SimpleGOEngine documentation.

  use Bio::Ontology::SimpleGOEngine;

  my $parser = Bio::Ontology::SimpleGOEngine->new
        ( -defs_file => "/home/czmasek/GO/GO.defs",
          -files     => ["/home/czmasek/GO/component.ontology",
                         "/home/czmasek/GO/function.ontology",
                         "/home/czmasek/GO/process.ontology"] );

  my $engine = $parser->parse();

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

sub _get_id {

    my ( $self, $term ) = @_;
    my $id = $term;

    if(ref($term)) {
        # use TermI standard API
        $self->throw("Object doesn't implement Bio::Ontology::TermI. ".
                     "Bummer.")
            unless $term->isa("Bio::Ontology::TermI");
        $id = $term->identifier();
        # if there is no ID, we need to fake one from ontology name and name
        # in order to achieve uniqueness
        if(!$id) {
            $id = $term->ontology->name() if $term->ontology();
            $id = $id ? $id.'|' : '';
            $id .= $term->name();
        }
    }
    # don't fuss if it looks remotely standard, and we trust GO terms
    return $id
#        if $term->isa("Bio::Ontology::GOterm")||($id =~ /^[A-Z_]{1,8}:\d{1,}$/);
        if $term->isa("Bio::Ontology::GOterm")||($id =~ /^\w+:\w+$/);
    # prefix with something if only numbers
    if($id =~ /^\d+$/) {
        $self->warn(ref($self).": identifier [$id] is only numbers - ".
                    "prefixing with 'GO:'");
        return "GO:" . $id;
    }
    # we shouldn't have gotten here if it's at least a remotely decent ID
    $self->throw(ref($self).": non-standard identifier '$id'\n")
        unless $id =~ /\|/;
    return $id;
} # _get_id

}

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.

  bioperl-l@bioperl.org                  - General discussion
  http://bioperl.org/wiki/Mailing_lists  - About the mailing lists

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:

  http://bugzilla.open-bio.org/

Christian M. Zmasek
Email: czmasek@gnf.org or cmzmasek@yahoo.com
WWW: http://www.genetics.wustl.edu/eddy/people/zmasek/
Address:

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