Bio2RDF - Make the most of Virtuoso Open Source


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Learn how to deploy Bio2RDF data in a triple store and SPARQL endpoint using Virtuoso Open Source

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Bio2RDF - Make the most of Virtuoso Open Source

  1. 1. Making the most of Virtuoso Opensource Tutorial @ ICBO 2013
  2. 2. Tutorial roadmap
  3. 3. Triplestores are Database Management System for data modeled in RDF ● Optimized for triples, queryable via the SPARQL query language ● There are three types of TripleStores: ○ Native Persistent storage systems with their own implementation of databases. Eg: Virtuoso ○ In Memory RDF Graph is stored as triples in RAM Eg: Jena ○ Non-native non-memory: Persistent storage systems setup to run on third party DBMS Eg. Jena SDB
  4. 4. Managing a VOS installation for Bio2RDF ● Each Bio2RDF dataset is loaded into a Virtuoso Triplestore and available at its own SPARQL endpoint ● We have developed a PHP manager script for creating and configuring Virtuoso installations that is publicly available at: https: //
  5. 5. ● Allows you to create, start, stop and change memory requirements of multiple VOS instances ○ manager.php is available for download here ● Requires: a tab-delimited file listing the desired instance names and the HTTP/ISQL ports they use Use manager.php to configure multiple VOS instances
  6. 6. ● Script options ○ create : creates a virtuoso instance binary for the specified instance name and starts it ○ start : stops, then starts the corresponding instance of VOS ○ stop : stops the specified instance ○ refresh : creates a fresh copy of the instance's virtuoso.ini file with default values ○ apacheconfig : create an Apache VirtualHost file ○ GB of memory to use : specifies the amount of RAM that an instance can use in GB manager.php cli options
  7. 7. Set up manager.php ● Set the location of local virtuoso installation ○ $virtuoso_dir = '/usr/local/virtuoso-opensource'; ● Set the location of your base directory ○ $base_dir = '/media/320/bio2rdf/manager'; ● Set the sub-directory where the virtuoso instances will live ○ $instance_dir = $base_dir.'/virtuoso'; ● Set the location of the file ○ $instance_file = $base_dir.'/'; make sure you have appropriate permissions to create target directories Live demo -> Using manager.php
  8. 8. Load Bio2RDF data into your VOS endpoint ● Loading data into a VOS endpoint can be done using web interface (Conductor) or ISQL: ○ ● You can also use the Bio2RDF loader script to load RDF into an endpoint ○ uses a tab-delimited instances file to specify VOS instance to load into ○ can load single files or recursively load files inside a given directory ○ will record loading errors/incorrectly formatted RDF ○ will re-try a certain number of times to reload data on error
  9. 9. loader.php cli options ● Script options ○ file: file to load ○ dir: directory of files to load ○ graph: name of graph to load into ○ instance: instance name from tab-delimited ○ port: ISQL port of VOS instance ○ user: username for VOS instance (default: dba) ○ pass: password for VOS instance (default: dba)
  10. 10. Using loader.php ● Script options cont'd: ○ threads: number of threads to use when loading ○ updatefacet: update VOS faceted browser (true|false) ○ deletegraph: delete graph before loading (true|false) ○ deleteonly: delete graph without loading (true|false) ○ setns: set namespaces for faceted browser ○ setpassword: set password for VOS conductor ○ format: format of RDF being loaded (default: N3) ○ ignoreerror: ignore RDF format errors (true|false)
  11. 11. Using loader.php with Bio2RDF DrugBank data ● Live demo -> load Drugbank into your newly installed VOS instance
  12. 12. How to install Virtuoso Opensource
  13. 13. 1. Download VOS 6.1.6 binary from here available via github: https://github. com/openlink/virtuoso-opensource 2. Verify that you have installed these packages 3. Uncompress the VOS binary, cd into that directory and run: ○ ./ (to prepare for building) ○ Set the appropriate compiler flags ○ ./configure ( > 20 minutes) 4. Install VOS by running: ○ sudo make install ■ install location: /usr/local/virtuoso-opensource How to build OpenLink Virtuoso OS: Ubuntu Reference:
  14. 14. VOS Post-installation setup 1. Go to your installation directory and copy ○ var/lib/virtuoso/db/virtuoso.ini to bin/virtuoso.ini 2. Allow virtuoso to read other (or all) directories in your filesystem ○ Edit virtuoso.ini and add '/' at the end of DirsAllowed ■ see example here 3. Start your virtuoso instance by running: ○ sudo ./virtuoso-t -f & (run from /usr/local/virtuoso-opensource/bin) ○ visit http://localhost:8890/conductor and login with default credentials: user:dba, pass:dba 4. Install Faceted Browser ○ Go to System Admin -> Packages, select the fct package and click on Install/Upgrade -> proceed ○ Verify that http://localhost:8890/fct responds Reference: Do I...