mjy / obo_parser

An OBO file parser.

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.

Installation

gem install obo_parser

Use

General

require 'obo_parser'
o = parse_obo_file(File.read('my_ontology.obo'))  # => An OboParser instance  
first_term = o.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 = o.typdefs.first                   # => An OboParser#Typdef instance 
first_typdef.id.value                               # => 'Some typedef id'
first_typdef.name.value                             # => 'Some typedef name'

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

o.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

o.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. 
o.id_hash                                         # => { id (String) => term (String), ... for each [Term] in the file. } 

See also /test/test_obo_parser.rb

Utilities

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.

Viz

OboParser::Utilities::Viz.mock_coordinate_space(o, size: 100) # => STDOUT tab delimited table with x, y, z, identifier, label 

Contributing

Fork, test, code, test, pull request.

Copyright

Copyright (c) 2010-2017 Matt Yoder. See LICENSE for details.

License

MIT

obo_parser's Issues

Does not parse GO ontology 1.2

Used this gem successfully on the TAIR (arabidopsis.org) GO slim for Arabidopsis thaliana. Worked really well!

Didn't work so well when I try to use it on the full Gene Ontology:

> parse_obo_file(File.read("GO.obo"))
RuntimeError: cytochrome c
from /home/jwoods/obo_parser/lib/tokens.rb:69:in `initialize'
from /home/jwoods/obo_parser/lib/lexer.rb:52:in `new'
from /home/jwoods/obo_parser/lib/lexer.rb:52:in `match'
from /home/jwoods/obo_parser/lib/lexer.rb:38:in `block in read_next_token'
from /home/jwoods/obo_parser/lib/lexer.rb:37:in `each'
from /home/jwoods/obo_parser/lib/lexer.rb:37:in `read_next_token'
from /home/jwoods/obo_parser/lib/lexer.rb:10:in `peek'
from /home/jwoods/obo_parser/lib/parser.rb:32:in `parse_term'
from /home/jwoods/obo_parser/lib/parser.rb:16:in `parse_file'
from /home/jwoods/obo_parser/lib/obo_parser.rb:169:in `parse_obo_file'
from (irb):3
from /home/jwoods/.rvm/gems/ruby-1.9.2-p180/bundler/gems/rails-f064664de72a/railties/lib/rails/commands/console.rb:45:in `start'
from /home/jwoods/.rvm/gems/ruby-1.9.2-p180/bundler/gems/rails-f064664de72a/railties/lib/rails/commands/console.rb:8:in `start'
from /home/jwoods/.rvm/gems/ruby-1.9.2-p180/bundler/gems/rails-f064664de72a/railties/lib/rails/commands.rb:44:in `<top (required)>'
from script/rails:6:in `require'
from script/rails:6:in `<main>'

I do notice that this has a lot of escaped characters in it, which the code says it can't handle. Is there a workaround?

Many thanks for this! And BTW, I'm working on a hacked-together fork that has some graph code.

Feature Request: OBO Enumerator

I just tried parsing the Gene Ontology which is pretty huge, and my MacBook almost had a heart attack. What do you think about adding a method that enables lazy parsing (i.e. only parse one Term at a time, whenever somebody asks for it), either as a separate method or perhaps with an option such as lazy=true? I've been using this super-simple python OBO-parser until now but now that I'm trying to package my software into a Ruby Gem, of course everything should be just Ruby. And I don't like the idea of having multiple obo_parser gem equivalents floating around or that everybody starts their own thing from scratch.
I understand this would make many of the sanity/crossref checks impossible but I only care about very specific parts of the terms anyway and would rather have it parse quickly than safely in this case.

Error parsing XREFS

I'm using your gem to parse Human Phenotype Ontology, exactly this version (https://raw.githubusercontent.com/obophenotype/human-phenotype-ontology/master/hp.obo).

When I try to load it using your example code I obtain a "Runtime Exception: Facebase is seemingly infinite".

Searching into your code, I observe that it happend at line 69 of your "Tokens.rb" file. It seems to be a conceptual error because there, you are parsing XREFS and the line which launch the error using hp.obo file is a "synonym" of term "HP:0000175".

Tell me if you need any other information to replicate the error