Bio::OntologyIO::goflat.3pm

Langue: en

Version: 2010-05-19 (ubuntu - 24/10/10)

Section: 3 (Bibliothèques de fonctions)

NAME

Bio::OntologyIO::goflat - a parser for the Gene Ontology flat-file format

SYNOPSIS

   use Bio::OntologyIO;
 
   # do not use directly -- use via Bio::OntologyIO
   my $parser = Bio::OntologyIO->new
         ( -format       => "go",
      -defs_file    => "/home/czmasek/GO/GO.defs",
           -files        => ["/home/czmasek/GO/component.ontology",
                             "/home/czmasek/GO/function.ontology",
                             "/home/czmasek/GO/process.ontology"] );
 
   my $go_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 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:
   http://bugzilla.open-bio.org/
 
 

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 => "go",
                              -defs_file => "/path/to/GO.defs",
                              -files => ["/path/to/component.ontology",
                                         "/path/to/function.ontology",
                                         "/path/to/process.ontology"] );
  Function: Creates a new goflat parser.
  Returns : A new goflat 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 (for GO, there will usually be
                           3 files: component.ontology, function.ontology,
                           process.ontology)
            -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::OntologyIO.