GOActive

Gene Ontology ActiveRecord models.

Description

GOActive is a gem/rails plugin containing ActiveRecord models for the Gene Ontology (GO) database and migrations to assist in setting up a local version of GO. GOActive is a part of the BioActive project.

Features/Problems

Currently the GOActive models have only been used in one tiny application. As such, very little work has gone into developing the models beyond defining obvious associations in the database. Nonetheless, the basic associations are numerous so GOActive is a good starting point for new ruby/rails projects that need them.

If you find your work improves these models, please do get in contact with me and pass your development back into the community. Additionally, if you have models for another biological database, see the BioActive project on RubyForge for a nice place to share them.

Installation

GOActive can be installed as a gem or as a rails plugin.

For the gem:

% gem install goactive

If you don’t have the activerecord gem, you’ll be prompted to install dependencies. Then in your scripts:

# load the gem
require 'goactive'
# create a connection to your GO database
ActiveRecord....
# now use the models as you please
dbxref = Dbxref.find :first, :conditions => ["xref_key = ? and xref_dbname = ?", "", "Uniprot"]
dbxref.gene_product.associated_terms.first.name # =>

For the plugin:

The plugin is most easily utilized by first installing the Rails Engines plugin.

Last I checked all you need to do is this (from your rails project of course):

% script/plugin install http://svn.rails-engines.org/plugins/engines

Check their website for details if this doesn’t work. Installing GOActive is similar:

% script/plugin install svn://rubyforge.org/var/svn/bioactive/goactive

Note: The goactive install command requires you have svn installed. Without it you’ll get no response or something like ‘Plugin not found’. On Windows, even if you have a Subversion client like TortoiseSVN, svn is often not available. Use whatever client you have to manually checkout the files from ‘svn://rubyforge…’ into your plugins directory.

Now you have the plugin which will be, like all plugins, automatically discovered by your application. Unless you do some fancy connection-magic, you’ll need to install and run migrations to setup the GO database on your computer.

% script/generate plugin_migration
% rake db:migrate

License

Developer: Simon Chiang, Biomolecular Structure Program
Support: UCHSC School of Medicine Deans Academic Enrichment Fund
Licence: MIT-Style