OLS

github.com/dazoakley/ols

OLS provides a simple interface to the EBI's Ontology Lookup Service (www.ebi.ac.uk/ontology-lookup/). It provides an easy lookup of ontology terms and automagically builds up ontology trees using RubyTree (rubytree.rubyforge.org/) as a base library.

PLEASE NOTE: The current version of this gem requires a local install of the OLS database running on MySQL. Please see www.ebi.ac.uk/ontology-lookup/databaseExport.do I will update the code in the future to run off the soap service.

Install

gem install ols

Usage

Include the module in your code:

require 'rubygems'
require 'ols'

Then, to lookup an ontology term:

ont = OLS::OntologyTerm.new('EMAP:3018')

This will create a simple tree object for the EMAP term EMAP:3018

ont.name          # => "EMAP:3018"
ont.term          # => "EMAP:3018"

ont.content       # => "TS18,nose"
ont.term_name     # => "TS18,nose"

Find out about your ontology term

ont.is_root?      # => false
ont.is_leaf?      # => false

NOTE: OntologyTerm's are lazily loaded, so upon initial build the OntologyTerm is just a single node in a tree - no parents, no children. See here (note the “Total Nodes Loaded” count):

ont.to_s          # => "Term: EMAP:3018 Term Name: TS18,nose Root Term?: false Leaf Node?: false  Total Nodes Loaded: 1"

The tree for the term is built up (parents) and down (children) as it is requested:

ont.parentage     # => Array of all parent terms (these will be loaded into the tree now)
ont.children      # => Array of all direct child terms (these will also be loaded into the tree now)
ont.to_s          # => "Term: EMAP:3018 Term Name: TS18,nose Root Term?: false Leaf Node?: false  Total Nodes Loaded: 4"

Alternatively, if you want to force load the tree:

ont.buld_tree     # => Will load both parents and children into the tree

Find out more about your tree:

ont.root                # => Gives you the root node - in this case: "EMAP:0"
ont.all_child_terms     # => An array of all child ontology terms
ont.all_child_name      # => An array of all child ontology term names

For more information on general usage, take a look in the test suite. Also, OLS::OntologyTerm is a child object of Tree::TreeNode (from the rubytree gem - rubytree.rubyforge.org/) and as such inherits all of its methods.

Database Connection Details

The default database connection details are:

{
  :database => 'ols',
  :host     => '127.0.0.1',
  :port     => 3306,
  :user     => 'ols',
  :password => 'ols'
}

If your local copy of the OLS database requires different details, simply do the following once in your code (substituting in your connection details) before any calls to OLS::OntologyTerm are made:

OLS.db_connection_details = {
  :database => 'my_ols',
  :host     => 'ols.example.com',
  :port     => 3307,
  :user     => 'user1',
  :password => 'pass1'
}

Meta

Written by Darren Oakley (daz dot oakley at gmail dot com)

github.com/dazoakley/ols

License

(The MIT License)

Copyright © 2011 Darren Oakley

Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the 'Software'), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions:

The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software.

THE SOFTWARE IS PROVIDED 'AS IS', WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.