX_URI_LENGTH, d.height));
+//            jComboBoxURI.setPreferredSize(new Dimension(MAX_URI_LENGTH, d.height));
+//            AnnotationsPanel.ComboboxToolTipRenderer renderer = new AnnotationsPanel.ComboboxToolTipRenderer();
+//            jComboBoxURI.setRenderer(renderer);
+//        }
+//        return jComboBoxURI;
+//    }
+
+}
diff --git a/vcell-client/src/main/java/cbit/vcell/client/desktop/biomodel/annotations/AnnotationsPanel.java b/vcell-client/src/main/java/cbit/vcell/client/desktop/biomodel/annotations/AnnotationsPanel.java
new file mode 100644
index 0000000000..51110c9496
--- /dev/null
+++ b/vcell-client/src/main/java/cbit/vcell/client/desktop/biomodel/annotations/AnnotationsPanel.java
@@ -0,0 +1,1204 @@
+/*
+ * Copyright (C) 1999-2011 University of Connecticut Health Center
+ *
+ * Licensed under the MIT License (the "License").
+ * You may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at:
+ *
+ *  http://www.opensource.org/licenses/mit-license.php
+ */
+
+package cbit.vcell.client.desktop.biomodel.annotations;
+
+import java.awt.BorderLayout;
+import java.awt.Color;
+import java.awt.Component;
+import java.awt.Dimension;
+import java.awt.GridBagConstraints;
+import java.awt.GridBagLayout;
+import java.awt.Insets;
+import java.awt.SystemColor;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.awt.event.FocusEvent;
+import java.awt.event.FocusListener;
+import java.awt.event.KeyEvent;
+import java.awt.event.KeyListener;
+import java.awt.event.MouseAdapter;
+import java.awt.event.MouseEvent;
+import java.awt.event.MouseListener;
+import java.beans.PropertyChangeEvent;
+import java.beans.PropertyChangeListener;
+import java.net.URI;
+import java.util.ArrayList;
+import java.util.Collections;
+import java.util.HashSet;
+import java.util.List;
+import java.util.Map;
+
+import javax.swing.*;
+import javax.swing.event.TreeSelectionEvent;
+import javax.swing.event.TreeSelectionListener;
+import javax.swing.tree.DefaultMutableTreeNode;
+import javax.swing.tree.DefaultTreeCellRenderer;
+import javax.swing.tree.DefaultTreeSelectionModel;
+import javax.swing.tree.TreePath;
+
+import cbit.vcell.client.desktop.biomodel.DocumentEditorSubPanel;
+import org.vcell.model.rbm.MolecularType;
+import org.vcell.pathway.BioPaxObject;
+import org.vcell.sybil.models.AnnotationQualifiers;
+import org.vcell.sybil.models.miriam.MIRIAMQualifier;
+import org.vcell.sybil.models.miriam.MIRIAMRef.URNParseFailureException;
+import org.vcell.util.Compare;
+import org.vcell.util.Displayable;
+import org.vcell.util.document.BioModelInfo;
+import org.vcell.util.document.Identifiable;
+import org.vcell.util.document.MathModelInfo;
+import org.vcell.util.gui.DialogUtils;
+
+import cbit.vcell.biomodel.BioModel;
+import cbit.vcell.biomodel.meta.MiriamManager;
+import cbit.vcell.biomodel.meta.VCMetaData;
+import cbit.vcell.biomodel.meta.VCMetaDataMiriamManager;
+import cbit.vcell.biomodel.meta.VCMetaDataMiriamManager.VCMetaDataDataType;
+import cbit.vcell.biomodel.meta.MiriamManager.DataType;
+import cbit.vcell.biomodel.meta.MiriamManager.MiriamRefGroup;
+import cbit.vcell.biomodel.meta.MiriamManager.MiriamResource;
+import cbit.vcell.client.PopupGenerator;
+import cbit.vcell.desktop.BioModelCellRenderer;
+import cbit.vcell.mapping.SimulationContext;
+import cbit.vcell.model.Model;
+import cbit.vcell.model.RbmObservable;
+import cbit.vcell.model.ReactionRule;
+import cbit.vcell.model.ReactionStep;
+import cbit.vcell.model.Species;
+import cbit.vcell.model.SpeciesContext;
+import cbit.vcell.model.Structure;
+import cbit.vcell.xml.gui.MiriamTreeModel;
+import cbit.vcell.xml.gui.MiriamTreeModel.LinkNode;
+/**
+ * Superclass for all the Annotation panels
+ * Creation date: (11/6/2018 3:44:00 PM)
+ * @author: Dan Vasilescu
+ */
+@SuppressWarnings("serial")
+public class AnnotationsPanel extends DocumentEditorSubPanel {
+	private BioModel bioModel = null;
+	private VCMetaData vcMetaData = null;
+	MiriamTreeModel miriamTreeModel = null;
+
+	private Identifiable selectedObject = null;
+
+	public static final String ACTION_ADD ="Add...";
+	public static final String ACTION_DELETE ="Delete";
+	public static final String ACTION_REMOVE_TEXT = "Delete";
+	public static final String ACTION_GOTO ="Go";
+	public static final int COMBO_QUALIFIER_WIDTH = 200;
+	public static final int MAX_DESCRIPTION_LENGTH = 145;
+	public static final int MAX_URI_LENGTH = 130;
+
+	private EventHandler eventHandler = new EventHandler();
+
+	private JTree jTreeMIRIAM = null;
+
+	private JPanel jPanelNewIdentifier = null;			// add new identity dialog
+	private JPanel jPanelIdentifierManager = null;		// upper panel with the identity provider combobox, Navigate and Add buttons
+	private JPanel jPanelLowerLeft = null;				// lower left panel with the  Delete buttons
+	private JPanel jBottomPanel = null;
+	private JSplitPane splitPane = null;
+	private JScrollPane jScrollPane = null;			// will show the MIRIAM JTree
+
+	private JComboBox jComboBoxURI = null;			// identity provider combo
+	private DefaultComboBoxModel defaultComboBoxModelURI = null;
+	private JComboBox jComboBoxQualifier = null;	// annotation qualifier combo (isDescribedBy, etc)
+	private DefaultComboBoxModel defaultComboBoxModelQualifier = new DefaultComboBoxModel();
+
+	private JTextField jTextFieldFormalID = null;	// immortal ID text
+	private JButton jButtonAddRef = null;			// add a cross-reference
+	private JButton jButtonDeleteRef = null;		// delete selected cross-reference
+	private JButton jButtonRemoveText = null;		// remove text annotation
+
+	JTextArea annotationTextArea = null;
+	private String emptyHtmlText = null;	// content of annotationTextArea after initialization with null
+	// will contain an empty html object "<html><header></header><body><p style="margin-top: 0"></p></body></html>"
+	private static String emptyHtmlText2 = "<html><header></header><body></body></html>";	// really empty
+
+	private AddAnnotationsPanel addAnnotationsPanel; //new window to add annotations from online DBs.
+
+
+	private class EventHandler extends MouseAdapter implements ActionListener, FocusListener, PropertyChangeListener, KeyListener {
+		public void focusGained(FocusEvent e) {
+		}
+		public void focusLost(FocusEvent e) {
+			if (e.getSource() == annotationTextArea) {
+				changeTextAnnotation();
+			}
+		}
+		@Override
+		public void mouseExited(MouseEvent e) {
+			super.mouseExited(e);
+			if(e.getSource() == annotationTextArea) {
+				changeTextAnnotation();
+			}
+		}
+		@Override
+		public void propertyChange(PropertyChangeEvent evt) {
+			if (evt.getSource() instanceof SpeciesContext
+					|| evt.getSource() instanceof MolecularType
+					|| evt.getSource() instanceof ReactionRule
+					|| evt.getSource() instanceof ReactionStep
+					|| evt.getSource() instanceof RbmObservable
+					|| evt.getSource() instanceof BioModel
+					|| evt.getSource() instanceof Structure
+					|| evt.getSource() instanceof Model.ModelParameter
+					|| evt.getSource() instanceof BioPaxObject
+
+					|| evt.getSource() instanceof SimulationContext
+//					|| evt.getSource() instanceof Simulation			// TODO: check why is not saving
+//					|| evt.getSource() instanceof SpeciesContextSpec	// TODO: can't use species name for spec too, need some hack
+//					|| evt.getSource() instanceof ReactionSpec
+			) {
+				initializeComboBoxURI();
+				updateInterface();
+			}
+		}
+		@Override
+		public void actionPerformed(ActionEvent evt) {
+			if (evt.getSource() == getJButtonAddRef()) {
+				initializeAddAnnotationsPanel();
+
+//				addIdentifier();
+			}
+			else if(evt.getSource() == addAnnotationsPanel.getOkButton()) {
+				annotationTextArea.setText("A test from the void");
+			}
+
+			else if(evt.getSource() == getJButtonDeleteRef()) {
+				removeIdentifier();
+			} else if(evt.getSource() == getJButtonRemoveText()) {
+				removeText();
+			}
+		}
+		@Override
+		public void keyPressed(KeyEvent e) {
+		}
+		@Override
+		public void keyReleased(KeyEvent e) {
+			// too expensive to parse it at each keystroke
+//			System.out.println("key released");
+//			if (e.getSource() == annotationTextArea) {
+//				String text = annotationTextArea.getText();
+//				text = text.replaceAll("(\n\r|\n|\r)", "");
+//				text = text.replaceAll(" ", "");
+//				System.out.println(text);
+//			}
+		}
+		@Override
+		public void keyTyped(KeyEvent e) {
+		}
+	}
+
+	public static class ComboboxToolTipRenderer extends DefaultListCellRenderer {
+		List<String> tooltips;
+		@SuppressWarnings("rawtypes")
+		@Override
+		public Component getListCellRendererComponent(JList list, Object value, int index, boolean isSelected, boolean cellHasFocus) {
+			Component comp;
+			if(value == null) {
+				comp = super.getListCellRendererComponent(list, value, index, isSelected, cellHasFocus);
+			} else if(value instanceof DataType) {
+				DataType dt = (DataType)value;
+				comp = super.getListCellRendererComponent(list,dt.getDataTypeName(),index,isSelected,cellHasFocus);
+			} else if(value instanceof MIRIAMQualifier) {
+				MIRIAMQualifier mc = (MIRIAMQualifier)value;
+				comp = super.getListCellRendererComponent(list,mc.getDescription(),index,isSelected,cellHasFocus);
+			} else {
+				comp = super.getListCellRendererComponent(list, value, index, isSelected, cellHasFocus);
+			}
+			if (-1 < index && null != value && null != tooltips) {
+				list.setToolTipText(tooltips.get(index));
+			}
+			return comp;
+		}
+		public void setTooltips(List<String> tooltips) {
+			this.tooltips = tooltips;
+		}
+	}
+
+
+	public AnnotationsPanel() {
+		super();
+		initialize();
+	}
+
+	private void handleException(java.lang.Throwable exception) {
+		System.out.println("--------- UNCAUGHT EXCEPTION ---------");
+		exception.printStackTrace(System.out);
+	}
+
+	private JPanel getJPanelNewIdentifier() {
+		jPanelNewIdentifier = new JPanel();
+		jPanelNewIdentifier.setLayout(new GridBagLayout());
+//	jPanelNewIdentifier.setPreferredSize(new Dimension(725, 37));
+//	jPanelNewIdentifier.setBorder(BorderFactory.createLineBorder(SystemColor.windowBorder, 2));
+////////////////////////////////////////////////////////////////////////////////////////////////////////
+//		VCMetaDataDataType mdt = (VCMetaDataDataType)getJComboBoxURI().getSelectedItem();
+		int gridx = 0;
+		int gridy = 0;
+		GridBagConstraints gbc = new GridBagConstraints();
+//		gbc.insets = new Insets(3, 15, 3, 0);		// top left bottom right
+//		gbc.gridx = gridx;
+//		gbc.gridy = gridy;
+//		gbc.anchor = GridBagConstraints.WEST;
+//		jPanelNewIdentifier.add(new JLabel("Provider: "), gbc);
+//
+//		gridx++;
+//		gbc = new GridBagConstraints();
+//		gbc.insets = new Insets(3, 5, 3, 4);
+//		gbc.gridx = gridx;
+//		gbc.gridy = gridy;
+//		gbc.anchor = GridBagConstraints.WEST;
+//		jPanelNewIdentifier.add(new JLabel("<html><b>" + mdt.getDataTypeName() + "</b></html>"), gbc);
+
+		// ------------------------------------- Qualifier combobox  -----------------------------
+
+		gridx++;
+		gbc = new GridBagConstraints();
+		gbc.insets = new Insets(3, 15, 3, 0);		// top left bottom right
+		gbc.gridx = gridx;
+		gbc.gridy = gridy;
+		jPanelNewIdentifier.add(new JLabel("Qualifier"), gbc);
+
+		gridx++;
+		gbc = new GridBagConstraints();
+		gbc.insets = new Insets(3, 5, 3, 4);
+		gbc.gridx = gridx;
+		gbc.gridy = gridy;
+		jPanelNewIdentifier.add(getJComboBoxQualifier(), gbc);
+
+		// -------------------------------------------------------------------------------
+		gridx++;
+		gbc = new GridBagConstraints();
+		gbc.insets = new Insets(3, 15, 3, 0);
+		gbc.gridx = gridx;
+		gbc.gridy = gridy;
+		gbc.anchor = GridBagConstraints.WEST;
+		jPanelNewIdentifier.add(new JLabel("Identifier ID"), gbc);
+
+		gridx++;
+		gbc = new GridBagConstraints();
+		gbc.insets = new Insets(3, 5, 3, 4);
+		gbc.gridx = gridx;
+		gbc.gridy = gridy;
+		gbc.anchor = GridBagConstraints.WEST;
+		jPanelNewIdentifier.add(getJTextFieldFormalID(), gbc);
+		getJTextFieldFormalID().setText("NewID");
+
+		gridx++;
+		gbc = new GridBagConstraints();
+		gbc.insets = new Insets(3, 15, 3, 0);
+		gbc.gridx = gridx;
+		gbc.gridy = gridy;
+		gbc.anchor = GridBagConstraints.WEST;
+//		jPanelNewIdentifier.add(new JLabel("<html>Example: <b>" + mdt.getExample() +"</b></html>"), gbc);
+
+		gridx++;
+		gbc = new GridBagConstraints();
+		gbc.insets = new Insets(3, 15, 3, 0);
+		gbc.gridx = gridx;
+		gbc.gridy = gridy;
+		gbc.weightx = 1.0;
+		gbc.anchor = GridBagConstraints.EAST;
+		jPanelNewIdentifier.add(new JLabel(), gbc);
+
+		// ---------------------------------------------------------------------
+		gridx = 0;
+		gridy++;
+
+		JLabel linkLabel = new JLabel();
+//		String s = "<html>" + "Navigate to" + "&nbsp;<font color=\"" + "blue" + "\"><a href=" + mdt.getDataTypeURL() + ">" + mdt.getDataTypeURL() + "</a></font>&nbsp;&nbsp;";
+//		s += "and find the identifier ID, then paste it in the box above." + "</html>";
+		linkLabel.setToolTipText("Double-click to open link");
+//		linkLabel.setText(s);
+		linkLabel.addMouseListener(new MouseAdapter() {
+			public void mousePressed(MouseEvent e) {
+				if(e.getClickCount() == 2) {
+//					showBrowseToLink(mdt);
+				}
+			}
+		});
+
+		gbc = new GridBagConstraints();
+		gbc.insets = new Insets(3, 15, 3, 0);
+		gbc.gridx = gridx;
+		gbc.gridy = gridy;
+		gbc.gridwidth = 8;
+		gbc.anchor = GridBagConstraints.WEST;
+		jPanelNewIdentifier.add(linkLabel, gbc);
+
+		// ---------------------------------------------------------------------
+		List <String> rows = new ArrayList<> ();
+//		String value = mdt.getDescription();
+//		StringTokenizer tokenizer = new StringTokenizer(value, " ");
+		String row = "";
+//		while(tokenizer.hasMoreTokens()) {
+//			String word = tokenizer.nextToken();
+//			if((row.length() + word.length()) > MAX_DESCRIPTION_LENGTH) {
+//				rows.add(row);
+//				row = word + " ";
+//			} else {
+//				row += word + " ";
+//			}
+//		}
+		if(!row.isEmpty()) {
+			rows.add(row);
+		}
+		for(String currentRow : rows) {
+			gridx = 0;
+			gridy++;
+			gbc = new GridBagConstraints();
+			gbc.insets = new Insets(3, 15, 3, 0);
+			gbc.gridx = gridx;
+			gbc.gridy = gridy;
+			gbc.gridwidth = 8;
+			gbc.fill = GridBagConstraints.HORIZONTAL;
+			gbc.weightx = 1.0;
+			jPanelNewIdentifier.add(new JLabel(currentRow), gbc);
+
+		}
+		return jPanelNewIdentifier;
+	}
+	private JPanel getJPanelLeftTitle() {
+		JPanel jPanelLeftTitle = new JPanel();
+		jPanelLeftTitle.setLayout(new GridBagLayout());
+		jPanelLeftTitle.setPreferredSize(new Dimension(260, 37));
+		jPanelLeftTitle.setBorder(BorderFactory.createLineBorder(SystemColor.windowBorder, 1));
+		int gridx = 0;
+		GridBagConstraints gbc = new GridBagConstraints();
+		gbc.insets = new Insets(3, 15, 3, 0);		// top left bottom right
+		gbc.gridx = gridx;
+		gbc.gridy = 0;
+		gbc.fill = GridBagConstraints.HORIZONTAL;
+		gbc.weightx = 1.0;
+		jPanelLeftTitle.add(new JLabel("User defined cross-references."), gbc);
+
+		gridx++;
+		gbc = new GridBagConstraints();
+		gbc.insets = new Insets(3, 6, 3, 8);
+		gbc.gridx = gridx;
+		gbc.gridy = 0;
+		jPanelLeftTitle.add(getJButtonAddRef(), gbc);
+		getJButtonAddRef().addActionListener(eventHandler);
+
+		return jPanelLeftTitle;
+	}
+	private JPanel getJPanelRightTitle() {
+		JPanel jPanelRightTitle = new JPanel();
+		jPanelRightTitle.setLayout(new GridBagLayout());
+		jPanelRightTitle.setBorder(BorderFactory.createLineBorder(SystemColor.windowBorder, 1));
+
+		int gridx = 0;
+		GridBagConstraints gbc = new GridBagConstraints();
+		gbc.gridx = gridx;
+		gbc.gridy = 0;
+		gbc.insets = new Insets(6, 8, 0, 0);		// top left bottom right
+		gbc.anchor = GridBagConstraints.NORTHWEST;
+		jPanelRightTitle.add(new JLabel("Text Annotations"), gbc);
+
+		gridx++;
+		gbc = new java.awt.GridBagConstraints();
+		gbc.gridx = gridx;
+		gbc.gridy = 0;
+		gbc.weightx = 1.0;
+		gbc.weighty = 1.0;
+		gbc.fill = java.awt.GridBagConstraints.BOTH;
+		jPanelRightTitle.add(new JLabel(), gbc);
+
+		gridx++;
+		gbc = new java.awt.GridBagConstraints();
+		gbc.gridx = gridx;
+		gbc.gridy = 0;
+		gbc.insets = new Insets(3, 0, 3, 3);
+		gbc.anchor = GridBagConstraints.NORTHEAST;
+		jPanelRightTitle.add(getJButtonRemoveText(), gbc);
+
+		getJButtonRemoveText().addActionListener(eventHandler);
+		return jPanelRightTitle;
+	}
+	private JPanel getJPanelIdentifierManager() {
+		if (jPanelIdentifierManager == null) {
+			jPanelIdentifierManager = new JPanel();
+//			jPanelIdentifierManager.setLayout(new GridBagLayout());
+//			jPanelIdentifierManager.setPreferredSize(new Dimension(260, 300)); //37
+//			jPanelIdentifierManager.setBorder(BorderFactory.createLineBorder(SystemColor.windowBorder, 1));
+//
+//			int gridx = 0;
+//			GridBagConstraints gbc = new GridBagConstraints();
+//		gbc.insets = new Insets(3, 15, 3, 0);		// top left bottom right
+//		gbc.gridx = gridx;
+//		gbc.gridy = 0;
+//		jPanelIdentifierManager.add(new JLabel("Provider"), gbc);
+
+//		gridx++;
+//		gbc = new GridBagConstraints();
+//			gbc.insets = new Insets(3, 5, 3, 4);
+//			gbc.gridx = gridx;
+//			gbc.gridy = 0;
+//			jPanelIdentifierManager.add(getJComboBoxURI(), gbc);
+
+//		gridx++;
+//		gbc = new GridBagConstraints();
+//		gbc.insets = new Insets(3, 5, 3, 5);
+//		gbc.gridx = gridx;
+//		gbc.gridy = 0;
+//		jPanelIdentifierManager.add(getJButtonAddRef(), gbc);
+
+//		gbc = new GridBagConstraints();
+//		gbc.insets = new Insets(3, 0, 3, 0);
+//		gbc.gridx = gridx;
+//		gbc.gridy = 0;
+//		gbc.fill = GridBagConstraints.HORIZONTAL;
+//		gbc.weightx = 1.0;
+//		jPanelIdentifierManager.add(new JLabel(""), gbc);
+//
+//		getJButtonAddRef().addActionListener(eventHandler);
+		}
+		return jPanelIdentifierManager;
+	}
+	private JPanel getJPanelLowerLeft() {
+		if (jPanelLowerLeft == null) {
+			jPanelLowerLeft = new JPanel();
+			jPanelLowerLeft.setLayout(new GridBagLayout());
+			jPanelLowerLeft.setPreferredSize(new Dimension(300, 37));
+			jPanelLowerLeft.setBorder(BorderFactory.createLineBorder(SystemColor.windowBorder, 1));
+
+			int gridx = 0;
+			GridBagConstraints gbc = new GridBagConstraints();
+			gbc.insets = new Insets(3, 3, 3, 3);
+			gbc.gridx = gridx;
+			gbc.gridy = 0;
+			jPanelLowerLeft.add(getJButtonDeleteRef(), gbc);
+
+			gridx++;
+			gbc = new GridBagConstraints();
+			gbc.insets = new Insets(3, 0, 3, 0);
+			gbc.gridx = gridx;
+			gbc.gridy = 0;
+			gbc.fill = GridBagConstraints.HORIZONTAL;
+			gbc.weightx = 1.0;
+			jPanelLowerLeft.add(new JLabel(""), gbc);
+
+			getJButtonDeleteRef().setEnabled(false);
+			getJButtonDeleteRef().addActionListener(eventHandler);
+		}
+		return jPanelLowerLeft;
+	}
+
+	public JComboBox getJComboBoxQualifier() {
+		if (jComboBoxQualifier == null) {
+			jComboBoxQualifier = new JComboBox();
+//		defaultComboBoxModelQualifier = new DefaultComboBoxModel();	// already allocated
+			jComboBoxQualifier.setModel(defaultComboBoxModelQualifier);
+			Dimension d = jComboBoxQualifier.getPreferredSize();
+			jComboBoxQualifier.setMinimumSize(new Dimension(COMBO_QUALIFIER_WIDTH, d.height));
+			jComboBoxQualifier.setPreferredSize(new Dimension(COMBO_QUALIFIER_WIDTH, d.height));
+			ComboboxToolTipRenderer renderer = new ComboboxToolTipRenderer();
+			jComboBoxQualifier.setRenderer(renderer);
+		}
+		return jComboBoxQualifier;
+	}
+	private JTextField getJTextFieldFormalID() {
+		if (jTextFieldFormalID == null) {
+			jTextFieldFormalID = new JTextField();
+			jTextFieldFormalID.setText("NewID");
+			Dimension d = jTextFieldFormalID.getPreferredSize();
+			jTextFieldFormalID.setMinimumSize(new Dimension(100, d.height));
+			jTextFieldFormalID.setPreferredSize(new Dimension(100, d.height));
+		}
+		return jTextFieldFormalID;
+	}
+
+	@SuppressWarnings({ "rawtypes", "unchecked" })
+	public JComboBox getJComboBoxURI() {
+		if (jComboBoxURI == null) {
+			jComboBoxURI = new JComboBox();
+			defaultComboBoxModelURI = new DefaultComboBoxModel();
+			jComboBoxURI.setModel(defaultComboBoxModelURI);
+			Dimension d = jComboBoxURI.getPreferredSize();
+			jComboBoxURI.setMinimumSize(new Dimension(MAX_URI_LENGTH, d.height));
+			jComboBoxURI.setPreferredSize(new Dimension(MAX_URI_LENGTH, d.height));
+			ComboboxToolTipRenderer renderer = new ComboboxToolTipRenderer();
+			jComboBoxURI.setRenderer(renderer);
+//		jComboBoxURI.setRenderer(new DefaultListCellRenderer() {
+//			public Component getListCellRendererComponent(JList list, Object value, int index, boolean isSelected, boolean cellHasFocus) {
+//				if(value == null) {
+//					return super.getListCellRendererComponent(list, value, index, isSelected, cellHasFocus);
+//				} else {
+//					DataType dt = (DataType)value;
+//					Component comp = super.getListCellRendererComponent(list,dt.getDataTypeName(),index,isSelected,cellHasFocus);
+//					return comp;
+//				}
+//			}
+//		});
+		}
+		return jComboBoxURI;
+	}
+
+	private JPanel getBottomPanel() {
+		if (jBottomPanel == null) {
+			jBottomPanel = new JPanel();
+			jBottomPanel.setLayout(new BorderLayout());
+			jBottomPanel.add(getSplitPane(), BorderLayout.CENTER);
+		}
+		return jBottomPanel;
+
+	}
+	private JSplitPane getSplitPane() {
+		if (splitPane == null) {
+
+			JPanel leftPanel = new JPanel();
+			leftPanel.setLayout(new GridBagLayout());
+			leftPanel.setBackground(Color.white);
+
+			int gridy = 0;
+			GridBagConstraints gbc = new java.awt.GridBagConstraints();
+			gbc.gridx = 0;
+			gbc.gridy = gridy;
+			gbc.weightx = 1.0;
+			gbc.weighty = 0;
+			gbc.insets = new Insets(3, 3, 1, 3);
+			gbc.fill = java.awt.GridBagConstraints.HORIZONTAL;
+			gbc.anchor = GridBagConstraints.NORTHWEST;
+			leftPanel.add(getJPanelLeftTitle(), gbc);
+
+//			gridy++;
+//			gbc = new java.awt.GridBagConstraints();
+//			gbc.gridx = 0;
+//			gbc.gridy = gridy;
+//			gbc.weightx = 1.0;
+//			gbc.weighty = 0;
+//			gbc.insets = new Insets(2, 3, 1, 3);
+//			gbc.fill = java.awt.GridBagConstraints.HORIZONTAL;
+//			gbc.anchor = GridBagConstraints.NORTHWEST;
+//			leftPanel.add(getJPanelIdentifierManager(), gbc);
+
+			gridy++;
+			gbc = new java.awt.GridBagConstraints();
+			gbc.gridx = 0;
+			gbc.gridy = gridy;
+			gbc.weightx = 1.0;
+			gbc.weighty = 1.0;
+			gbc.insets = new Insets(2, 3, 1, 3);
+			gbc.fill = java.awt.GridBagConstraints.BOTH;
+			gbc.anchor = GridBagConstraints.SOUTHWEST;
+			leftPanel.add(getJScrollPane(), gbc);
+
+			gridy++;
+			gbc = new java.awt.GridBagConstraints();
+			gbc.gridx = 0;
+			gbc.gridy = gridy;
+			gbc.weightx = 1.0;
+			gbc.weighty = 0;
+			gbc.insets = new Insets(2, 3, 3, 3);
+			gbc.fill = java.awt.GridBagConstraints.BOTH;
+			gbc.anchor = GridBagConstraints.SOUTHWEST;
+			leftPanel.add(getJPanelLowerLeft(), gbc);
+			// -----------------------------------------------------------------------
+
+			JPanel rightPanel = new JPanel();
+			rightPanel.setLayout(new GridBagLayout());
+			rightPanel.setBackground(Color.white);
+
+			gridy = 0;
+			gbc = new java.awt.GridBagConstraints();
+			gbc.gridx = 0;
+			gbc.gridy = gridy;
+			gbc.insets = new Insets(3, 3, 2, 2);
+			gbc.fill = java.awt.GridBagConstraints.HORIZONTAL;
+			gbc.anchor = GridBagConstraints.NORTHWEST;
+			rightPanel.add(getJPanelRightTitle(), gbc);
+
+			annotationTextArea = new JTextArea();
+//		annotationTextArea.setContentType("text/html");
+			annotationTextArea.setEditable(false);
+			annotationTextArea.addFocusListener(eventHandler);
+			annotationTextArea.addMouseListener(eventHandler);
+			annotationTextArea.setLineWrap(true);
+			annotationTextArea.setWrapStyleWord(true);
+			annotationTextArea.setCaretPosition(0);
+			JScrollPane annotationPanel = new JScrollPane(annotationTextArea);
+
+			gridy++;
+			gbc = new java.awt.GridBagConstraints();
+			gbc.gridx = 0;
+			gbc.gridy = gridy;
+			gbc.weightx = 1.0;
+			gbc.weighty = 1.0;
+			gbc.insets = new Insets(1, 3, 1, 2);
+			gbc.fill = java.awt.GridBagConstraints.BOTH;
+			gbc.anchor = GridBagConstraints.NORTHWEST;
+			rightPanel.add(annotationPanel, gbc);
+			// ----------------------------------------------------------------------------------
+
+			splitPane = new JSplitPane(JSplitPane.HORIZONTAL_SPLIT);
+			splitPane.setOneTouchExpandable(true);
+			splitPane.setLeftComponent(leftPanel);
+			splitPane.setRightComponent(rightPanel);
+			splitPane.setResizeWeight(0.1);
+			splitPane.setDividerLocation(0.3);
+
+			annotationTextArea.addKeyListener(eventHandler);
+		}
+		return splitPane;
+	}
+
+	private JScrollPane getJScrollPane() {
+		if (jScrollPane == null) {
+			jScrollPane = new JScrollPane();
+			jScrollPane.setViewportView(getJTreeMIRIAM());
+		}
+		return jScrollPane;
+	}
+	private JTree getJTreeMIRIAM() {
+		if (jTreeMIRIAM == null) {
+			try {
+				DefaultTreeSelectionModel ivjLocalSelectionModel;
+				ivjLocalSelectionModel = new DefaultTreeSelectionModel();
+				ivjLocalSelectionModel.setSelectionMode(1);
+				jTreeMIRIAM = new JTree();
+				jTreeMIRIAM.setName("JTree1");
+				jTreeMIRIAM.setToolTipText("");
+				jTreeMIRIAM.setBounds(0, 0, 357, 405);
+				jTreeMIRIAM.setMinimumSize(new java.awt.Dimension(100, 72));
+				jTreeMIRIAM.setSelectionModel(ivjLocalSelectionModel);
+				jTreeMIRIAM.setRowHeight(0);
+				jTreeMIRIAM.setRootVisible(false);
+
+				// Add cellRenderer
+				DefaultTreeCellRenderer dtcr = new BioModelCellRenderer(null) {
+					@Override
+					public Component getTreeCellRendererComponent(JTree tree, Object value, boolean sel, boolean expanded, boolean leaf, int row, boolean hasFocus) {
+						// default for LinkNode is in BioModelCellRenderer.java
+						JLabel component = (JLabel)super.getTreeCellRendererComponent(tree, value, sel, expanded, leaf, row, hasFocus);
+						// TODO: here
+						component.setIcon(null);
+						return component;
+					}
+				};
+				jTreeMIRIAM.setCellRenderer(dtcr);
+
+				MouseListener mouseListener = new MouseAdapter() {
+					@Override
+					public void mouseClicked(MouseEvent e) {
+						super.mouseClicked(e);
+//					TreePath closestMousePath =jTreeMIRIAM.getClosestPathForLocation(e.getPoint().x, e.getPoint().y);
+//					showPopup(e, closestMousePath);
+					}
+
+					@Override
+					public void mouseReleased(MouseEvent e) {
+						super.mouseReleased(e);
+//					TreePath closestMousePath =jTreeMIRIAM.getClosestPathForLocation(e.getPoint().x, e.getPoint().y);
+//					showPopup(e,closestMousePath);
+					}
+
+					public void mousePressed(MouseEvent e) {
+						TreePath closestMousePath =jTreeMIRIAM.getClosestPathForLocation(e.getPoint().x, e.getPoint().y);
+						jTreeMIRIAM.setSelectionPath(closestMousePath);
+//					showPopup(e,closestMousePath);
+						if(e.getClickCount() == 2) {
+							DefaultMutableTreeNode node = (DefaultMutableTreeNode)jTreeMIRIAM.getLastSelectedPathComponent();
+							if (node instanceof LinkNode) {
+								showBrowseToLink((LinkNode)node);
+							}
+						}
+					}
+				};
+				jTreeMIRIAM.addMouseListener(mouseListener);
+
+			} catch (java.lang.Throwable ivjExc) {
+				ivjExc.printStackTrace(System.out);
+			}
+		}
+		return jTreeMIRIAM;
+	}
+	private void showBrowseToLink(LinkNode linkNode) {
+		String link = linkNode.getLink();
+		if (link != null) {
+			DialogUtils.browserLauncher(jTreeMIRIAM, link, "failed to launch");
+		}else{
+			DialogUtils.showWarningDialog(this, "No Web-site link available");
+		}
+	}
+	private void showBrowseToLink(VCMetaDataDataType md) {
+		String link = md.getDataTypeURL();
+		if (link != null) {
+			DialogUtils.browserLauncher(getJComboBoxURI(), link, "Failed to launch");
+		} else {
+			DialogUtils.showWarningDialog(this, "No Web-site link available");
+		}
+	}
+
+	private void initialize() {
+		try {
+			setLayout(new GridBagLayout());
+			setBackground(Color.white);
+
+			int gridy = 0;
+			GridBagConstraints gbc = new java.awt.GridBagConstraints();
+			gbc.gridx = 0;
+			gbc.gridy = gridy;
+			gbc.weightx = 1.0;
+			gbc.weighty = 1.0;
+			gbc.insets = new Insets(4, 4, 4, 4);
+			gbc.fill = java.awt.GridBagConstraints.BOTH;
+			gbc.anchor = GridBagConstraints.SOUTHWEST;
+			add(getBottomPanel(), gbc);
+
+			JTextPane tenpTextPane = new JTextPane();	// used just to initialize emptyText once
+			tenpTextPane.setContentType("text/html");
+			tenpTextPane.setText(null);
+			emptyHtmlText = tenpTextPane.getText();
+
+			initializeComboBoxQualifier();
+			initializeComboBoxURI();
+
+			getJTreeMIRIAM().addTreeSelectionListener(new TreeSelectionListener() {
+				public void valueChanged(TreeSelectionEvent e) {
+					TreePath tp = ((JTree)e.getSource()).getSelectionPath();
+					if(tp == null) {
+						getJButtonDeleteRef().setEnabled(false);
+					} else {
+						Object lastPathComponent = tp.getLastPathComponent();
+						getJButtonDeleteRef().setEnabled(tp != null && lastPathComponent instanceof LinkNode);
+					}
+				}
+			});
+
+		} catch (java.lang.Throwable ivjExc) {
+			handleException(ivjExc);
+		}
+	}
+
+	public void addToAnnotationTextArea(String annotDescription) {
+//		annotationTextArea.setText("Text can be set from addToAnnotation method");
+		String existingTest = annotationTextArea.getText();
+		if (annotationTextArea.getText().length() != 0) {
+			annotationTextArea.setText(existingTest + "\n" + annotDescription);
+		} else {
+			annotationTextArea.setText(annotDescription);
+		}
+
+//		String existingText = "";
+//		if (annotationTextArea != null || annotationTextArea.getText().length() != 0) {
+//			existingText = annotationTextArea.getText();
+//		}
+//		annotationTextArea.setText("\n" + existingText + annotDescription);
+		changeTextAnnotation();
+	}
+
+	private void changeTextAnnotation() {
+		try{
+			if (bioModel == null || selectedObject == null) {
+				return;
+			}
+			Identifiable entity = getIdentifiable(selectedObject);
+			String textAreaStr = (annotationTextArea.getText() == null || annotationTextArea.getText().length()==0?null:annotationTextArea.getText());
+			String oldText = bioModel.getVCMetaData().getFreeTextAnnotation(entity);
+
+			if(textAreaStr == null || textAreaStr.isEmpty() || emptyHtmlText.equals(textAreaStr)) {	// no annotation now, the field is empty
+				bioModel.getVCMetaData().deleteFreeTextAnnotation(entity);	// delete, if there's something previously saved
+				if(selectedObject instanceof ReactionStep) {
+					// we tell ReactionPropertiesPanel to refresh the annotation icon
+					((ReactionStep) selectedObject).firePropertyChange("addIdentifier", false, true);
+				}
+			} else if(!Compare.isEqualOrNull(oldText,textAreaStr)) {		// some text annotation different from what's already saved
+				bioModel.getVCMetaData().setFreeTextAnnotation(entity, textAreaStr);	// overwrite
+				if(selectedObject instanceof ReactionStep) {
+					// we tell ReactionPropertiesPanel to refresh the text annotation icon
+					((ReactionStep) selectedObject).firePropertyChange("addIdentifier", false, true);
+				}
+			}
+		} catch(Exception e) {
+			e.printStackTrace(System.out);
+			PopupGenerator.showErrorDialog(this,"Annotation Error\n"+e.getMessage(), e);
+		}
+	}
+	private void removeText() {
+		if (bioModel == null || selectedObject == null) {
+			return;
+		}
+		Identifiable entity = getIdentifiable(selectedObject);
+		annotationTextArea.setText(null);
+		bioModel.getVCMetaData().deleteFreeTextAnnotation(entity);	// delete, if there's something previously saved
+		if(selectedObject instanceof ReactionStep) {
+			((ReactionStep) selectedObject).firePropertyChange("addIdentifier", false, true);
+		}
+	}
+
+	public void setBioModel(BioModel newValue) {
+		if (newValue == bioModel) {
+			return;
+		}
+		bioModel = newValue;
+		vcMetaData = bioModel.getVCMetaData();
+
+		// set tree model on jTableMIRIAM here, since we have access to miriamDescrHeir here
+		miriamTreeModel = new MiriamTreeModel(new DefaultMutableTreeNode("Object Annotations",true), vcMetaData, false);
+		jTreeMIRIAM.setModel(miriamTreeModel);
+
+		initializeComboBoxURI();
+		getJTextFieldFormalID().setText("NewID");
+		updateInterface();
+	}
+
+	private void updateInterface() {
+		if (bioModel == null) {
+			return;
+		}
+		Identifiable entity = getIdentifiable(selectedObject);
+		if(selectedObject != null && entity != null) {
+			getJComboBoxURI().setEnabled(true);
+			getJTextFieldFormalID().setEnabled(true);
+			getJButtonAddRef().setEnabled(true);
+			getJButtonRemoveText().setEnabled(true);
+			VCMetaDataDataType mdt = (VCMetaDataDataType)getJComboBoxURI().getSelectedItem();
+			miriamTreeModel.createTree(entity);
+
+			String freeText = bioModel.getVCMetaData().getFreeTextAnnotation(entity);
+			if(freeText == null || freeText.isEmpty()) {
+				annotationTextArea.setText(null);
+			} else {
+				annotationTextArea.setText(freeText);
+			}
+			annotationTextArea.setEditable(true);
+			annotationTextArea.setCaretPosition(0);
+		} else {
+			getJComboBoxURI().setEnabled(false);
+			getJTextFieldFormalID().setEnabled(false);
+			getJButtonAddRef().setEnabled(false);
+			getJButtonRemoveText().setEnabled(false);
+			miriamTreeModel.createTree(null);
+
+			annotationTextArea.setText(null);
+			annotationTextArea.setEditable(false);
+		}
+	}
+	public static Identifiable getIdentifiable(Identifiable selectedObject) {
+		//
+		// for SpeciesContext objects:
+		//		MIRIAM tree needs the Species				!!!
+		//		text Annotation needs the SpeciesContext
+		//
+		// !!!	use this only for the tree !!!
+		//
+		if(selectedObject == null) {
+			return null;
+		}
+		if(selectedObject instanceof SpeciesContext) {
+			return (Species)((SpeciesContext)selectedObject).getSpecies();
+		} else if(selectedObject instanceof MolecularType) {
+			return (MolecularType)selectedObject;
+		} else if(selectedObject instanceof ReactionRule) {
+			return (ReactionRule)selectedObject;
+		} else if(selectedObject instanceof ReactionStep) {
+			return (ReactionStep)selectedObject;
+		} else if(selectedObject instanceof RbmObservable) {
+			return (RbmObservable)selectedObject;
+		} else if(selectedObject instanceof BioModel) {
+			return (BioModel)selectedObject;
+		} else if(selectedObject instanceof Structure) {
+			return (Structure)selectedObject;
+		} else if(selectedObject instanceof BioPaxObject) {
+			return null;
+		} else if(selectedObject instanceof Model.ModelParameter) {
+			return (Model.ModelParameter)selectedObject;
+		} else if(selectedObject instanceof SimulationContext) {
+			return (SimulationContext)selectedObject;
+//	} else if(selectedObject instanceof Simulation) {
+//		return (Simulation)selectedObject;
+//	} else if(selectedObject instanceof SpeciesContextSpec) {
+//		return (SpeciesContextSpec)selectedObject;
+//	} else if(selectedObject instanceof ReactionSpec) {
+//		return (ReactionSpec)selectedObject;
+		} else {
+			return null;
+		}
+	}
+
+	@Override
+	protected void onSelectedObjectsChange(Object[] selectedObjects) {
+		if (selectedObjects != null && selectedObjects.length == 1) {
+			if(selectedObjects[0] instanceof BioModelInfo || selectedObjects[0] instanceof MathModelInfo) {
+				return;
+			}
+			if(selectedObjects[0] instanceof Identifiable && selectedObjects[0] instanceof Displayable) {
+				selectedObject = (Identifiable)selectedObjects[0];
+				System.out.println("AnnotationsPanel: class: " + selectedObject.getClass().getSimpleName() + ", selected object: " + ((Displayable)selectedObject).getDisplayName());
+			} else {
+				selectedObject = null;
+				System.out.println("Unsupported or null entity");
+			}
+			initializeComboBoxURI();		// if selectedObject or entity are null we just empty the combobox
+			getJButtonDeleteRef().setEnabled(false);
+			getJTextFieldFormalID().setText("NewID");
+			updateInterface();
+		}
+	}
+
+	// -------------------------------------------------------------------------------------------------------
+	private void initializeAddAnnotationsPanel() {
+		//generate addAnnotationPanel with URI and Qualifier ComboBox
+		if (addAnnotationsPanel == null) {
+			addAnnotationsPanel =  new AddAnnotationsPanel(this, getJComboBoxURI(), getJComboBoxQualifier());
+		}
+		else {
+			addAnnotationsPanel.dispose();
+			addAnnotationsPanel = new AddAnnotationsPanel(this, getJComboBoxURI(), getJComboBoxQualifier());
+		}
+	}
+
+	protected void addIdentifier(SearchElement searchElement) {
+//	if(PopupGenerator.showComponentOKCancelDialog(AnnotationsPanel.this, getJPanelNewIdentifier(), "Define New Formal Identifier") != JOptionPane.OK_OPTION) {
+//		return;
+//	}
+/////////////////////////////////////////////////////////////////////////////////////////////////////
+		MIRIAMQualifier qualifier = (MIRIAMQualifier)getJComboBoxQualifier().getSelectedItem();
+
+		MiriamManager.DataType objectNamespace = (MiriamManager.DataType)getJComboBoxURI().getSelectedItem();
+
+//		String objectID = getJTextFieldFormalID().getText();
+		String objectID = getId(searchElement.getDbLink(), objectNamespace.getDataTypeName());
+//		if(objectID.compareTo("NewID") == 0) {
+//			return;
+//		}
+		MiriamManager miriamManager = vcMetaData.getMiriamManager();
+		HashSet<MiriamResource> miriamResources = new HashSet<>();
+		try {
+			Identifiable entity = getIdentifiable(selectedObject);
+			MiriamResource mr = miriamManager.createMiriamResource(objectNamespace.getBaseURN()+":"+objectID);
+			miriamResources.add(mr);
+			miriamManager.addMiriamRefGroup(entity, qualifier, miriamResources);
+//		System.out.println(vcMetaData.printRdfStatements());
+			updateInterface();
+			if(selectedObject instanceof ReactionStep) {
+				// we tell ReactionPropertiesPanel to refresh the annotation icon
+				((ReactionStep) selectedObject).firePropertyChange("addIdentifier", false, true);
+			}
+		} catch (Exception e) {
+			e.printStackTrace();
+			DialogUtils.showErrorDialog(this,"Add Identifier failed:\n"+e.getMessage(), e);
+		}
+	}
+	private String getId(URI uri, String dataTypeName) {
+		String id = "Wrong ID";
+
+		if (uri.toString().contains("BTO"))
+			id = uri.getPath().replace("/obo/BTO_","");
+		else if (uri.toString().contains("CHEBI"))
+			id = uri.getPath().replace("/obo/CHEBI_","");
+		else if (uri.toString().contains("CL"))
+			id = uri.getPath().replace("/obo/CL_","");
+		else if (uri.toString().contains("EFO"))
+			id = uri.getPath().replace("/efo/EFO_","");
+		else if (uri.toString().contains("GO"))
+			id = uri.getPath().replace("/obo/GO_","");
+		else if (uri.toString().contains("ncit"))
+			id = uri.toString().replace("https://ncit.nci.nih.gov/ncitbrowser/ConceptReport.jsp?dictionary=NCI_Thesaurus&ns=ncit&code=","");
+		else if (uri.toString().contains("PATO"))
+			id = uri.getPath().replace("/obo/PATO_","");
+		else if (uri.toString().contains("PR"))
+			id = uri.getPath().replace("/obo/PR_","");
+
+		return id;
+	}
+	private void removeIdentifier() {
+		Object treeNode = jTreeMIRIAM.getLastSelectedPathComponent();
+		if (treeNode instanceof LinkNode) {
+			LinkNode linkNode = (LinkNode)treeNode;
+			MiriamResource resourceToDelete = linkNode.getMiriamResource();
+			Identifiable entity = getIdentifiable(selectedObject);
+			//Map<MiriamRefGroup, MIRIAMQualifier> refGroupsToRemove = vcMetaData.getMiriamManager().getAllMiriamRefGroups(entity);
+			MiriamManager mm = vcMetaData.getMiriamManager();
+			Map<MiriamRefGroup,MIRIAMQualifier> refGroupsToRemove = mm.getMiriamTreeMap().get(entity);
+
+			boolean found = false;
+			for (MiriamRefGroup refGroup : refGroupsToRemove.keySet()){
+				MIRIAMQualifier qualifier = refGroupsToRemove.get(refGroup);
+				for (MiriamResource miriamResource : refGroup.getMiriamRefs()) {
+
+					if(!isEqual(miriamResource, resourceToDelete)) {
+						continue;
+					}
+					try {
+						mm.remove2(entity, qualifier, refGroup);	// remove the ref group for this resource
+						System.out.println(vcMetaData.printRdfStatements());
+
+						found = true;
+						break;
+					} catch (URNParseFailureException e) {
+						e.printStackTrace(System.out);
+					}
+				}
+				if(found == true) {
+					updateInterface();
+					if(selectedObject instanceof ReactionStep) {
+						((ReactionStep) selectedObject).firePropertyChange("addIdentifier", true, false);
+					}
+					break;
+				}
+			}
+		}
+	}
+
+	private boolean isEqual(MiriamResource aThis, MiriamResource aThat) {
+		if (aThis == aThat) {
+			return true;
+		}
+		if (!(aThis instanceof MiriamResource)) {
+			return false;
+		}
+		if (!(aThat instanceof MiriamResource)) {
+			return false;
+		}
+		MiriamResource athis = (MiriamResource)aThis;
+		MiriamResource athat = (MiriamResource)aThat;
+
+		if (athis.getDataType() != null && athat.getDataType() != null && !athis.getDataType().equals(athat.getDataType())) {
+			return false;
+		}
+		if (!Compare.isEqual(athis.getMiriamURN(), athat.getMiriamURN())) {
+			return false;
+		}
+		if (!Compare.isEqual(athis.getIdentifier(), athat.getIdentifier())) {
+			return false;
+		}
+		return true;
+	}
+
+	@SuppressWarnings("unchecked")
+	private void initializeComboBoxURI() {
+		jComboBoxURI = getJComboBoxURI();
+		Identifiable entity = getIdentifiable(selectedObject);
+		defaultComboBoxModelURI.removeAllElements();
+		List<String> tooltips = new ArrayList<> ();
+		List<DataType> dataTypeList = new ArrayList<>();
+		if(entity == null) {
+			for (DataType dt : vcMetaData.getMiriamManager().getAllDataTypes().values()) {
+				dataTypeList.add(dt);
+			}
+		} else {
+			for (DataType dt : VCMetaDataMiriamManager.getSpecificDataTypes(entity)) {
+				dataTypeList.add(dt);
+			}
+		}
+		Collections.sort(dataTypeList);
+		for(DataType dt : dataTypeList) {
+			tooltips.add(dt.getDescription());
+			defaultComboBoxModelURI.addElement(dt);
+		}
+		((ComboboxToolTipRenderer)getJComboBoxURI().getRenderer()).setTooltips(tooltips);
+	}
+	private void initializeComboBoxQualifier() {
+		//Set<MIRIAMQualifier> MIRIAM_all;
+		//AnnotationQualifiers.MIRIAM_all;
+		List<MIRIAMQualifier> qualifierList = new ArrayList<>();
+		for(MIRIAMQualifier qualifier : AnnotationQualifiers.MIRIAM_all) {
+			qualifierList.add(qualifier);
+		}
+		Collections.sort(qualifierList);
+		for(MIRIAMQualifier qualifier : qualifierList) {
+			defaultComboBoxModelQualifier.addElement(qualifier);
+		}
+	}
+
+	private JButton getJButtonAddRef() {
+		if (jButtonAddRef == null) {
+			jButtonAddRef = new JButton();
+			jButtonAddRef.setText(ACTION_ADD);
+			jButtonAddRef.setToolTipText("Add a new reference with this provider");
+		}
+		return jButtonAddRef;
+	}
+	private JButton getJButtonDeleteRef() {
+		if (jButtonDeleteRef == null) {
+			jButtonDeleteRef = new JButton();
+			jButtonDeleteRef.setText(ACTION_DELETE);
+			jButtonDeleteRef.setToolTipText("Delete the selected cross-reference");
+
+		}
+		return jButtonDeleteRef;
+	}
+	private JButton getJButtonRemoveText() {
+		if (jButtonRemoveText == null) {
+			jButtonRemoveText = new JButton();
+			jButtonRemoveText.setText(ACTION_REMOVE_TEXT);
+			jButtonRemoveText.setToolTipText("Remove the entire text annotation");
+		}
+		return jButtonRemoveText;
+	}
+	/*
+
+Universal (goes in all types of annotations):
+PubMed ID https://www.ncbi.nlm.nih.gov/pubmed
+DOI: https://www.doi.org/
+
+Model
+BioModels Database https://www.ebi.ac.uk/biomodels/
+Reactome: https://reactome.org/
+Grey: NeuronDB: https://senselab.med.yale.edu/neurondb/
+Grey: https://senselab.med.yale.edu/modeldb/
+Grey: CellML Model Repository: https://models.cellml.org/cellml
+
+Species/Molecules/Observables:
+CheBI: https://www.ebi.ac.uk/chebi/
+Kegg Compound: https://www.genome.jp/kegg/compound/
+Uniprot: https://www.uniprot.org/
+Enzyme Nomenclature: http://www.sbcs.qmul.ac.uk/iubmb/enzyme/
+Gene Ontology: http://www.geneontology.org/
+Reactome: https://reactome.org/
+
+Reactions
+Kegg Reaction: https://www.genome.jp/kegg/reaction/
+Kegg Pathway: https://www.genome.jp/kegg/pathway.html
+Reactome: https://reactome.org/
+Grey: BRENDA: https://www.brenda-enzymes.org/
+Grey: BIND  https://www.bindingdb.org/bind/index.jsp
+
+Parameters (all grey for now)
+Grey:BIND https://www.bindingdb.org/bind/index.jsp
+
+Structures
+Grey: BRENDA: https://www.brenda-enzymes.org/
+Grey: Gene Ontology  http://geneontology.org/
+
+
+DataType DataType_PIR 			"PIRSF"
+DataType DataType_DOI 			"DOI"
+DataType DataType_BIOMODELS 	"BioModels Database"
+DataType DataType_Chebi 		"ChEBI"
+DataType DataType_IntAct 		"IntAct"
+DataType DataType_InterPro 		"InterPro"
+DataType DataType_ECCODE 		"Enzyme Nomenclature"
+DataType DataType_ENSEMBLE 		"Ensembl"
+DataType DataType_GO 			"Gene Ontology"
+DataType DataType_KEGGCOMPOUND 	"KEGG Compound"
+DataType DataType_KEGGPATHWAY 	"KEGG Pathway"
+DataType DataType_KEGGREACTION 	"KEGG Reaction"
+DataType DataType_PUBMED 		"PubMed"
+DataType DataType_TAXONOMY 		"Taxonomy"
+DataType DataType_REACTOME 		"Reactome"
+DataType DataType_UNIPROT 		"UniProt"
+DataType DataType_ICD 			"ICD"
+
+
+
+
+*/
+
+
+
+
+
+}
diff --git a/vcell-client/src/main/java/cbit/vcell/client/desktop/biomodel/annotations/BioPortalSearch.java b/vcell-client/src/main/java/cbit/vcell/client/desktop/biomodel/annotations/BioPortalSearch.java
new file mode 100644
index 0000000000..4149b79434
--- /dev/null
+++ b/vcell-client/src/main/java/cbit/vcell/client/desktop/biomodel/annotations/BioPortalSearch.java
@@ -0,0 +1,182 @@
+package cbit.vcell.client.desktop.biomodel.annotations;
+
+import org.xml.sax.Attributes;
+import org.xml.sax.InputSource;
+import org.xml.sax.SAXException;
+import org.xml.sax.helpers.DefaultHandler;
+
+import javax.xml.parsers.ParserConfigurationException;
+import javax.xml.parsers.SAXParser;
+import javax.xml.parsers.SAXParserFactory;
+import java.io.*;
+import java.net.HttpURLConnection;
+import java.net.URISyntaxException;
+import java.net.URL;
+import java.util.ArrayList;
+import java.util.List;
+
+public class BioPortalSearch {
+    // base URL for class search
+    private final String REST_URL = "http://data.bioontology.org/search?q=";
+    private final String API_KEY = "d77db9ae-3fb4-4cc9-b95a-5ea18b1bfda4";
+    private String format;
+    private final List<SearchElement> SearchElements = new ArrayList<>();
+
+    public List<SearchElement> search(String searchTerm) throws IOException, URISyntaxException, ParserConfigurationException, InterruptedException, SAXException {
+        return search(searchTerm, 5000, "", false);
+    }
+
+    public List<SearchElement> search(String searchTerm, int pageSize, String ontologyNicknames, boolean requireExactMatch) throws IOException, SAXException, URISyntaxException, ParserConfigurationException, InterruptedException {
+        //Advanced Search Attributes
+        String includeAttr = "prefLabel,synonym,definition"; //,notation,cui,semanticType,properties
+        format = "xml";
+//        String pageSize = "500"; //max page size
+//        boolean requireExactMatch = false;
+
+        // GET request returns xml string for processing
+//        HttpResponse<String> response = get(REST_URL +
+        String response = get(REST_URL +
+                searchTerm +
+                "&include=" + includeAttr +
+                "&pagesize=" + pageSize +
+                "&display_context=false" +
+                "&display_links=false" +
+                "&ontologies=" + ontologyNicknames +
+                "&require_exact_match=" + requireExactMatch
+        );
+//        System.out.println("Status Code: " + response.statusCode());
+//        System.out.println("Response Body:\n" + response.body());
+        System.out.println();
+
+        SAXParserFactory fact = SAXParserFactory.newInstance();
+        SAXParser saxParser = fact.newSAXParser();
+
+        //List to hold all search results
+
+
+//        boolean collectionEnds = false;
+        DefaultHandler handle = new DefaultHandler() {
+            boolean bTotalCount=false, bPrefLabel=false, bSynonym=false, bDefinition=false, bId=false, collectionEnds=false;
+            String prefLabel, definition, id;
+            final ArrayList<String> synonyms = new ArrayList<>();
+            @Override
+            public void startElement(String uri, String localName, String qName, Attributes attributes) {
+                //System.out.println("Start Element: " + qName);
+                switch (qName) {
+                    case "totalCount":
+                        bTotalCount = true;
+                        break;
+                    case "class":
+                        prefLabel = "";
+                        synonyms.clear();
+                        definition = "";
+                        id = "";
+                        break;
+                    case "prefLabel":
+                        bPrefLabel = true;
+                        break;
+                    case "synonym":
+                        bSynonym = true;
+                        break;
+                    case "definition":
+                        bDefinition = true;
+                        break;
+                    case "id":
+                        bId = true;
+                        break;
+                }
+            }
+
+            @Override
+            public void endElement(String uri, String localName, String qName) {
+                //System.out.println("End Element: " + qName);
+                if (qName.equals("collection")) collectionEnds = true;
+//                if (searchElements.size()-1 < noOfElements) {
+//                    if (qName.equals("class")) {
+                if (qName.equals("class") && !collectionEnds) {
+                    SearchElements.add(new SearchElement(prefLabel, synonyms, definition, id));
+//                    }
+                }
+
+            }
+
+            @Override
+            public void characters(char[] ch, int start, int length) {
+//                if (bTotalCount) {
+//                    noOfElements = Integer.parseInt(new String(ch,start,length));
+//                    System.out.println("totalCount: " + noOfElements +"\n");
+//                    bTotalCount = false;
+//                }
+                if (bPrefLabel) {
+                    prefLabel = new String(ch,start,length);
+                    //System.out.println("prefLabel: " + prefLabel);
+                    bPrefLabel = false;
+                }
+                if (bSynonym) {
+                    String synonym = new String(ch,start,length);
+                    synonyms.add(synonym);
+                    //System.out.println("synonym: " + synonym);
+                    bSynonym = false;
+                }
+                if (bDefinition) {
+                    definition = new String(ch,start,length);
+                    //System.out.println("definition: " + definition);
+                    bDefinition = false;
+                }
+                if (bId) {
+                    id = new String(ch,start,length);
+                    //System.out.println("id: " + id);
+                    bId = false;
+                    //System.out.println();
+                }
+
+            }
+        };
+
+        saxParser.parse(new InputSource(new StringReader(response)), handle);
+        for (SearchElement element: SearchElements) {
+            System.out.println(element.toString());
+        }
+        return SearchElements;
+    }
+
+    //    private HttpResponse<String> get(String urlToGet) throws URISyntaxException, IOException, InterruptedException {
+    private String get(String urlToGet) throws IOException {
+        //build request
+        URL url;
+        HttpURLConnection conn;
+        BufferedReader rd;
+        String line;
+        StringBuilder result = new StringBuilder();
+
+        url = new URL(urlToGet);
+        conn = (HttpURLConnection) url.openConnection();
+        conn.setRequestMethod("GET");
+        conn.setRequestProperty("Authorization", "apikey token=" + API_KEY);
+        conn.setRequestProperty("Accept", "application/" + format);
+        System.out.println("Status Code: " + conn.getResponseCode());
+
+        rd = new BufferedReader(new InputStreamReader(conn.getInputStream()));
+        while ((line = rd.readLine()) != null) {
+            result.append(line);
+        }
+        rd.close();
+
+        return result.toString();
+        /////////////////////////////////////////////////////////////////////////////////////
+//        HttpRequest GET_Request = HttpRequest.newBuilder()
+//                .uri(new URI(urlToGet))
+//                .header("Authorization", "apikey token=" + API_KEY)
+//                .header("Accept", "application/" + format)
+//                .GET()
+//                .build();
+//        System.out.println("GET Request Built: " + GET_Request);
+//
+//        //instantiate client to send request
+//        HttpClient httpClient = HttpClient.newHttpClient();
+//
+//        //use client to send request and store response
+//        return httpClient.send(GET_Request, HttpResponse.BodyHandlers.ofString());
+    }
+}
+
diff --git a/vcell-client/src/main/java/cbit/vcell/client/desktop/biomodel/annotations/SearchElement.java b/vcell-client/src/main/java/cbit/vcell/client/desktop/biomodel/annotations/SearchElement.java
new file mode 100644
index 0000000000..40d54a7d1d
--- /dev/null
+++ b/vcell-client/src/main/java/cbit/vcell/client/desktop/biomodel/annotations/SearchElement.java
@@ -0,0 +1,53 @@
+package cbit.vcell.client.desktop.biomodel.annotations;
+
+
+import java.net.URI;
+import java.util.ArrayList;
+import java.util.List;
+
+public class SearchElement {
+    private final String entityName;
+    private final List<String> synonyms;
+    private final String definition;
+    private final URI dbLink;
+
+    public SearchElement(String entityName, List<String> synonyms, String definition, String dbLink) {
+        this.entityName = entityName;
+        this.synonyms = new ArrayList<>(synonyms);
+        this.definition = definition;
+
+        if (dbLink.contains("http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#")) {
+            String newDbLink = dbLink.replace("http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#",
+                    "https://ncit.nci.nih.gov/ncitbrowser/ConceptReport.jsp?dictionary=NCI_Thesaurus&ns=ncit&code=");
+            this.dbLink = URI.create(newDbLink);
+        } else  {
+            this.dbLink = URI.create(dbLink);
+        }
+
+    }
+
+    public String getEntityName() {
+        return entityName;
+    }
+
+    public List<String> getSynonyms() {
+        return synonyms;
+    }
+
+    public String getDefinition() {
+        return definition;
+    }
+
+    public URI getDbLink() {
+        return dbLink;
+    }
+
+    @Override
+    public String toString() {
+        return  "Name: " + entityName +
+                "\nSynonyms: " + synonyms.toString() +
+                "\nDefinition: " + definition +
+                "\nLink: " + dbLink;
+    }
+}
+
diff --git a/vcell-client/src/main/java/cbit/vcell/graph/gui/ReactionCartoonTool.java b/vcell-client/src/main/java/cbit/vcell/graph/gui/ReactionCartoonTool.java
index d315ad8822..cf7895037f 100644
--- a/vcell-client/src/main/java/cbit/vcell/graph/gui/ReactionCartoonTool.java
+++ b/vcell-client/src/main/java/cbit/vcell/graph/gui/ReactionCartoonTool.java
@@ -33,7 +33,6 @@
 import java.util.ArrayList;
 import java.util.Arrays;
 import java.util.Collection;
-import java.util.Collections;
 import java.util.Comparator;
 import java.util.HashMap;
 import java.util.HashSet;
@@ -46,13 +45,11 @@
 import javax.swing.AbstractAction;
 import javax.swing.ActionMap;
 import javax.swing.DefaultComboBoxModel;
-import javax.swing.DefaultListCellRenderer;
 import javax.swing.InputMap;
 import javax.swing.JComboBox;
 import javax.swing.JComponent;
 import javax.swing.JFileChooser;
 import javax.swing.JLabel;
-import javax.swing.JList;
 import javax.swing.JMenuItem;
 import javax.swing.JOptionPane;
 import javax.swing.JPanel;
@@ -66,7 +63,6 @@
 import org.vcell.model.rbm.MolecularType;
 import org.vcell.model.rbm.MolecularTypePattern;
 import org.vcell.model.rbm.SpeciesPattern;
-import org.vcell.sybil.models.miriam.MIRIAMQualifier;
 import org.vcell.util.BeanUtils;
 import org.vcell.util.Compare;
 import org.vcell.util.Matchable;
@@ -98,16 +94,12 @@
 import cbit.gui.graph.visualstate.VisualState.PaintLayer;
 import cbit.vcell.biomodel.BioModel;
 import cbit.vcell.biomodel.meta.VCMetaData;
-import cbit.vcell.biomodel.meta.MiriamManager.DataType;
-import cbit.vcell.biomodel.meta.VCMetaDataMiriamManager.VCMetaDataDataType;
 import cbit.vcell.client.BioModelWindowManager;
 import cbit.vcell.client.ChildWindowManager;
 import cbit.vcell.client.PopupGenerator;
 import cbit.vcell.client.ChildWindowManager.ChildWindow;
 import cbit.vcell.client.desktop.DocumentWindow;
-import cbit.vcell.client.desktop.biomodel.AnnotationsPanel;
 import cbit.vcell.client.desktop.biomodel.BioModelEditor;
-import cbit.vcell.client.desktop.biomodel.AnnotationsPanel.ComboboxToolTipRenderer;
 import cbit.vcell.client.server.ClientServerManager;
 import cbit.vcell.client.server.UserPreferences;
 import cbit.vcell.desktop.VCellTransferable;
diff --git a/vcell-core/src/main/java/cbit/vcell/biomodel/meta/VCMetaDataMiriamManager.java b/vcell-core/src/main/java/cbit/vcell/biomodel/meta/VCMetaDataMiriamManager.java
index fb3399c4d9..c331af3f2d 100644
--- a/vcell-core/src/main/java/cbit/vcell/biomodel/meta/VCMetaDataMiriamManager.java
+++ b/vcell-core/src/main/java/cbit/vcell/biomodel/meta/VCMetaDataMiriamManager.java
@@ -83,16 +83,15 @@ public static class VCMetaDataDataType implements DataType {
 				"urn:miriam:doi",
 				"The Digital Object Identifier System is for identifying content objects in the digital environment.",
 				"10.1038/nbt1156");
-		public final static DataType DataType_BIOMODELS 	= new VCMetaDataDataType("BioModels Database",
+		public final static DataType DataType_BIOMODELS 	= new VCMetaDataDataType("BIOMODELS",
 				"http://www.ebi.ac.uk/biomodels/",
 				biomodelsDbWebAccessBaseURL,																// ^((BIOMD|MODEL)\d{10})|(BMID\d{12})$
 				"urn:miriam:biomodels.db",
 				"BioModels Database is a data resource that allows biologists to store, search and retrieve published mathematical models of biological interests.",
 				"BIOMD0000000048");
-		public final static DataType DataType_Chebi 		= new VCMetaDataDataType("ChEBI",
+		public final static DataType DataType_Chebi 		= new VCMetaDataDataType("CHEBI",
 				"http://www.ebi.ac.uk/chebi/",
-//				"http://www.ebi.ac.uk/chebi/searchFreeText.do?searchString=",								// old
-				"https://www.ebi.ac.uk/ols/ontologies/chebi/terms?obo_id=",									// ^CHEBI:\d+$
+				"https://www.ebi.ac.uk/ols/ontologies/chebi/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FCHEBI_",									// ^CHEBI:\d+$
 				"urn:miriam:chebi",
 				"Chemical Entities of Biological Interest (ChEBI) is a freely available dictionary of molecular entities focused on 'small' chemical compounds.",
 				"CHEBI:36927");																				// CHEBI:36927
@@ -121,10 +120,9 @@ public static class VCMetaDataDataType implements DataType {
 				"urn:miriam:ensembl",
 				"Ensembl is a joint project between EMBL - EBI and the Sanger Institute to develop a software system which produces and maintains automatic annotation on selected eukaryotic genomes.",
 				"ENSG00000139618");
-		public final static DataType DataType_GO 			= new VCMetaDataDataType("Gene Ontology",
+		public final static DataType DataType_GO 			= new VCMetaDataDataType("GO",
 				"http://www.geneontology.org/",
-				//"http://www.ebi.ac.uk/ego/GTerm?id=",														// old
-				"https://www.ebi.ac.uk/ols/ontologies/go/terms?obo_id=",									// ^GO:\d{7}$
+				"https://www.ebi.ac.uk/ols/ontologies/go/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FGO_",									// ^GO:\d{7}$
 				"urn:miriam:obo.go",
 				"The Gene Ontology project provides a controlled vocabulary to describe gene and gene product attributes in any organism.",
 				"GO:0006915");																				// GO:0006915
@@ -216,7 +214,7 @@ public static class VCMetaDataDataType implements DataType {
 //				"urn:miriam:",
 //				"BindingDB Description",
 //				null);
-		public final static DataType DataType_Mamo 			= new VCMetaDataDataType("Mamo",
+		public final static DataType DataType_Mamo 			= new VCMetaDataDataType("MAMO",
 				"http://bioportal.bioontology.org/ontologies/MAMO/",
 				"http://identifiers.org/mamo/",
 				"urn:miriam:mamo",
@@ -240,7 +238,7 @@ public static class VCMetaDataDataType implements DataType {
 				"urn:miriam:pubchem.substance",
 				"PubChem is the collection of freely accessible chemical information.",
 				"3324");
-		public final static DataType DataType_Doid			= new VCMetaDataDataType("Doid",
+		public final static DataType DataType_Doid			= new VCMetaDataDataType("DOID",
 				"http://disease-ontology.org/",
 				"http://purl.bioontology.org/ontology/DOID/",		// http://disease-ontology.org/term/
 				"urn:miriam:doid",
@@ -258,9 +256,9 @@ public static class VCMetaDataDataType implements DataType {
 				"urn:miriam:3dmet",
 				"3DMET is a database collecting three-dimensional structures of natural metabolites.",
 				"B00006");
-		public final static DataType DataType_CL			= new VCMetaDataDataType("Cell Ontology",
+		public final static DataType DataType_CL			= new VCMetaDataDataType("CL",
 				"http://bioportal.bioontology.org/ontologies/CL/",
-				"http://purl.bioontology.org/ontology/CL/",
+				"https://www.ebi.ac.uk/ols/ontologies/cl/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FCL_",
 				"urn:miriam:cl",
 				"The Cell Ontology is a structured controlled vocabulary for cell types.",
 				"CL:0000145");
@@ -271,14 +269,14 @@ public static class VCMetaDataDataType implements DataType {
 				"CAS (Chemical Abstracts Service) is a comprehensive database of chemical information.",
 				"50-78-2");
 		public final static DataType DataType_BTO			= new VCMetaDataDataType("BTO",
-				"http://bioportal.bioontology.org/ontologies/BTO/",
-				"http://purl.bioontology.org/ontology/BTO/",
+				"https://www.ebi.ac.uk/ols/ontologies/bto/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FBTO_",
+				"https://www.ebi.ac.uk/ols/ontologies/bto/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FBTO_",
 				"urn:miriam:bto",
 				"The Brenda Tissue Ontology is a structured controlled vocabulary used to identify the source of an enzyme cited in the Brenda enzyme database. It comprises terms of tissues, cell lines, cell types and cell cultures.",
 				"BTO:0000028");
-		public final static DataType DataType_Pato			= new VCMetaDataDataType("Pato",
+		public final static DataType DataType_Pato			= new VCMetaDataDataType("PATO",
 				"http://bioportal.bioontology.org/ontologies/PATO/",
-				"http://purl.bioontology.org/ontology/PATO/",
+				"https://www.ebi.ac.uk/ols/ontologies/pato/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FPATO_",
 				"urn:miriam:pato",
 				"PATO is an ontology of phenotypic qualities.",
 				"PATO:0002220");
@@ -300,15 +298,15 @@ public static class VCMetaDataDataType implements DataType {
 				"urn:miriam:fma",
 				"The Foundational Model of Anatomy Ontology (FMA) represents a coherent body of explicit declarative knowledge about human anatomy.",
 				"FMA:74531");
-		public final static DataType DataType_Pr			= new VCMetaDataDataType("Pr",
+		public final static DataType DataType_Pr			= new VCMetaDataDataType("PR",
 				"https://proconsortium.org/",
-				"http://purl.bioontology.org/ontology/PR/",	// or https://proconsortium.org/app/entry/  or  https://www.ebi.ac.uk/ols/ontologies/pr/terms?obo_id=
+				"https://www.ebi.ac.uk/ols/ontologies/pr/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FPR_",	// or https://proconsortium.org/app/entry/  or  https://www.ebi.ac.uk/ols/ontologies/pr/terms?obo_id=
 				"urn:miriam:pr",
 				"The PRotein Ontology (PRO) describes the relationships of proteins and protein evolutionary classes, to delineate the multiple protein forms of a gene locus.",
 				"PR:000007300");
-		public final static DataType DataType_Ncit			= new VCMetaDataDataType("Ncit",
+		public final static DataType DataType_Ncit			= new VCMetaDataDataType("NCIT",
 				"http://www.ontobee.org/ontology/NCIT/",
-				"http://purl.obolibrary.org/obo/NCIT_",
+				"https://www.ebi.ac.uk/ols/ontologies/ncit/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FNCIT_",
 				"urn:miriam:ncit",
 				"NCIt is a reference terminology that includes broad coverage of the cancer domain, including cancer related diseases, findings and abnormalities.",
 				"C67381");
@@ -483,57 +481,58 @@ public Map<String,DataType> getAllDataTypes() {
 	
 	public static List<DataType> getSpecificDataTypes(Identifiable entity) {
 		List<DataType> list = new ArrayList<>();
-		list.add(VCMetaDataDataType.DataType_PUBMED);
-		list.add(VCMetaDataDataType.DataType_DOI);
+		//temp comment ontologies not supported by search feature
+//		list.add(VCMetaDataDataType.DataType_PUBMED);
+//		list.add(VCMetaDataDataType.DataType_DOI);
 		list.add(VCMetaDataDataType.DataType_Ncit);
 		list.add(VCMetaDataDataType.DataType_GO);
 		
 		if(entity instanceof BioModel) {
 			list.add(VCMetaDataDataType.DataType_BIOMODELS);
-			list.add(VCMetaDataDataType.DataType_REACTOME);
-			list.add(VCMetaDataDataType.DataType_NeuronDB);
-			list.add(VCMetaDataDataType.DataType_SenseLab);
+//			list.add(VCMetaDataDataType.DataType_REACTOME);
+//			list.add(VCMetaDataDataType.DataType_NeuronDB);
+//			list.add(VCMetaDataDataType.DataType_SenseLab);
 			list.add(VCMetaDataDataType.DataType_Mamo);
 			list.add(VCMetaDataDataType.DataType_EFO);
 			list.add(VCMetaDataDataType.DataType_Doid);
 
 		} else if(entity instanceof Species || entity instanceof MolecularType || entity instanceof RbmObservable) {
 			list.add(VCMetaDataDataType.DataType_Chebi);
-			list.add(VCMetaDataDataType.DataType_KEGGCOMPOUND);
-			list.add(VCMetaDataDataType.DataType_UNIPROT);
-			list.add(VCMetaDataDataType.DataType_ECCODE);
-			list.add(VCMetaDataDataType.DataType_REACTOME);
+//			list.add(VCMetaDataDataType.DataType_KEGGCOMPOUND);
+//			list.add(VCMetaDataDataType.DataType_UNIPROT);
+//			list.add(VCMetaDataDataType.DataType_ECCODE);
+//			list.add(VCMetaDataDataType.DataType_REACTOME);
 			list.add(VCMetaDataDataType.DataType_CL);
 			list.add(VCMetaDataDataType.DataType_EFO);
 			list.add(VCMetaDataDataType.DataType_BTO);
-			list.add(VCMetaDataDataType.DataType_TAXONOMY);
+//			list.add(VCMetaDataDataType.DataType_TAXONOMY);
 			list.add(VCMetaDataDataType.DataType_Pato);
 			list.add(VCMetaDataDataType.DataType_Pr);
 			
 		} else if(entity instanceof Model.ModelParameter) {
 			list.add(VCMetaDataDataType.DataType_Chebi);
-			list.add(VCMetaDataDataType.DataType_KEGGCOMPOUND);
-			list.add(VCMetaDataDataType.DataType_UNIPROT);
-			list.add(VCMetaDataDataType.DataType_ECCODE);
-			list.add(VCMetaDataDataType.DataType_REACTOME);
+//			list.add(VCMetaDataDataType.DataType_KEGGCOMPOUND);
+//			list.add(VCMetaDataDataType.DataType_UNIPROT);
+//			list.add(VCMetaDataDataType.DataType_ECCODE);
+//			list.add(VCMetaDataDataType.DataType_REACTOME);
 			list.add(VCMetaDataDataType.DataType_CL);
 			list.add(VCMetaDataDataType.DataType_EFO);
 			list.add(VCMetaDataDataType.DataType_BTO);
-			list.add(VCMetaDataDataType.DataType_TAXONOMY);
+//			list.add(VCMetaDataDataType.DataType_TAXONOMY);
 			list.add(VCMetaDataDataType.DataType_Pato);
 			list.add(VCMetaDataDataType.DataType_Pr);
 			list.add(VCMetaDataDataType.DataType_SBO);
 			
 		} else if(entity instanceof ReactionRule || entity instanceof ReactionStep) {
-			list.add(VCMetaDataDataType.DataType_KEGGPATHWAY);
-			list.add(VCMetaDataDataType.DataType_KEGGREACTION);
-			list.add(VCMetaDataDataType.DataType_REACTOME);
-			list.add(VCMetaDataDataType.DataType_Brenda);
-			list.add(VCMetaDataDataType.DataType_IntAct);
+//			list.add(VCMetaDataDataType.DataType_KEGGPATHWAY);
+//			list.add(VCMetaDataDataType.DataType_KEGGREACTION);
+//			list.add(VCMetaDataDataType.DataType_REACTOME);
+//			list.add(VCMetaDataDataType.DataType_Brenda);
+//			list.add(VCMetaDataDataType.DataType_IntAct);
 			list.add(VCMetaDataDataType.DataType_SBO);
 			
 		} else if(entity instanceof Structure) {
-			list.add(VCMetaDataDataType.DataType_Brenda);
+//			list.add(VCMetaDataDataType.DataType_Brenda);
 			list.add(VCMetaDataDataType.DataType_BTO);
 			list.add(VCMetaDataDataType.DataType_EFO);