GeneOntology
Parses gene ontology .obo files, links terms through is_a and provides
methods to find levels and traverse the tree.
Installation
Add this line to your application's Gemfile:
gem 'gene_ontology'And then execute:
$ bundle
Or install it yourself as:
$ gem install gene_ontology
Usage
require 'gene_ontology'
# download from http://purl.obolibrary.org/obo/go.obo
go = GeneOntology.from_file("go.obo")
go.header # => a GeneOntology::Header object
go.id_to_term # => a hash from GO id to the GeneOntology::Term
some_term = go.id_to_term.values.first
# traverse the tree upwards, beginning with the current Term
some_term.each do |term|
term.name =~ /Plasma Membrane/i
end
some_term.level # => how many levels down from the top 3
# molecular_function, biol comp. etc are level 0
Testing
rake test
Note: will download http://purl.obolibrary.org/obo/go.obo to a tempfile unless 'go.obo' is already in package root. Just for testing.
License
MIT License -- see LICENSE for copyright info.