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<h1><a name="ntView" id="ntView"></a>i2b2 Navigate Terms View</h1>
<p>The Navigate Terms view is designed to display the i2b2 vocabulary concepts that are maintained in the <b>Ontology Management Cell</b> of the <b>i2b2 Hive</b>. These concepts are used in many of the i2b2 views and plug-ins, such as the <i>Query Tool view</i>.
</p>
<p></p>
<h2><a name="ntIntro" id="ntIntro"></a>Introduction</h2>
<p>This section describes the layout and contents of this view.</p>
<p>&nbsp;</p>
<h3><a name="ntLayout" id="ntLayout"></a>Layout of the Navigate Terms View</h3>
<p>The <b>Navigate Terms view</b> displays the terms listed in the metadata table(s). These terms are grouped (categorized) with other similar items. These groupings are displayed in a hierarchal tree that can be expanded to view all the concepts and modifiers in the associated category.
</p>
<p>&nbsp;</p>
<p><img src="images/ntView.png" alt="ntView" width="301" height="172" /></p>
<p>&nbsp;</p>
<p>&nbsp;</p>
<p>As stated above, the <b>Navigate Terms view</b> is hierarchical display of the concepts and modifiers in the metadata table(s). The modifiers will always appear with their associated concept.
</p>
<p>&nbsp;</p>
<p>There are several branches or components of the tree that display.</p>
<p>&nbsp;</p>
<h4><a name="ntTableName" id="ntTableName"></a>Table Name</h4>
<p>The highest level is the <b>name</b> of the metadata table that stores the vocabulary. This level cannot be used when creating a query.
</p>
<p>&nbsp;</p>
<h4><a name="ntContainers" id="ntContainers"></a>Containers</h4>
<p>A <b>container</b> <span style="color:#CCCCCC">(<img src="images/container.png" width="16" height="18" alt="container" />)</span> has other folders, concepts and / or modifiers. It can be expanded and collapsed by clicking on the <i>plus sign</i> <span style="color:#CCCCCC">(<img src="images/plusSign.png" alt="plusSign" width="11" height="11" />) </span>or <i>minus sign</i> <span style="color:#CCCCCC">(<img src="images/minusSign.png" alt="minusSign" width="9" height="9" />)</span> next to it. It can not be dragged to other views.
</p>
<p>&nbsp;</p>
<p>&nbsp;</p>
<h4><a name="ntModContainers" id="ntModContainers"></a>Modifier Containers</h4>
<p>A <b>modifier container</b> <span style="color:#CCCCCC">(<img src="images/modifierContainer.png" width="16" height="18" alt="modifierContainer" />)</span> has other modifier folders and / or modifiers. It can be expanded and collapsed by clicking on the <i>plus sign</i> <span style="color:#CCCCCC">(<img src="images/plusSign.png" alt="plusSign" width="11" height="11" />) </span>or <i>minus sign</i> <span style="color:#CCCCCC">(<img src="images/minusSign.png" alt="minusSign" width="9" height="9" />)</span> next to it. It can not be dragged to other views.
</p>
<p>&nbsp;</p>
<h4><a name="ntFolders" id="ntFolders"></a>Folders</h4>
<p>A <b>folder</b> <span style="color:#CCCCCC">(<img src="images/folder.png" width="16" height="18" alt="folder" />)</span> contains other folders, concepts and / or modifiers. It can be expanded and collapsed by clicking on the <i>plus sign</i> <span style="color:#CCCCCC">(<img src="images/plusSign.png" alt="plusSign" width="11" height="11" />) </span>or <i>minus sign</i> <span style="color:#CCCCCC">(<img src="images/minusSign.png" alt="minusSign" width="9" height="9" />)</span> next to it. It can also be dragged to other views.
</p>
<p>&nbsp;</p>
<h4><a name="ntModFolders" id="ntModFolders"></a>Modifier Folders</h4>
<p>A <b>modifier folder</b> <span style="color:#CCCCCC">(<img src="images/modifierFolder.png" width="16" height="18" alt="modifierFolder" />)</span> contains other modifier folders and / or modifiers. It can be expanded and collapsed by clicking on the <i>plus sign</i> <span style="color:#CCCCCC">(<img src="images/plusSign.png" alt="plusSign" width="11" height="11" />) </span>or <i>minus sign</i> <span style="color:#CCCCCC">(<img src="images/minusSign.png" alt="minusSign" width="9" height="9" />)</span> next to it. It can also be dragged to other views.
</p>
<p>&nbsp;</p>
<h4><a name="ntConcepts" id="ntConcepts"></a>Concepts</h4>
<p>The <b>concept</b> <span style="color:#CCCCCC">(<img src="images/leaf.png" alt="leaf" width="16" height="17" />)</span> is the lowest level of the hierarchy and cannot be expanded further.
</p>
<p>&nbsp;</p>
<h4><a name="ntModifiers" id="ntModifiers"></a>Modifiers</h4>
<p>The <b>modifier</b> <span style="color:#CCCCCC">(<img src="images/modifier.png" alt="modifier" width="16" height="17" />)</span> is the lowest level of the hierarchy and cannot be expanded further.
</p>
<p>&nbsp;</p>
<p>&nbsp;</p>
<p>&nbsp;</p>
<h2><a name="ntNavigation" id="ntNavigation"></a>Navigation</h2>
<p>&nbsp;</p>
<h3><a name="ntExpCollFolder" id="ntExpCollFolder"></a>Expand / Collapse a Folder</h3>
<p>Users can expand or collapse a folder by clicking on the plus sign <span style="color:#CCCCCC">(<img src="images/plusSign.png" alt="plusSign" />)</span> or negative sign <span style="color:#CCCCCC">(<img src="images/minusSign.png" alt="minusSign" />)</span> next to the folder icon.
</p>
<p>&nbsp;</p>
<h4><a name="ntExpFolder" id="ntExpFolder"></a>Expand (Open) a Folder</h4>
<ol>
<li>Click on the <b>plus sign</b> <span style="color:#CCCCCC">(<img src="images/plusSign.png" alt="plusSign" />)</span> next to the folder in the <i>Navigate Terms view.</i>
</li>
<li>The folder will open and all the items in the folder will display.</li>
</ol>
<p>&nbsp;</p>
<h4><a name="ntCollFolder" id="ntCollFolder"></a>Collapse (Close) a Folder</h4>
<ol>
<li>Click on the <b>negative sign</b> <span style="color:#CCCCCC">(<img src="images/minusSign.png" alt="minusSign" />)</span> next to the folder in the <i>Navigate Terms view.</i>
</li>
<li>The folder will close and all the items in the folder will display.</li>
</ol>
<p></p>
<p>&nbsp;</p>
<p>&nbsp;</p>
<h3><a name="ntOptions" id="ntOptions"></a>Options</h3>
<p>Users can define how many concepts to display and whether or not to show hidden terms and/or synonyms. The display options are set in the Navigate Terms Options dialog window, which can be accessed by clicking on the <b>Show Options button</b> <span style="color:#CCCCCC">(<img src="images/options.png" alt="options" />)</span>.
</p>
<p>&nbsp;</p>
<p><img src="images/ntOptions.png" alt="ntOptions" /></p>
<p>&nbsp;</p>
<p>&nbsp;</p>
<p>&nbsp;</p>
<h4><a name="ntDisplayMax" id="ntDisplayMax"></a>Maximum to Display</h4>
<p>The <b>Maximum number of children to display</b> is used when expanding a folder in the <b>Navigate Terms view</b>. Once the maximum number is reached a message will appear informing you that you have reached the maximum and continuing to retrieve all the concepts in the list may affect performance. You will have the option to continue or to cancel the action.
</p>
<p>&nbsp;</p>
<p><img src="images/ntMaxExceedMsg.png" alt="ntMaxExceed" /></p>
<p>&nbsp;</p>
<p>&nbsp;</p>
<p>&nbsp;</p>
<h4><a name="ntShowHidden" id="ntShowHidden"></a>Show Hidden Terms</h4>
<p>In the metadata table, an attribute is set to determine whether or not a term is active, inactive or hidden. If an item is marked as hidden it will not appear in the list of terms. Selecting <b>Show Hidden Terms</b> will display those items marked to be hidden. For easy identification, hidden terms will be <span style="color:#FF0000">red</span> when displayed in the results list.
</p>
<p>&nbsp;</p>
<p>&nbsp;</p>
<h4><a name="ntShowSynonym" id="ntShowSynonym"></a>Show Synonymous Terms</h4>
<p>Some terms may be flagged in the metadata table as a synonym of another term. Selecting <b>Show Synonymous Terms</b> will display both the original term and the synonym in the <i>Find Terms view</i>. For easy identification, synonymous terms will be <span style="color:#000099">blue</span> when displayed in the results list.
</p>
<p>&nbsp;</p>
<p>&nbsp;</p>
<h4><a name="ntEnablePtCounts" id="ntEnablePtCounts"></a>Enable Patient Counts</h4>
<p>The <b>Enable patient counts</b> option will display the total number of patients that have an observation fact entered for that item.
</p>
<p>&nbsp;</p>
<p>&nbsp;</p>
<h4><a name="ntUseShortTooltips" id="ntUseShortTooltips"></a>Use Short Tooltips</h4>
<p>By default, the tooltip that displays when you hover over an item will contain the entire path name and the tooltip that is specific to that item. Enabling the <b>Use short tooltips</b> option will only display the tooltip information; the path will not be included.
</p>
<p>&nbsp;</p>
<p>&nbsp;</p>
<h4><a name="ntShowConceptCd" id="ntShowConceptCd"></a>Show Concept Codes in Tooltips</h4>
<p>In addition to showing the tooltip, this option will also display the concept_cd associated to the item.
</p>
<p>&nbsp;</p>
<p>&nbsp;</p>
<h4><a name="ntDisableModifiers" id="ntDisableModifiers"></a>Disable Modifiers</h4>
<p>The ability to search for modifiers will not be available if the <b>Disable modifiers </b> option is checked off.
</p>
<p>&nbsp;</p>
<p></p>
<p></p>
<p>&nbsp;</p>
<h2><a name="ntUseTerms" id="ntUseTerms"></a>Using Terms</h2>
<p>This section describes how to use a group of concepts, a single concept, and a modifier.</p>
<p>&nbsp;</p>
<h3><a name="ntDragItems" id="ntDragItems"></a>Draggable Items</h3>
<p>Individual as well as groups of concepts can be dragged and dropped (copied) from the Navigate Terms view to other views in the i2b2 Web Client.
</p>
<p>&nbsp;</p>
<ol>
<li>Folder</li>
<p>A <b>folder</b> <span style="color:#CCCCCC">(<img src="images/folder.png" width="16" height="18" alt="folder" />)</span> and all its concepts (children) can be added to other views by dragging the folder name from <b>Navigate Terms</b> to one of the following views.
</p>
<p>&nbsp;</p>
<ul>
<li><b>Query Tool view;</b> drop in the <i>panel</i>.</li>
<li><b>Workplace view;</b> drop in a <i>user</i> or <i>shared folder</i></li>
</ul>
<p>&nbsp;</p>
<p>&nbsp;</p>
<li>Modifier Folder</li>
<p>A <b>modifier folder</b> <span style="color:#CCCCCC">(<img src="images/modifierFolder.png" width="16" height="18" alt="modifierFolder" />)</span> and all its concepts (children) can be added to other views by dragging the modifier folder name from <b>Navigate Terms</b> to one of the following views.
</p>
<p>&nbsp;</p>
<ul>
<li><b>Query Tool view;</b> drop in the <i>panel</i>.</li>
<li><b>Workplace view;</b> drop in a <i>user</i> or <i>shared folder</i></li>
</ul>
<p>&nbsp;</p>
<p>&nbsp;</p>
<li>Concept</li>
<p> A <b>concept</b> <span style="color:#CCCCCC">(<img src="images/leaf.png" alt="leaf" width="16" height="17" />)</span> can be added to other views by dragging the name of the concept from <b>Navigate Terms</b> to one of the following views.
</p>
<p>&nbsp;</p>
<ul>
<li><b>Query Tool view;</b> drop in the <i>panel</i>.</li>
<li><b>Workplace view;</b> drop in a <i>user</i> or <i>shared folder</i></li>
</ul>
<p>&nbsp;</p>
<p>&nbsp;</p>
<li>Modifier</li>
<p> A <b>modifier</b> <span style="color:#CCCCCC">(<img src="images/modifier.png" alt="modifier" width="16" height="17" />)</span> can be added to other views by dragging the name of the modifier from <b>Navigate Terms</b> to one of the following views.
</p>
<p>&nbsp;</p>
<ul>
<li><b>Query Tool view;</b> drop in the <i>panel</i>.</li>
<li><b>Workplace view;</b> drop in a <i>user</i> or <i>shared folder</i></li>
</ul>
</ol>
<p>&nbsp;</p>
<h3><a name="ntAddToQt" id="ntAddToQt"></a>Add to Query Tool View</h3>
<p>A folder, individual concept, or modifier can be added to the query tool view by simply dragging the item from <b>Navigate Terms view</b> and dropping it into one of the panels in the <b>Query Tool view</b>.
</p>
<h4><a name="ntAddFolderToQt" id="ntAddFolderToQt"></a>Add Folder to Query Tool View</h4>
<ol>
<li>Highlight the <b>folder</b> <span style="color:#CCCCCC">(<img src="images/folder.png" width="16" height="18" alt="folder" />)</span> by clicking on the name of the folder.
</li>
<li>While holding the <i>left mouse button</i> down, drag the item over to the <b>Query Tool view</b>.</li>
<li>Drop the item into the <b>panel</b> labeled <b>Group 1</b>.</li>
<p>&nbsp;</p>
<p><img src="images/qtDragFolderMI.png" alt="qtDragFolderMI" width="526" height="362" /></p>
<p>&nbsp;</p>
<p>&nbsp;</p>
<li>The folder will now display in the panel for Group 1.</li>
<p>&nbsp;</p>
<p><img src="images/qtDropFolderMI.png" alt="qtDropFolderMI" width="172" height="232" /></p>
</ol>
<p>&nbsp;</p>
<h4><a name="ntAddConceptToQt" id="ntAddConceptToQt"></a>Add Concept to Query Tool View</h4>
<ol>
<li>Highlight the <b>concept</b> <span style="color:#CCCCCC">(<img src="images/leaf.png" alt="leaf" width="16" height="17" />)</span> by clicking on the name of the concept.
</li>
<li>While holding the <i>left mouse button</i> down, drag the item over to the <b>Query Tool view</b>.</li>
<li>Drop the item into the <b>panel</b> labeled <b>Group 1</b>.</li>
<p>&nbsp;</p>
<p><img src="images/qtDragConceptMI.png" alt="qtDragConceptMI" width="524" height="359" /></p>
<p>&nbsp;</p>
<p>&nbsp;</p>
<li>The concept will now display in the panel for Group 1.</li>
<p>&nbsp;</p>
<p><img src="images/qtDropConceptMI.png" alt="qtDropConceptMI" width="172" height="232" /></p>
</ol>
<p>&nbsp;</p>
<p>&nbsp;</p>
<p>&nbsp;</p>
<h4><a name="ntAddModToQt" id="ntAddModToQt"></a>Add Modifier to Query Tool View</h4>
<ol>
<li>Highlight the <b>modifier</b> <span style="color:#CCCCCC">(<img src="images/modifier.png" alt="modifier" width="16" height="17" />)</span> by clicking on the name of the modifier.
</li>
<li>While holding the <i>left mouse button</i> down, drag the item over to the <b>Query Tool view</b>.</li>
<li>Drop the item into the <b>panel</b> labeled <b>Group 1</b>.</li>
<p>&nbsp;</p>
<p><img src="images/qtDragModPrincDx.png" alt="qtDragModPrincDx" width="524" height="359" /></p>
<p>&nbsp;</p>
<p>&nbsp;</p>
<li>The name of the concept associated to the modifier plus the modifier will now display in the panel for Group 1.
</li>
<p>&nbsp;</p>
<p><img src="images/qtDropModPrincDx.png" alt="qtDropModPrincDx" /></p>
</ol>
<p>&nbsp;</p>
<p>&nbsp;</p>
<p></p>
<p>&nbsp;</p>
<h3><a name="ntAddToWp" id="ntAddToWp"></a>Add to Workplace View</h3>
<p>Information in the workplace is related to the most common concepts and queries that an individual uses and in essence becomes their personal workplace.
</p>
<p>&nbsp;</p>
<p><img src="images/wpView.png" alt="wpView" width="296" height="164" /></p>
<p>&nbsp;</p>
<p>&nbsp;</p>
<h4><a name="ntAddFolderToWp" id="ntAddFolderToWp"></a>Add Folder to Workplace View</h4>
<ol>
<li>Highlight the <b>folder</b> <span style="color:#CCCCCC">(<img src="images/folder.png" width="16" height="18" alt="folder" />)</span> by clicking on the name of the folder.
</li>
<li>While holding the <i>left mouse button</i> down, drag the item over to the <b>Workplace view</b>.</li>
<li>Drop the item into either your workplace folder or the shared folder.</li>
<p>&nbsp;</p>
<p><img src="images/wpDragFolder.png" alt="wpDragFolder" width="303" height="170" /></p>
<p>&nbsp;</p>
<p>&nbsp;</p>
<li>The folder will now display in the <b>Workplace view</b> with the same name.</li>
<p>&nbsp;</p>
<p><img src="images/wpDropFolder.png" alt="wpDropFolder" width="304" height="171" /></p>
</ol>
<p>&nbsp;</p>
<h4><a name="ntAddConceptToWp" id="ntAddConceptToWp"></a>Add Concept to Workplace View</h4>
<ol>
<li>Highlight the <b>concept</b> <span style="color:#CCCCCC">(<img src="images/leaf.png" alt="leaf" />)</span> by clicking on the name of the concept.
</li>
<li>While holding the <i>left mouse button</i> down, drag the item over to the <b>Workplace view</b>.</li>
<li>Drop the item into either your workplace folder or the shared folder.</li>
<p>&nbsp;</p>
<p><img src="images/wpDragConcept.png" alt="wpDragConcept" width="303" height="170" /></p>
<p>&nbsp;</p>
<p>&nbsp;</p>
<li>The concept will now display in the <b>Workplace view</b> with the same name.</li>
<p>&nbsp;</p>
<p><img src="images/wpDropConcept.png" alt="wpDropConcept" width="303" height="170" /></p>
</ol>
<p>&nbsp;</p>
<p>&nbsp;</p>
<p>&nbsp;</p>
<p>&nbsp;</p>
<h4><a name="ftAddModToWp" id="ftAddModToWp"></a>Add Modifier to Workplace View</h4>
<p>&nbsp;</p>
<ol>
<li>Highlight the <b>modifier</b> <span style="color:#CCCCCC">(<img src="images/modifier.png" alt="leaf" />)</span> by clicking on the name of the modifier.
</li>
<li>While holding the <i>left mouse button</i> down, drag the item over to the <b>Workplace view</b>.</li>
<li>Drop the item into either your workplace folder or the shared folder.</li>
<p>&nbsp;</p>
<p><img src="images/wpDragModifier.png" alt="wpDragModifier" width="303" height="170" /></p>
<p>&nbsp;</p>
<p>&nbsp;</p>
<li>The name of the concept associated to modifier and the modifier will now display in the <b>Workplace view</b>.
</li>
<p>&nbsp;</p>
<p><img src="images/wpDropModifier.png" alt="wpDropModifier" width="303" height="170" /></p>
</ol>
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