obo_parser¶ ↑

A simple Ruby gem for parsing OBO 1.2 (?4) formatted ontology files. Useful for reporting, comparing, and mapping data to other databases. There is presently no functionality for logical inference across the ontology.

@powerpak updated this to support Ruby >1.9 by simply removing references to ‘ruby-debug`.

Installation¶ ↑

RubyGems only has version 0.3.7, so to install this version you need to clone this repo and then:

gem build obo_parser.gemspec
gem install obo_parser-0.3.8.gem

Use¶ ↑

General ¶ ↑

require 'rubygems'
require 'obo_parser'
foo = parse_obo_file(File.read('my_ontology.obo'))  # => An OboParser instance
first_term = foo.terms.first                        # => An OboParser#Term instance

first_term.id.value                                 # => 'HAO:1234'

d = first_term.def                                  # => An OboParser#Tag instance
d.tag                                               # => 'def'
d.value                                             # => 'Some defintition'
d.xrefs                                             # => ['xref:123', 'xref:456']
d.comment                                           # => 'Some comment'

t = first_term.name                                 # => An OboParser#Tag instance
t.tag                                               # => 'name'
t.value                                             # => 'Some Term name'

o = first_term.other_tags                           # => [OboParser#Tag, ... ] An array of tags that are not specially referenced in an OboParser::Stanza
o.first                                             # => An OboParser#Tag instance

first_typedef = foo.typdefs.first                   # => An OboParser#Typdef instance
first_typdef.id.value                               # => 'Some typedef id'
first_typdef.name.value                             # => 'Some typedef name'

foo.terms.first.tags_named('synonym')               # => [OboParser#Tag, ... ]
foo.terms.first.tags_named('synonym').first.tag     # => 'synonym'
foo.terms.first.tags_named('synonym').first.value   # => 'Some label'

foo.terms.first.relationships                       # => [['relationship', 'FOO:123'], ['other_relationship', 'FOO:456'] ...] An array of [relation, related term id], includes 'is_a', 'disjoint_from' and Typedefs

Convenience methods ¶ ↑

foo.term_hash                                       # => { term (String) => id (String), ... for each [Term] in the file. } !! Assumes names terms are unique, they might not be, in which case you get key collisions.
foo.id_hash                                         # => { id (String) => term (String), ... for each [Term] in the file. }

Utilties¶ ↑

A small set of methods (e.g. comparing OBO ontologies) utilizing the gem are included in /lib/utilities.rb. For example: 1) shared labels across sets of ontologies can be found and returned, 2) ontologies can be dumped into a simple Cytoscape node/edge format; 3) given a set of correspondances between two ontologies various reports can be made.

Documentation¶ ↑

Code documentation is slowly being formalized using Yard.

powerpak/obo_parser