Updated with viz changes.
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2 changed files with 80 additions and 56 deletions
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@ -66,12 +66,13 @@ h5{
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}
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a {
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text-decoration: underline
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text-decoration: underline;
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color: #2485ae;
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}
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code {
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padding: 0 0 0 20px;
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margin: 10px;
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a:visited {
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text-decoration: underline;
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color: #5e6363;
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}
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/* HEADER ------> */
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@ -127,16 +127,16 @@
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your values for "dbname", "username", and "password". Most of the time,
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the "hostname" will equal "localhost".
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</p>
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<code>
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<pre>
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CREATE DATABASE dbname CHARACTER SET utf8;
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</code>
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</pre>
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<p>
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Grant access to a database user.
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For example:
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</p>
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<code>
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<pre>
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GRANT ALL ON dbname.* TO 'username'@'hostname' IDENTIFIED BY 'password';
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</code>
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</pre>
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<p>
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Keep track of the database name, username, and password for Step IV.
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</p>
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@ -351,15 +351,33 @@
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http://vivo.mydomain.edu/ns#networkId
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</td>
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</tr>
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<tr>
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<td>
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Temporal Graph Visualization is used to compare different organizations/people within
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an organization on different parameters like number of publications, grants. This parameter will be
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used as a default in case a URI is not provided. It will be also used whenever this visualization is to be rendered for top level organization.
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In absence of this parameter a SPARQL query will be fired which will attempt to provide a top level organization.The name of a property
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that can be used to associate an Individual with a user account. When a user logs in with a name that matches the value of this property,
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the user will be authorized to edit that Individual.
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</td>
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</tr>
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<tr class="odd_row">
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<td>
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visualization.topLevelOrg
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</td>
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<td>
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http://vivo-trunk.indiana.edu/individual/topLevelOrgURI
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</td>
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</tr>
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</table>
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<h3 id="deploy">V. Compile and deploy</h3>
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<p>
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At the command line, from the top level of the unpacked distribution
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directory, type:
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</p>
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<code>
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<pre>
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ant all
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</code>
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</pre>
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<p>
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to build VIVO and deploy to Tomcat's webapps
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directory.
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@ -367,7 +385,7 @@
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<h3 id="tomcat_settings">VI. Set Tomcat JVM parameters and security limits</h3>
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<p>
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Currently, VIVO copies the contents of your RDF database into memory
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in order to serve Web requests quickly (the in-memory copy and the
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in order to serve Web requests quickly (the in-memory copy and the
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underlying databaseare kept in synch as edits are performed).
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<p>
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VIVO will
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@ -377,9 +395,9 @@
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<br/>
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For example:
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</p>
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<code>
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<pre>
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export CATALINA_OPTS="-Xms2048m -Xmx1024m -XX:MaxPermSize=128m"
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</code>
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</pre>
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<p>
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This sets Tomcat to allocate an initial heap of 2048 megabytes, a
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maximum heap of 1024 megabytes, and a PermGen space of 128 megs. 1024
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@ -400,13 +418,10 @@
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that your installation can support the required number of threads
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by making the following edits to "/etc/security/limits.conf":
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</p>
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<code>
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apache hard nproc 400
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</code>
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<br>
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<code>
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tomcat6 hard nproc 1500
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</code>
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<pre>
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apache hard nproc 400
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tomcat6 hard nproc 1500
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</pre>
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<h3 id="start_tomcat">VII. Start Tomcat </h3>
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<p>
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Most Tomcat installations can be started by running "startup.sh" or
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@ -427,11 +442,11 @@
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<p>
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After verifying your new password, you will be presented with a menu of
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editing options. Here you can create OWL classes, object properties,
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data properties, and configure the display of data. Currently,
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any classes you wish to make visible on your website must be part of a
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class group, and there a number of visibility and display options
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data properties, and configure the display of data. Currently,
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any classes you wish to make visible on your website must be part of a
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class group, and there a number of visibility and display options
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available for each ontology entity. VIVO comes with a core VIVO
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ontology, but you may also upload other ontologies from an RDF
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ontology, but you may also upload other ontologies from an RDF
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file.
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</p>
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<p>
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@ -442,8 +457,10 @@
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machine. Ensure that the "add RDF" radio button is selected. You
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will also likely want to check "create classgroups automatically."
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</p>
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Clicking the "Index" tab in the navigation bar at the top left of
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the page will show a simple index of the knowledge base.
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<p>
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Clicking the "Index" tab in the navigation bar at the top left of
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the page will show a simple index of the knowledge base.
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</p>
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<p>
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See more
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documentation for configuring VIVO, ingesting data, and manually adding
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@ -483,9 +500,9 @@
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</p>
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<p>
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Using the mod_jk connector allows for communication between Tomcat
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and the primary web server. The
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<a href="http://tomcat.apache.org/connectors-doc/generic_howto/quick.html">Quick
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Start HowTo</a> on the Apache site describes the minimum server configurations
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and the primary web server. The <a href="http://tomcat.apache.org/connectors-doc/generic_howto/quick.html">Quick
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Start HowTo</a>
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on the Apache site describes the minimum server configurations
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for several popular web servers.
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</p>
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<p>
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@ -494,9 +511,9 @@
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requests from Apache via the connector. Look for the
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<connector> directive and add the following properties:
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</p>
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<code>
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<pre>
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connectionTimeout="20000" maxThreads="320" keepAliveTimeout="20000"
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</code>
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</pre>
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<p>
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Note: the value for maxThreads (320) is equal to the value for MaxClients
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in the apache's "httpd.conf" file.
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@ -505,51 +522,57 @@
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Locate the <Host name="localhost"...> directive and update as
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follows:
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</p>
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<!-- ELLY IS WORKING HERE. -->
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<!-- ELLY IS WORKING HERE. -->
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<pre>
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<Host name="localhost" appBase="webapps"
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DeployOnStartup="false"
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unpackWARs="true" autoDeploy="false"
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xmlValidation="false" xmlNamespaceAware="false">
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<Alias>example.com</Alias>
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<Context path=""
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<Host name="localhost" appBase="webapps"
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DeployOnStartup="false"
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unpackWARs="true" autoDeploy="false"
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xmlValidation="false" xmlNamespaceAware="false">
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<Alias>example.com</Alias>
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<Context path=""
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docBase="/usr/local/tomcat/webapps/vivo"
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reloadable="true"
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cookies="true" >
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<Manager pathname="" />
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<Environment type="java.lang.String" override="false"
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cookies="true" >
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<Manager pathname="" />
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<Environment type="java.lang.String" override="false"
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name="path.configuration"
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value="deploy.properties"
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/>
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</Context>
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</pre>
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/>
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</Context>
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...
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</pre>
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<h3 id="pellet">XI. Configure Pellet Reasoner </h3>
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<p>
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VIVO uses the Pellet engine to perform reasoning, which runs in the
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<p><em>Do we need this section still? - elly</em></p>
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<p>VIVO uses the Pellet engine to perform reasoning, which runs in the
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background at startup and also when the knowledge base is edited. VIVO
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continues serving pages while the reasoner continues working; when the
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reasoner finishes, the new inferences appear. Inferred statements are
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cached in a database graph so that they are available immediately when
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VIVO is restarted. By default, Pellet is fed only an incomplete view of
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VIVO is restarted.</p>
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<p>By default, Pellet is fed only an incomplete view of
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your ontology and only certain inferences are materialized. These
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include rdf:type, rdfs:subClassOf,owl:equivalentClass, and
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owl:disjointWith. This mode is typically suitable for ontologies with a
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lot of instance data. If you would like to keep the default mode,
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skip to the next step. To enable "complete" OWL inference (materialize
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all significant entailed statements), open
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"vitro-core/webapp/config/web.xml" and search for PelletReasonerSetup.
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Then change the name of the listener class to
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skip to the next step. </p>
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<p>
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To enable "complete" OWL inference (materialize
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all significant entailed statements), open
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"vitro-core/webapp/config/web.xml" and search for PelletReasonerSetup.
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</p>
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<p>Then change the name of the listener class to
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PelletReasonerSetupComplete. Because "complete" reasoning can be very
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resource intensive, there is also an option to materialize nearly
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all inferences except owl:sameAs and owl:differentFrom. This is enabled
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all inferences except owl:sameAs and owl:differentFrom. </p>
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<p>This is enabled
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by specifying PelletReasonerSetupPseudocomplete. For ontologies with
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large numbers of individuals, this mode can offer enormous performance
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improvements over the "complete" mode. Finally, a class called
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improvements over the "complete" mode. </p>
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<p>Finally, a class called
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PelletReasonerSetupPseudocompleteIgnoreDataproperties is provided to
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improve performance on ontologies with large literals where data
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property entailments are not needed.
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property entailments are not needed.</p>
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</p>
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<h3 id="external_auth">XII. Using an External Authentication System with VIVO </h3>
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<p>
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