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Bio::Ontology::SimpleGOEngine.3pm

NAME

Bio::Ontology::SimpleGOEngine - a Ontology Engine for GO implementing OntologyEngineI

SYNOPSIS

   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" );
 
 

DESCRIPTION

This class is deprecated and instead Bio::Ontology::OBOEngine should be used.

Needs Graph.pm from CPAN.

FEEDBACK

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.

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

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:

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

AUTHOR

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
 
 

APPENDIX

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