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Written by Francois   
The following instructions are a guide about how to install the Bio2RDF software locally and optionally host your own local mirror. Your mirror will be private by default, but if it has a public IP address this can be shared with other users through the distribution of this software, and through the wiki page about Public Bio2RDF SPARQL Endpoints

Basic Install

Install Tomcat and the Bio2RDF webapp


Download Apache Tomcat (Apache License), and install it locally, making sure that it runs on port 80 if you wish to have the smoothest experience. Running on the default 8080 is possible, but the Bio2RDF URL's (http://bio2rdf.org/database:identifier) which assume the default HTTP port 80, will not be directly resolvable. On Windows you can configure Apache Tomcat to run on port 80 by changing a line in the server.xml file (in the conf directory) from 8080 to 80. On Linux/Mac OSX/Unix environments you might want to consider other options such as running Apache HTTPD on port 80, with mod_ajp_proxy redirecting requests to the Apache Tomcat ajp port.

Download the Bio2RDF Tomcat Webapp which contains a single file called ROOT.war, which you should uncompress. Delete the ROOT directory in the Tomcat webapps folder, and the ROOT.war file if it exists. Copy the ROOT.war file to the webapps directory of your Tomcat installation.

Testing the servers

http://localhost/ (gets the Bio2RDF application which responds to HTTP GET requests for rdfised versions of popular biological database web pages). You might want to install the Firefox extension Tabulator (or other RDF browsers) at this point so that you can browse through the RDF data as if it were HTML.

DNS configuration

In order to utilise your local mirror, any clients who will use it should insert the following line in their Hosts file (See the Wikipedia article on Hosts file for more information about how to do this on your operating system). You need to replace 127.0.0.1 with the IP address of your server which is hosting the software. 127.0.0.1 is an appropriate entry for the Hosts file on the actual computer hosting your Bio2RDF software.
127.0.0.1 bio2rdf.org
You now have a functioning installation that you can use to proxy communications between you and the public mirrors. If you wish to host a local mirror, you can continue with the following instructions.

Optional Advanced Install

Install Virtuoso Open source community edition

Virtuoso (GPL)
Install information for compiling Virtuoso can be found at the following addresses:
If your server is windows, executables are provided and can be configured according to the following instructions:

Check that Virtuoso is installed correctly

http://localhost:8890/ (gets the Rdf database application which responds to HTTP GET SPARQL database queries)

Database population

The data files that are required to load the bio2rdf atlas are available at http://bio2rdf.org/download/. You do not require all of these to have a functional atlas, particularly you do not need to download the complete atlas (bio2rdf-atlas-080414.n3.gz) if you are downloading the other databases individually. If you want to be a public mirror we recommend that you do download all of the individual databases that bio2rdf support.
The uncompressed .n3 files can then be loaded into the virtuoso database using the instructions in 'Loading the atlas.'

Configuring the Bio2RDF software to use your local mirror

You will then need to configure your bio2rdf.properties file in order to make your local server use your system for the datasets that you have loaded. It is recommended for this step that you download the source zip and configure the src/war/WEB-INF/src/org/bio2rdf/bio2rdf.properties file following the examples and guidelines at bio2rdf.properties. You will then need to run the following command in the directory containing the build.xml file, in order to generate a new ROOT.war with your properties file:
ant zip-war

Configure Virtuoso for optimal performance after loading

  1. Ensure the vital Bitmap indexes and Full Text indexes http://docs.openlinksw.com/virtuoso/rdfsparqlrulefulltext.html are created (as per this post http://www.openlinksw.com/blog/%7Ekidehen/?id=1298), you can verify this via the Conductor (http://localhost:8890/conductor ) You can use the script from http://quebec.bio2rdf.org/download/virtuoso/create_index.sql for this
  2. If you don't want to use FROM and you don't want to set up a Graph IRI in the INI then follow the instructions in this post http://www.openlinksw.com/weblog/oerling/?id=1358.
  3. Virtuoso RDF tunning guide http://docs.openlinksw.com/virtuoso/rdfperformancetuning.html