NAME

OBO::Parser::OBOParser - An OBO (Open Biomedical Ontologies) file parser.

SYNOPSIS

use OBO::Parser::OBOParser;

use strict;

my $my_parser = OBO::Parser::OBOParser->new;

my $ontology = $my_parser->work("cco.obo");

$ontology->has_term($ontology->get_term_by_id("CCO:B9999993"));

$ontology->has_term($ontology->get_term_by_name("small molecule"));

$ontology->get_relationship_by_id("CCO:B9999998_is_a_CCO:B0000000")->type() eq "is_a";

$ontology->get_relationship_by_id("CCO:B9999996_part_of_CCO:B9999992")->type() eq "part_of";

my $ontology2 = $my_parser->work("cco.obo");

$ontology2->has_term($ontology2->get_term_by_id("CCO:B9999993"));

$ontology2->has_term($ontology2->get_term_by_name("cell cycle"));

$ontology2->get_relationship_by_id("CCO:P0000274_is_a_CCO:P0000262")->type() eq "is_a";

$ontology2->get_relationship_by_id("CCO:P0000274_part_of_CCO:P0000271")->type() eq "part_of";

DESCRIPTION

An OBOParser object works on parsing an OBO file.

AUTHOR

Erick Antezana, <erant@psb.ugent.be>

COPYRIGHT AND LICENSE

Copyright (C) 2006, 2007, 2008 by Erick Antezana

This library is free software; you can redistribute it and/or modify it under the same terms as Perl itself, either Perl version 5.8.7 or, at your option, any later version of Perl 5 you may have available.

work

  Usage    - $OBOParser->work($obo_file_path)
  Returns  - the parsed OBO ontology
  Args     - the OBO file to be parsed
  Function - parses an OBO file