use Bio::OntologyIO;

  # do not use directly -- use via Bio::OntologyIO
  my $parser = Bio::OntologyIO->new
	( -format       => "go",
          -defs_file    => "/home/czmasek/GO/GO.defs",
	  -files        => ["/home/czmasek/GO/component.ontology",
	                    "/home/czmasek/GO/function.ontology",
	                    "/home/czmasek/GO/process.ontology"] );

  my $go_ontology = $parser->next_ontology();

  my $IS_A    = Bio::Ontology::RelationshipType->get_instance( "IS_A" );
  my $PART_OF = Bio::Ontology::RelationshipType->get_instance( "PART_OF" );

    my ($self, @args) = @_;
    
    $self->SUPER::_initialize( @args );

    # default term object factory
    $self->term_factory(Bio::Ontology::TermFactory->new(
					  -type => "Bio::Ontology::GOterm"))
	unless $self->term_factory();

} # _initialize

  
1;

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  Genomics Institute of the Novartis Research Foundation
  10675 John Jay Hopkins Drive
  San Diego, CA 92121

 Hilmar Lapp, hlapp at gmx.net

 Title   : new
 Usage   : $parser = Bio::OntologyIO->new(
                             -format => "go",
                             -defs_file => "/path/to/GO.defs",
                             -files => ["/path/to/component.ontology",
                                        "/path/to/function.ontology",
                                        "/path/to/process.ontology"] );
 Function: Creates a new goflat parser.
 Returns : A new goflat parser object, implementing Bio::OntologyIO.
 Args    : -defs_file  => the name of the file holding the term
                          definitions
           -files      => a single ontology flat file holding the
                          term relationships, or an array ref holding
                          the file names (for GO, there will usually be
                          3 files: component.ontology, function.ontology,
                          process.ontology)
           -file       => if there is only a single flat file, it may
                          also be specified via the -file parameter
           -ontology_name => the name of the ontology; if not specified the
                          parser will auto-discover it by using the term
                          that starts with a '$', and converting underscores
                          to spaces
           -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
                          former.