Provided by: libbio-perl-perl_1.7.2-2_all bug


       Bio::OntologyIO::obo - parser for OBO flat-file format


         use Bio::OntologyIO;

         # do not use directly -- use via Bio::OntologyIO
         my $parser = Bio::OntologyIO->new
               ( -format => "obo",
                 -file   =>  "gene_ontology.obo");

         while(my $ont = $parser->next_ontology()) {
         print "read ontology ",$ont->name()," with ",
                      scalar($ont->get_root_terms), " root terms, and ",
                      scalar($ont->get_all_terms),  " total terms, and ",
                      scalar($ont->get_leaf_terms), " leaf terms\n";


       Parser for OBO flat-file format. 'obo' example:

        format-version: 1.2
        ontology: so/dev/externalDerived
        property_value: owl:versionInfo "$Revision: 80 $" xsd:string
        default-namespace: SO

        id: SO_0000343
        name: match
        def: "A region of sequence, aligned to another sequence." []

        id: SO_0000039
        name: match_part
        def: "A part of a match." []
        is_a: SO_0000343

       Specification: <>.


   Mailing Lists
       User feedback is an integral part of the evolution of this and other Bioperl modules. Send
       your comments and suggestions preferably to the Bioperl mailing lists  Your participation
       is much appreciated.
                  - General discussion  - About the mailing lists

       Please direct usage questions or support issues to the mailing list:

       rather than to the module maintainer directly. Many experienced and reponsive experts will
       be able look at the problem and quickly address it. Please include a thorough description
       of the problem with code and data examples if at all possible.

   Reporting Bugs
       Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their
       resolution.  Bug reports can be submitted via the web:


       Sohel Merchant



         Northwestern University
         Center for Genetic Medicine (CGM), dictyBase
         Suite 1206,
         676 St. Clair st
         Chicago IL 60611

        Hilmar Lapp, hlapp at
        Chris Mungall, cjm at
        Brian Osborne,


       The rest of the documentation details each of the object methods. Internal methods are
       usually preceded with a _

        Title   : new
        Usage   : $parser = Bio::OntologyIO->new(
                                    -format => "obo",
                                    -file => "gene_ontology.obo");
        Function: Creates a new dagflat parser.
        Returns : A new dagflat parser object, implementing Bio::OntologyIO.
        Args    : -file      => a single ontology flat file holding the
                                terms, descriptions and relationships
                  -ontology_name => the name of the ontology; if not specified the
                                 parser will assign the name of the ontology as the
                                 default-namespace header value from the OBO file.
                  -engine     => the Bio::Ontology::OntologyEngineI object
                                 to be reused (will be created otherwise); note
                                 that every Bio::Ontology::OntologyI will
                                 qualify as well since that one inherits from the

       See Bio::OntologyIO.

        Title   : ontology_name
        Usage   : $obj->ontology_name($newval)
        Function: Get/set the name of the ontology parsed by this module.
        Example :
        Returns : value of ontology_name (a scalar)
        Args    : on set, new value (a scalar or undef, optional)

        Title   : parse()
        Usage   : $parser->parse();
        Function: Parses the files set with "new" or with methods
                  defs_file and _flat_files.

                  Normally you should not need to call this method as it will
                  be called automatically upon the first call to

        Returns : Bio::Ontology::OntologyEngineI
        Args    :

        Title   : next_ontology
        Usage   :
        Function: Get the next available ontology from the parser. This is the
                  method prescribed by Bio::OntologyIO.
        Example :
        Returns : An object implementing Bio::Ontology::OntologyI, and nothing if
                  there is no more ontology in the input.
        Args    :

        Title   : close
        Usage   :
        Function: Closes this ontology stream and associated file handles.

                  Clients should call this method especially when they write

                  We need to override this here in order to close the file
                  handle for the term definitions file.

        Example :
        Returns : none
        Args    : none