This document provides instructions for setting up and using Virtuoso Opensource Triplestore (VOS) and related tools. It describes how to install VOS, configure it using a PHP manager script to run multiple instances, load Bio2RDF data into the instances using a loader script, and access the data via SPARQL endpoints. Step-by-step instructions are given for installing VOS, loading DrugBank data as an example, and a live demo is referenced.

1. Making the most of
Virtuoso Opensource
Tutorial @ ICBO 2013

2. Tutorial roadmap

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. 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:
//github.com/micheldumontier/php-lib/blob/master/apps/manager.php

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. ● 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. 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 instances.tab file
○ $instance_file = $base_dir.'/instances.tab';
make sure you have appropriate permissions to create
target directories
Live demo -> Using manager.php

8. Load Bio2RDF data into your VOS
endpoint
● Loading data into a VOS endpoint can be
done using web interface (Conductor) or
ISQL:
○ http://virtuoso.openlinksw.com/dataspace/doc/dav/wiki/Main/VirtBulkRDFLoader
● 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. 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. 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. Using loader.php with Bio2RDF
DrugBank data
● Live demo -> load Drugbank into your newly
installed VOS instance

12. How to install Virtuoso Opensource

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:
○ ./autotogen.sh (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: http://virtuoso.openlinksw.com/dataspace/doc/dav/wiki/Main/VOSMake#Requirements

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: http://virtuoso.openlinksw.com/dataspace/doc/dav/wiki/Main#How Do I...