%VOSWARNING%
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---+  Prepopulated Virtuoso hosting of Bio2RDF on EC2 AMI

---++ What is the <nowiki>Bio2RDF</nowiki> Project?

A Bio Informatics knowledgebase available in RDF based Linked Data form. For additional information see:
   * [[http://bio2rdf.org][Project Home Page]]
   * [[http://www.freebase.com/view/user/bio2rdf/public/sparql][SPARQL Endpoints collection]]
   * [[http://bio2rdf.wiki.sourceforge.net/Demo+queries][Sample Queries]]


---++ <nowiki>Bio2RDF</nowiki> Installation on Virtuoso EC2 AMI instance
OpenLink Software provides a backup up of the current <nowiki>Bio2RDF</nowiki> knowledgebase currently exposed at
&lt;<code>[[http://lod.openlinksw.com/sparql][http://lod.openlinksw.com/sparql]]</code>&gt;.
Users can restore a backup of this knowledgebase into a Virtuoso AMI instance in the  
Amazon EC2 cloud thereby obtaining a personal or service-specific rendition of the <nowiki>Bio2RDF</nowiki> Knowledgebase.

---+++ Installation

   1 Start a [[VirtInstallationEC2][Virtuoso EC2 AMI instance]]. Note a Virtuoso Release 5 AMI instance ( ami-ids ami-59628630 or ami-c46084ad ) *must* be used with this backup. A 64-bit large image AMI instance with 8GB of memory, which is the <code>m1.large</code> EC2 instance type, is the minimum recommended for <nowiki>Bio2RDF</nowiki>. 
For best performance, particularly under extensive usage, the 16GB <code>m1.xlarge</code> EC2 instance type is preferred.
%BR%%BR%<img src="%ATTACHURLPATH%/EC2_AWS_Console_M1Large_Instance.png" style="wikiautogen"/>%BR%%BR%
   1 Load the Virtuoso Conductor administration interface of the running EC2 AMI instance with a URL of the form 
<code><nowiki>http://your-ec2-instance-cname/conductor</nowiki></code>.
%BR%%BR%<img src="%ATTACHURLPATH%/EC2_Conductor.png" style="wikiautogen"/>%BR%%BR%
   1 From the Virtuoso Conductor, navigate to the "System Admin" -> "Packages" tab to obtain a list of available 
Virtuoso packages (VADs) to install.
%BR%%BR%<img src="%ATTACHURLPATH%/EC2_VADPackages.png" style="wikiautogen"/>%BR%%BR%
   1 Click the "Install" button to initiate installation of the "EC2 Extensions" VAD package for use in performing backup 
and restore tasks.
%BR%%BR%<img src="%ATTACHURLPATH%/EC2_VADEc2Exts.png" style="wikiautogen"/>%BR%%BR% 
   1 Click the "Proceed" button to install the "EC2 Extensions" VAD package.%BR%%BR%
   1 Go to the URL <code><nowiki>http://your-ec2-instance-cname/ec2exts</nowiki></code> to load the Virtuoso 
Extensions for Amazon EC2 Images login page and log in as the "<code>dba</code>" user.
%BR%%BR%<img src="%ATTACHURLPATH%/EC2_ExtLogin.png" style="wikiautogen"/>%BR%%BR%
   1 From the Virtuoso Extensions for Amazon EC2 Images main page, click the "Restore a Remote Backup" link.
%BR%%BR%<img src="%ATTACHURLPATH%/EC2_MainPage.png" style="wikiautogen"/>%BR%%BR%
   1 On the "Restore a Remote Backup" page, set the follow options &mdash;
<verbatim>
          Protocol:  WebDAV/HTTP
              Host:  s3.amazonaws.com
    Path or Bucket:  bio2rdf-virtuoso-bundle
Backup File Prefix:  bio2rdf-bundle
</verbatim>
<img src="%ATTACHURLPATH%/EC2_RestoreBio2rdf.png" style="wikiautogen"/>
   1 Click the "Restore" button to begin the restoration of the <nowiki>Bio2RDF</nowiki> database from backup.
%BR%%BR%<img src="%ATTACHURLPATH%/EC2_RestoreBio2rdfProgress.png" style="wikiautogen"/>%BR%
.
%BR%
.
%BR%
.
%BR%<img src="%ATTACHURLPATH%/EC2_RestoreBio2rdfProgressDone.png" style="wikiautogen"/>%BR%%BR%
   1 Click on the "Continue" button to begin the re-assembly of the database from the restored backup files. Output 
similar to the following will be displayed when the re-assembly of the database is complete.
%BR%%BR% <img src="%ATTACHURLPATH%/EC2_ReassembleBio2rdf.png" style="wikiautogen"/>%BR%%BR%

Once complete the server will have been restarted automatically with the restored <nowiki>Bio2RDF</nowiki> database and is ready for use.

---+++Usage Examples

You can then access pages such as these on your <nowiki>Bio2RDF</nowiki> server:%BR%%BR%
      *  <code><nowiki>http://your-ec2-instance-cname/interpro:IPR008543</nowiki></code>
%BR%%BR%<img src="%ATTACHURLPATH%/EC2_Bio2rdfIPR008543.png" style="wikiautogen"/>%BR%%BR% 
      *  <code><nowiki>http://your-ec2-instance-cname/geneid:4421783</nowiki></code>
%BR%%BR%<img src="%ATTACHURLPATH%/EC2_Bio2rdf4421783.png" style="wikiautogen"/>%BR%%BR% 
      *  <code><nowiki>http://your-ec2-instance-cname/uniprot:A0A358</nowiki></code>
%BR%%BR%<img src="%ATTACHURLPATH%/EC2_Bio2rdfA0A358.png" style="wikiautogen"/>%BR%%BR% 

---+++<nowiki>Bio2RDF</nowiki> VAD Application Package

For those running a <nowiki>Bio2RDF</nowiki> Virtuoso EC2 AMI instance created before December 18, 2008, 
you will need to update the installed <nowiki>Bio2RDF</nowiki>
VAD Application package to obtain the latest enhancements, by taking the following steps &mdash;

   1 Download the <a href="%ATTACHURLPATH%/bio2rdf_dav.vad" style="wikiautogen">Bio2RDF VAD Application</a> 
(<code><nowiki>bio2rdf_dav.vad</nowiki></code>) package.
   1 Navigate to the "System Admin" -> "Packages" tab of the Virtuoso Conductor.
%BR%%BR%<img src="%ATTACHURLPATH%/EC2_VADInstall.png" style="wikiautogen"/>%BR%%BR%
   1 Scroll down to the "Install Package" section of the tab, use the "Upload Package" option  "browse" button.
%BR%%BR%<img src="%ATTACHURLPATH%/EC2_VADUploadFileBio.png" style="wikiautogen"/>%BR%%BR%
   1 Navigate to the location of the downloaded <code><nowiki>bio2rdf_dav.vad</nowiki></code> file and click the "open" button to select it.
%BR%%BR%<img src="%ATTACHURLPATH%/EC2_VADBio.png" style="wikiautogen"/>%BR%%BR%
   1 Click the "Proceed" button to begin the installation process.
%BR%%BR%<img src="%ATTACHURLPATH%/EC2_VADBioInstall.png" style="wikiautogen"/>%BR%%BR%
   1 Once the VAD installation is complete, the <nowiki>Bio2RDF</nowiki> installation is up-to-date and ready for use.

---+++ Results

   * The <nowiki>Bio2RDF</nowiki> SPARQL endpoint can be accessed on <nowiki>http://your-ec2-instance-cname/sparql</nowiki>
   * The OpenLink [[http://wikis.openlinksw.com/dataspace/owiki/wiki/OATWikiWeb/InteractiveSparqlQueryBuilder][Interactive SPARQL Query Builder]] can be accessed on <nowiki>http://your-ec2-instance-cname/isparql</nowiki>, enabling the visual construction of queries (Graph Patterns).

---++ Related

   * [[VirtSPARQLEndpointProtection][Safeguarding your Virtuoso-hosted SPARQL Endpoint]]
   * [[VirtEBSBackedBYOLAMI][EBS-backed BYOL ("Bring Your Own License") Virtuoso EC2 AMI]]
   * [[VirtTipsAndTricksGuideSPARQLEndpointProtection][SPARQL Endpoint Protection Methods Collection]]
   * [[http://docs.openlinksw.com/virtuoso/][Virtuoso documentation]]
      * [[http://docs.openlinksw.com/virtuoso/rdfsparql.html#rdfsupportedprotocolendpoint][SPARQL Service Endpoint]] 
      * [[http://docs.openlinksw.com/virtuoso/rdfsparql.html#rdfsupportedprotocolendpointuri][Service Endpoint Security]] 
      * [[http://docs.openlinksw.com/virtuoso/rdfsparql.html#sparqwebservicetbl][Managing a SPARQL Web Service Endpoint]] 
      * [[http://docs.openlinksw.com/virtuoso/rdfsparql.html][SPARQL]]
   * [[VirtTipsAndTricksGuide][Virtuoso Tips and Tricks Collection]]
      * [[VirtSPARQLDET][SPARQL Endpoint DET Configuration Guide]]       
      * [[VirtSPARQLSecurityWebID][WebID Protocol & SPARQL Endpoint ACLs Tutorial]]
      * [[VirtOAuthSPARQL][SPARQL OAuth Tutorial]]
      * [[VirtTipsAndTricksGuideSPARQLEndpoints][Securing SPARQL endpoints]]
   * [[http://ods.openlinksw.com/wiki/ODS/OdsSPARQLAuth][SPARUL over SPARQL using the http://cname:port/sparql-auth endpoint]]
   * [[VirtAuthServerUI][Virtuoso Authentication Server UI]]
   * [[VirtSPARQLSSL][Manage a SPARQL-WebID based Endpoint]]
   * [[VirtSetupSSL][Configure Virtuoso instance as an X.509 Certificate Authority and HTTPS listener]]
   * [[http://ods.openlinksw.com/wiki/ODS/ODSSetupSSL][Configure Virtuoso+ODS instance as an X.509 Certificate Authority and HTTPS listener]]  
   * [[http://ods.openlinksw.com/wiki/ODS/VirtODSSecurityWebID][WebID Protocol Support in OpenLink Data Spaces]].
   * Manage ODS Datadspaces Objects WebID Access Control Lists (ACLs):
      * [[http://ods.openlinksw.com/wiki/ODS/ODSBriefcaseWebID][ODS Briefcase WebID based ACL Guide]]
         * [[http://ods.openlinksw.com/wiki/ODS/ODSBriefcaseWebIDPerson][Person Entity WebID based ACL Guide]]
         * [[http://ods.openlinksw.com/wiki/ODS/ODSBriefcaseWebIDGroup][Group Entity WebID based ACL Guide]]
         * [[http://ods.openlinksw.com/wiki/ODS/ODSBriefcaseWebIDPublic][Public WebID based ACL Guide]]      
      * [[http://ods.openlinksw.com/wiki/ODS/ODSFeedManagerWebIDACL][ODS Feed Manager WebID based ACL Guide]]
         * [[http://ods.openlinksw.com/wiki/ODS/ODSFeedManagerWebIDACLPerson][Person Entity Specific ACL]]
         * [[http://ods.openlinksw.com/wiki/ODS/ODSFeedManagerWebIDACLGroup][Group Entity Specific ACL]]
         * [[http://ods.openlinksw.com/wiki/ODS/ODSFeedManagerWebIDACLPublic][Public Specific ACL for anyone with a WebID]]
      * [[http://ods.openlinksw.com/wiki/ODS/ODSCalendarWebIDACL][ODS Calendar WebID based ACL Guide]]
         * [[http://ods.openlinksw.com/wiki/ODS/ODSCalendarWebIDACLPerson][Person Entity Specific ACL]]
         * [[http://ods.openlinksw.com/wiki/ODS/ODSCalendarWebIDACLGroup][Group Entity Specific ACL]]
         * [[http://ods.openlinksw.com/wiki/ODS/ODSCalendarWebIDACLPublic][Public Specific ACL for anyone with a WebID]]
      * [[http://ods.openlinksw.com/wiki/ODS/ODSBookmarksWebIDACL][ODS Bookmark Manager WebID based ACL Guide]]
         * [[http://ods.openlinksw.com/wiki/ODS/ODSBookmarksWebIDACLPerson][Person Entity Specific ACL]]
         * [[http://ods.openlinksw.com/wiki/ODS/ODSBookmarksWebIDACLGroup][Group Entity Specific ACL]]
         * [[http://ods.openlinksw.com/wiki/ODS/ODSBookmarksWebIDACLPublic][Public Specific ACL for anyone with a WebID]]
      * [[http://ods.openlinksw.com/wiki/ODS/ODSAddressBookWebIDACL][ODS Addressbook  WebID based ACL Guide]]
         * [[http://ods.openlinksw.com/wiki/ODS/ODSAddressBookWebIDACLPerson][Person Entity Specific ACL]]
         * [[http://ods.openlinksw.com/wiki/ODS/ODSAddressBookWebIDACLGroup][Group Entity Specific ACL]]
         * [[http://ods.openlinksw.com/wiki/ODS/ODSAddressBookWebIDACLPublic][Public Specific ACL for anyone with a WebID]]
   * [[http://ods.openlinksw.com/wiki/ODS/ODSPkiSetup][Guide for Set up a X.509 certificate issuer and HTTPS listener and generate ODS user certificates.]]
   * [[http://ods.openlinksw.com/wiki/ODS/VirtODSPubSubHub][Setting up PubSubHub in ODS]]
   * [[http://ods.openlinksw.com/wiki/ODS/VirtPubSubHub][PubSubHubBub Demo Client Example]]
   * [[http://ods.openlinksw.com/wiki/ODS/VirtFeedPubSubHub][Feed subscription via PubSubHub protocol Example ]]
   * [[http://ods.openlinksw.com/wiki/ODS/VirtPubSubHubACL][Setting Up PubSubHub to use WebID Protocol or IP based control lists]]
   * [[http://ods.openlinksw.com/wiki/ODS/OdsKeyImport][CA Keys Import using Conductor]]
   * [[http://ods.openlinksw.com/wiki/ODS/ODSGenerateX509Certificate][Generate an X.509 Certificate hosted WebID Guide]]
   * [[http://ods.openlinksw.com/wiki/ODS/ODSGenerateWebIDX509CertOSKeystore][Generate an X.509 Certificate (with a WebID watermark) to be managed by host operating system keystore]]
   * [[http://ods.openlinksw.com/wiki/ODS/ODSGenerateWebIDX509CertBrsKeystore][Generate an X.509 Certificate (with a WebID watermark) to be managed by a browser-based keystore]]
   * [[http://ods.openlinksw.com/wiki/ODS/ODSWebIDIdP][Using Virtuoso's WebID Verification Proxy Service with a WebID-bearing X.509 certificate]]
   * [[http://ods.openlinksw.com/wiki/ODS/ODSWebIDIdpProxy][Using Virtuoso's WebID Identity Provider (IdP) Proxy Service with an X.509 certificate]]
   * [[http://ods.openlinksw.com/wiki/ODS/ODSBriefcaseWebIDShareFile][ODS Briefcase WebID Protocol Share File Guide]]
   * [[http://esw.w3.org/topic/foaf+ssl][WebID Protocol Specification]]
   * [[https://foaf.me/simpleLogin.php][Test WebID Protocol Certificate page]]
   * [[http://test.foafssl.org/cert/][WebID Protocol Certificate Generation page]]