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



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Module Version: 1.007001   Source  




  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";


Parser for OBO flat-file format. 'obo' example:

 format-version: 1.2
 ontology: so/dev/externalDerived
 property_value: owl:versionInfo "$Revision: 80 $" xsd:string
 default-namespace: SO

 id: SO_0000343
 name: match
 def: "A region of sequence, aligned to another sequence." []

 id: SO_0000039
 name: match_part
 def: "A part of a match." []
 is_a: SO_0000343



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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
 Brian Osborne,


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
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