Bio::OntologyIO::soflat(3pm)				User Contributed Perl Documentation			      Bio::OntologyIO::soflat(3pm)

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://redmine.open-bio.org/projects/bioperl/

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.

perl v5.14.2							    2012-03-02					      Bio::OntologyIO::soflat(3pm)