gene_ontology¶ ↑

Parses gene ontology .obo files, links terms through is_a and provides methods to find levels and traverse the tree.

Examples¶ ↑

go = GeneOntology.new.from_file("gene_ontology.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

Copyright¶ ↑

See LICENSE