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Bio::OntologyIO - Parser factory for Ontology formats


    use Bio::OntologyIO;

    my $parser = Bio::OntologyIO->new(-format => "go",
                                      -file=> $file);

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


This is the parser factory for different ontology sources and formats. Conceptually, it is very similar to Bio::SeqIO, but the difference is that the chunk of data returned as an object is an entire ontology.


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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.

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


 Title   : new
 Usage   : my $parser = Bio::OntologyIO->new(-format => 'go', @args);
 Function: Returns a stream of ontologies opened on the specified input
           for the specified format.
 Returns : An ontology parser (an instance of Bio::OntologyIO) initialized
           for the specified format.
 Args    : Named parameters. Common parameters are

              -format    - the format of the input; the following are
                           presently supported:
                  goflat: DAG-Edit Gene Ontology flat files
                  go    : synonymous to goflat
                  soflat: DAG-Edit Sequence Ontology flat files
                  so    : synonymous to soflat
                  simplehierarchy: text format with one term per line
                          and indentation giving the hierarchy
                  evoc  : synonymous to simplehierarchy
                  interpro: InterPro XML
                  interprosax: InterPro XML - this is actually not a
                          Bio::OntologyIO compliant parser; instead it
                          persists terms as they are encountered.
                  obo   : OBO format style from Gene Ontology Consortium
              -file      - the file holding the data
              -fh        - the stream providing the data (-file and -fh are
                          mutually exclusive)
              -ontology_name - the name of the ontology
              -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
              -term_factory - the ontology term factory to use. Provide a
                          value only if you know what you are doing.

           DAG-Edit flat file parsers will usually also accept the
           following parameters.

              -defs_file - the name of the file holding the term
              -files     - an array ref holding the file names (for GO,
                          there will usually be 3 files: component.ontology,
                          function.ontology, process.ontology)

           Other parameters are specific to the parsers.


 Title   : format
 Usage   : $format = $parser->format()
 Function: Get the ontology format
 Returns : ontology format
 Args    : none


 Title   : next_ontology
 Usage   : $ont = $stream->next_ontology()
 Function: Reads the next ontology object from the stream and returns it.
 Returns : a L<Bio::Ontology::OntologyI> compliant object, or undef at the
           end of the stream
 Args    : none


 Title   : term_factory
 Usage   : $obj->term_factory($newval)
 Function: Get/set the ontology term factory to use.

           As a user of this module it is not necessary to call this
           method as there will be default. In order to change the
           default, the easiest way is to instantiate
           L<Bio::Ontology::TermFactory> with the proper -type
           argument. Most if not all parsers will actually use this
           very implementation, so even easier than the aforementioned
           way is to simply call

 Example :
 Returns : value of term_factory (a Bio::Factory::ObjectFactoryI object)
 Args    : on set, new value (a Bio::Factory::ObjectFactoryI object, optional)

Private Methods

  Some of these are actually 'protected' in OO speak, which means you
  may or will want to utilize them in a derived ontology parser, but
  you should not call them from outside.


 Title   : _load_format_module
 Usage   : *INTERNAL OntologyIO stuff*
 Function: Loads up (like use) a module at run time on demand
 Example :
 Returns :
 Args    :