Provided by: libbio-perl-perl_1.7.6-3_all bug


       Bio::OntologyIO::soflat - a parser for the Sequence Ontology flat-file format


         use Bio::OntologyIO;

         # do not use directly -- use via Bio::OntologyIO
         my $parser = Bio::OntologyIO->new
               ( -format       => "so", # or soflat
            -defs_file    => "/home/czmasek/SO/SO.defs",
                 -file         => "/home/czmasek/SO/sofa.ontology" );

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

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


       Needs from CPAN.

       This is essentially a very thin derivation of the dagflat base-parser.


   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:


       Christian M. Zmasek

       Email:  or



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

        Hilmar Lapp, hlapp at


       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 => "soflat",
                                    -files => ["/path/to/sofa.ontology"] );
        Function: Creates a new soflat parser.
        Returns : A new soflat parser object, implementing Bio::OntologyIO.
        Args    : -defs_file  => the name of the file holding the term
                  -files      => a single ontology flat file holding the
                                 term relationships, or an array ref holding
                                 the file names
                  -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

       See Bio::Ontology::OntologyI.