NAME

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://bio.perl.org/MailList.html             - 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 email or the web:

bioperl-bugs@bio.perl.org
http://bugzilla.bioperl.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

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 L<Bio::Ontology::OntologyEngineI> object
                         to be reused (will be created otherwise); note
                         that every L<Bio::Ontology::OntologyI> will
                         qualify as well since that one inherits from the
                         former.