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

CONTRIBUTOR¶

 Hilmar Lapp, hlapp at gmx.net
 Chris Mungall, cjm at fruitfly.org
 Brian Osborne, briano@bioteam.net

new¶

 Title   : new
 Usage   : $parser = Bio::OntologyIO->new(
                             -format => "obo",
                             -file => "gene_ontology.obo");
 Function: Creates a new dagflat parser.
 Returns : A new dagflat parser object, implementing Bio::OntologyIO.
 Args    : -file      => a single ontology flat file holding the
                         terms, descriptions and relationships
           -ontology_name => the name of the ontology; if not specified the
                          parser will assign the name of the ontology as the
                          default-namespace header value from the OBO file.
           -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.

ontology_name¶

 Title   : ontology_name
 Usage   : $obj->ontology_name($newval)
 Function: Get/set the name of the ontology parsed by this module.
 Example :
 Returns : value of ontology_name (a scalar)
 Args    : on set, new value (a scalar or undef, optional)

parse¶

 Title   : parse()
 Usage   : $parser->parse();
 Function: Parses the files set with "new" or with methods
           defs_file and _flat_files.
           Normally you should not need to call this method as it will
           be called automatically upon the first call to
           next_ontology().
 Returns : Bio::Ontology::OntologyEngineI
 Args    :

next_ontology¶

 Title   : next_ontology
 Usage   :
 Function: Get the next available ontology from the parser. This is the
           method prescribed by Bio::OntologyIO.
 Example :
 Returns : An object implementing Bio::Ontology::OntologyI, and nothing if
           there is no more ontology in the input.
 Args    :

close¶

 Title   : close
 Usage   :
 Function: Closes this ontology stream and associated file handles.
           Clients should call this method especially when they write
           ontologies.
           We need to override this here in order to close the file
           handle for the term definitions file.
 Example :
 Returns : none
 Args    : none