Christopher Fields > BioPerl-1.6.901 > Bio::OntologyIO::obo



Annotate this POD


New  12
Open  4
View/Report Bugs
Module Version: 1.006901   Source   Latest Release: BioPerl-1.6.924


Bio::OntologyIO::obo - a parser for OBO flat-file format from Gene Ontology Consortium


  use Bio::OntologyIO;

  # do not use directly -- use via Bio::OntologyIO
  my $parser = Bio::OntologyIO->new
        ( -format       => "obo",
          -file        =>  "gene_ontology.obo");

  while(my $ont = $parser->next_ontology()) {
  print "read ontology ",$ont->name()," with ",
               scalar($ont->get_root_terms)," root terms, and ",
               scalar($ont->get_all_terms)," total terms, and ",
               scalar($ont->get_leaf_terms)," leaf terms\n";


Needs from CPAN.


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.                  - General discussion  - About the mailing lists


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

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:


Sohel Merchant



  Northwestern University
  Center for Genetic Medicine (CGM), dictyBase
  Suite 1206,
  676 St. Clair st
  Chicago IL 60611


 Hilmar Lapp, hlapp at
 Chris Mungall,   cjm at


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


 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

See Bio::OntologyIO.


 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)


 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

 Returns : Bio::Ontology::OntologyEngineI
 Args    :


 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    :


 Title   : close
 Usage   :
 Function: Closes this ontology stream and associated file handles.

           Clients should call this method especially when they write

           We need to override this here in order to close the file
           handle for the term definitions file.

 Example :
 Returns : none
 Args    : none
syntax highlighting: