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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Reporting Bugs
Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web: http://bugzilla.bioperl.org/ Email hlapp at gmx.net Describe contact details here Additional contributors names and emails here The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _

new
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; supported right now are 'go' (synonymous with goflat), 'so' (synonymous with soflat), and 'interpro' -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 former. -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 definitions -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.

next_ontology
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

term_factory
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 $ontio->term_factory->type("Bio::Ontology::MyTerm"). Example : Returns : value of term_factory (a Bio::Factory::ObjectFactoryI object) Args : on set, new value (a Bio::Factory::ObjectFactoryI object, optional) 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.

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