bel-rdf-jena

This implements an RdfRepository plugin for bel.rb using Apache Jena' TDB Storage. This plugin relies on rdf-jena to interface with Apache Jena as an RDF.rb repository.

Features

  • Plugs in rdf-jena as an Rdf Repository plugin.
  • rdf-jena executable that allows creation of Apache Jena TDB database.

Requirements

  • JRuby 1.7 or 9k series (due to rdf-jena).

Install

First install the gem using:

gem install bel-rdf-jena

Now the plugin is installed and can be used by bel.rb.

Getting started

bel-rdf-jena executable

This gem includes an executable that can create an RDF database (Apache Jena TDB) from one or more RDF files.

You will have the bel-rdf-jena executable available to you (i.e. on your PATH) once you install this gem. Keep in mind that you may have to add $GEM_HOME/bin to your PATH to pick up installed executables.

Now to create an Apache Jena TDB database provide a directory and one or more.

Example:

bel-rdf-jena --dir /opt/data/resources_rdf --file biological-concepts-rdf.ttl

Note: It may take a while to load your RDF data. Apache Jena does a good job of balancing performance and memory allocation. You can increase memory allocation for the process by specifying the -J-Xmx4g (i.e. max heap size of 4 Gb) option in JRUBY_OPTS.

Example:

JRUBY_OPTS="-J-Xmx4g" bel-rdf-jena --dir /opt/data/resources_rdf --file biological-concepts-rdf.ttl

Tip: For the biological-concepts-rdf.ttl file found on the OpenBEL build server try setting this to -J-Xmx4g or -J-Xmx8g if possible.

Plugin to bel.rb for accessing Annotations and Namespaces

bel.rb provides an approach to plugins that is meant to be uncomplicated. The following steps will get you started:

  • Build gem with gem build .gemspec and install with gem install bel-rdf-jena-0.4.0.beta1-java.gem.
  • Now you have this plugin installed and ready for use in bel.rb!
  • With bel.rb installed run the command bel plugins to list available plugins.
$ bel plugins

RDF Repository plugins
----------------------

 Name:        Apache Jena RDF Repository
 Description: A repository of RDF data on Apache Jena using TDB storage.
  • To create the search implementation in Ruby try:
rdf_jena_plugin = BEL::RdfRepository.plugins[:jena]

rdf_jena_plugin.create_repository(:tdb_directory => 'data')
  • Enjoy access to RDF datasets through Apache Jena!

Development

branches

  • master branch

    • Contains stable code. Releases are created from this branch using a tag (e.g. MAJOR.MINOR.PATCH).

  • next branch

    • Contains unstable code. Commits should be merged into master after it stabilizes.

releases

Releases of bel-rdf-jena should follow these steps:

  1. Update the version in the VERSION file.

  2. Add changes for this version to the CHANGELOG file. This file is modelled after http://keepachangelog.com/.

  3. Push the changes for VERSION and CHANGELOG on the master branch.

  4. Ensure the master branch has all of the required changes.

  5. Create a git tag, named after the version, on the master branch. Push this tag to GitHub.

  6. Create the Ruby and Java RubyGem for bel-rdf-jena.

gem build .gemspec

  1. Create a release on GitHub for this version and attach the gem file.

  2. Push gems to RubyGems.

gem push bel-rdf-jena-VERSION-java.gem