Erick Antezana > ONTO-PERL > OBO::Parser::OBOParser

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ONTO-PERL/ONTO-PERL-1.41.tar.gz

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work

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

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("apo.obo");

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

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

$ontology->get_relationship_by_id("APO:B9999998_is_a_APO:B0000000")->type() eq 'is_a';

$ontology->get_relationship_by_id("APO:B9999996_part_of_APO:B9999992")->type() eq 'part_of';

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

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

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

$ontology2->get_relationship_by_id("APO:P0000274_is_a_APO:P0000262")->type() eq 'is_a';

$ontology2->get_relationship_by_id("APO:P0000274_part_of_APO:P0000271")->type() eq 'part_of';

DESCRIPTION ^

An OBOParser object parses an OBO-formatted file:

        http://www.geneontology.org/GO.format.obo-1_4.shtml
        
        http://berkeleybop.org/~cjm/obo2owl/obo-syntax.html

AUTHOR ^

Erick Antezana, <erick.antezana -@- gmail.com>

COPYRIGHT AND LICENSE ^

Copyright (c) 2006-2013 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.

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