NAME

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

SYNOPSIS

  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" );

DESCRIPTION

Needs Graph.pm from CPAN.

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

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

Support

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

bioperl-l@bioperl.org

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:

  https://github.com/bioperl/bioperl-live/issues

AUTHOR

Christian M. Zmasek

Email: czmasek-at-burnham.org or cmzmasek@yahoo.com

WWW: http://monochrome-effect.net/

Address:

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

CONTRIBUTOR

 Hilmar Lapp, hlapp at gmx.net

APPENDIX

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

new

 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
                          definitions
           -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
                          former.

See Bio::Ontology::OntologyI.