Minor editorial changes applied to the docs.
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display and navigation, plus improvements to address scalability. The
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display and navigation, plus improvements to address scalability. The
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release also features two new visualization options: temporal graphing
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release also features two new visualization options: temporal graphing
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for organizations, and personal visualizations extended to cover grants
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for organizations, and personal visualizations extended to cover grants
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as well as publications. The VIVO Harvester library has also been
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as well as publications. The VIVO Harvester library has also been
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significantly improved and expanded in scope for its 1.0 release
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significantly improved and expanded in scope for its 1.0 release
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through the VIVO SourceForge project at <a href="http://sourceforge.net/projects/vivo">http://sourceforge.net/projects/vivo</a>.
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through the VIVO SourceForge project at <a href="http://sourceforge.net/projects/vivo">http://sourceforge.net/projects/vivo</a>.
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</p>
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</p>
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@ -77,16 +77,16 @@
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<h4>Ontology</h4>
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<h4>Ontology</h4>
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<p>
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<p>
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VIVO 1.2 includes a new ontology module representing research
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VIVO 1.2 includes a new ontology module representing research
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resources including biological specimens, human studies, instruments,
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resources including biological specimens, human studies, instruments,
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organisms, protocols, reagents, and research opportunities. This module
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organisms, protocols, reagents, and research opportunities. This module
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is aligned with the top-level ontology classes and properties from the
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is aligned with the top-level ontology classes and properties from the
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NIH-funded <a href="https://www.eagle-i.org/home/">eagle-i Project</a>.
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NIH-funded <a href="https://www.eagle-i.org/home/">eagle-i Project</a>.
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</p>
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</p>
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<h3>Associated VIVO releases</h3>
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<h3>Associated VIVO releases</h3>
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<h4>VIVO Harvester</h4>
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<h4>VIVO Harvester</h4>
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<p>
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<p>
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The Harvester development team is releasing version 1.0 of the VIVO
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The Harvester development team is releasing version 1.0 of the VIVO
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Harvester library, an extensible data ingest and updating framework
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Harvester library, an extensible data ingest and updating framework
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with sample configurations for loading PubMed publication, grants, and
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with sample configurations for loading PubMed publication, grants, and
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human resources data. The Harvester is available at <a href="http://sourceforge.net/projects/vivo">http://sourceforge.net/projects/vivo</a>.
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human resources data. The Harvester is available at <a href="http://sourceforge.net/projects/vivo">http://sourceforge.net/projects/vivo</a>.
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</p>
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</p>
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@ -567,13 +567,19 @@
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The temporal graph visualization can require extensive machine resources.
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The temporal graph visualization can require extensive machine resources.
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This can have a particularly noticable impact on memory usage if
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This can have a particularly noticable impact on memory usage if
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<ul>
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<ul>
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<li> VIVO is configured to use Jena SDB, </li>
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<li>
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<li> The organization tree is deep, </li>
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VIVO is configured to use Jena SDB,
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<li> The number of grants and publications is large. </li>
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</li>
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<li>
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The organization tree is deep,
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</li>
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<li>
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The number of grants and publications is large.
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</li>
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</ul>
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</ul>
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The VIVO developers are working to make this visualization more efficient.
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The VIVO developers are working to make this visualization more efficient.
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In the meantime, VIVO release 1.2 guards against this impact by disabling
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In the meantime, VIVO release 1.2 guards against this impact by disabling
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temporal graph visualization unless the "visualization.temporal" flag is
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temporal graph visualization unless the "visualization.temporal" flag is
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set to "enabled".
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set to "enabled".
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</td>
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</td>
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</tr>
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</tr>
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@ -782,12 +788,13 @@
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<h3 id="pellet">XII. Configure Pellet Reasoner </h3>
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<h3 id="pellet">XII. Configure Pellet Reasoner </h3>
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<p>
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<p>
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This optional configuration step is only applicable to VIVO installations
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This optional configuration step is only applicable to VIVO installations
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running in RDB mode (See section <a href="triple_store">Choose Triple Store</a> for details).
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running in RDB mode (See section <a href="triple_store">Choose Triple Store</a>
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VIVO uses the Pellet engine to perform reasoning, which runs in the
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for details).
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background at startup and also when the knowledge base is edited. VIVO
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VIVO uses the Pellet engine to perform reasoning, which runs in the
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continues serving pages while the reasoner continues working; when the
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background at startup and also when the knowledge base is edited. VIVO
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reasoner finishes, the new inferences appear. Inferred statements are
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continues serving pages while the reasoner continues working; when the
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cached in a database graph so that they are available immediately when
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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.
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VIVO is restarted.
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</p>
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</p>
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<p>
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<p>
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@ -863,17 +870,21 @@
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<li>
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<li>
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<h5>The name of the HTTP header that will hold the external user's
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<h5>The name of the HTTP header that will hold the external user's
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network ID.</h5>
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network ID.</h5>
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When a user completes the authentication process, the Apache server
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<p>
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will put the user's network ID into one of the headers of the HTTP
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When a user completes the authentication process, the Apache server
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request. The instructions from your institution should tell you which
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will put the user's network ID into one of the headers of the HTTP
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header is used for this purpose.
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request. The instructions from your institution should tell you which
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header is used for this purpose.
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</p>
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<p>
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<p>
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You need to tell VIVO the name of that HTTP header. Insert a
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You need to tell VIVO the name of that HTTP header. Insert a
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line like this in the deploy.properties file:
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line like this in the deploy.properties file:
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</p>
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</p>
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<pre>externalAuth.netIdHeaderName = [the header name]</pre>
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<pre>externalAuth.netIdHeaderName = [the header name]</pre>
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<p>For example:</p>
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<p>
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<pre>externalAuth.netIdHeaderName = remote_userID</pre>
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For example:
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</p>
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<pre>externalAuth.netIdHeaderName = remote_userID</pre>
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</li>
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</li>
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<li>
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<li>
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<h5>The text for the Login button.</h5>
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<h5>The text for the Login button.</h5>
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@ -885,13 +896,17 @@
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externalAuth.buttonText = [the text for your login button] For example:
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externalAuth.buttonText = [the text for your login button] For example:
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</p>
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</p>
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<pre>externalAuth.buttonText = Log in using BearCat Shibboleth</pre>
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<pre>externalAuth.buttonText = Log in using BearCat Shibboleth</pre>
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The VIVO login form will display a button labelled "Log in using
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<p>
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BearCat Shibboleth".
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The VIVO login form will display a button labelled "Log in using
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BearCat Shibboleth".
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</p>
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</li>
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</li>
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<li>
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<li>
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<h5>Associating a User with a profile page</h5>
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<h5>Associating a User with a profile page.</h5>
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If VIVO has an account for the user, the user will be given the
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<p>
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privileges assigned to that account.
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If VIVO has an account for the user, the user will be given the
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privileges assigned to that account.
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</p>
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<p>
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<p>
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In addition, VIVO will try to associate the user with a profile
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In addition, VIVO will try to associate the user with a profile
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page, so the user may edit his own profile data. VIVO will search the
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page, so the user may edit his own profile data. VIVO will search the
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Insert a line like this in the deploy.properties file:
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Insert a line like this in the deploy.properties file:
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</p>
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</p>
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<pre>selfEditing.idMatchingProperty = [the URI of the property]</pre>
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<pre>selfEditing.idMatchingProperty = [the URI of the property]</pre>
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For example:<pre>selfEditing.idMatchingProperty = http://vivo.mydomain.edu/ns#networkId</pre>
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<p>
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For example:
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</p>
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<pre>selfEditing.idMatchingProperty = http://vivo.mydomain.edu/ns#networkId</pre>
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</li>
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</li>
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</ul>
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</ul>
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<h3 id="installation_check">XIV. Was the installation successful? </h3>
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<h3 id="installation_check">XIV. Was the installation successful? </h3>
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Enter the name "test individual" under the field "Individual
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Enter the name "test individual" under the field "Individual
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Name," scroll to the bottom, and click "Create New Record." You will be
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Name," scroll to the bottom, and click "Create New Record." You will be
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taken to the "Individual Control Panel." Make note of the value of the
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taken to the "Individual Control Panel." Make note of the value of the
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field "URI" it will be used in the next step.
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field "URI" - it will be used in the next step.
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</li>
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</li>
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<li>
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<li>
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Open a new web browser or browser tab to the page <a href="http://marbles.sourceforge.net/">http://marbles.sourceforge.net/</a>.
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Open a new web browser or browser tab to the page <a href="http://marbles.sourceforge.net/">http://marbles.sourceforge.net/</a>.
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@ -117,7 +117,7 @@
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<a href="#upgrade_process">The Upgrade Process</a>
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<a href="#upgrade_process">The Upgrade Process</a>
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</li>
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</li>
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<li>
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<li>
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<a href="#ontology">Ontology Upgrade</a>
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<a href="#ontology">Ontology Changes</a>
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<ol class="roman2">
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<ol class="roman2">
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<li>
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<li>
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<a href="#verify_ontology_upgrade">Verify Ontology upgrade
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<a href="#verify_ontology_upgrade">Verify Ontology upgrade
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</ol>
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</ol>
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</li>
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</li>
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<li>
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<li>
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<a href="#theme">Theme Modifications</a>
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<a href="#theme">Theme Changes</a>
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</li>
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</li>
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<li>
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<li>
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<a href="#setup_sdb">Set Up SDB Store in the Background (Optional)</a>
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<a href="#setup_sdb">Set Up SDB Store in the Background (Optional)</a>
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@ -621,7 +621,7 @@
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is included in the built-in theme. This file serves only as an example,
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is included in the built-in theme. This file serves only as an example,
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and you must replace the tracking code shown with your institution's own
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and you must replace the tracking code shown with your institution's own
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tracking code. For additional information about the GATC for the NIH-funded
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tracking code. For additional information about the GATC for the NIH-funded
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VIVO implementation sites and a copy your institution's tracking code, see
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VIVO implementation sites and a copy of your institution's tracking code, see
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the <a href="https://confluence.cornell.edu/display/ennsrd/Google+Analytics+for+UI">VIVO Google Analytics wiki page</a>.
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the <a href="https://confluence.cornell.edu/display/ennsrd/Google+Analytics+for+UI">VIVO Google Analytics wiki page</a>.
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</li>
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</li>
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<li>
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<li>
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