Bio::Ontology::OntologyStore - A repository of ontologies # see documentation of methods The primary purpose of this module is that of a singleton repository of Bio::Ontology::OntologyI instances from which an Ontology instance can be retrieved by name or identifier. This enables TermI implementations to return their corresponding OntologyI through using this singleton store instead of storing a direct reference to the Ontology object. The latter would almost inevitably lead to memory cycles, and would therefore potentially blow up an application. As a user of Ontology objects and Term objects you almost certainly will not need to deal with this module.

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 list. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/MailList.shtml - About the mailing lists

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 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 $obj = new Bio::Ontology::OntologyStore(); Function: Returns the Bio::Ontology::OntologyStore object. Unlike usual implementations of new, this implementation will try to return a previously instantiated store, if there is any. It is just a synonym for get_instance. In order to avoid ambiguities in your code, you may rather want to call rather get_instance explicitly, which also usually is better associated with this kind of behaviour. Returns : an instance of Bio::Ontology::OntologyStore Args :

get_instance
Title : get_instance Usage : Function: Get an instance of this class for perusal. Since by design this class is meant to be used as a singleton, the implementation will return a previously instantianted store if there is one, and instantiate a new one otherwise. In order to use this class by means of an instance, call this method for added code clarity, not new(). Example : Returns : an instance of this class Args : named parameters, if any (currently, there are no class-specific parameters other than those accepted by L<Bio::Root::Root>.

get_ontology
Title : get_ontology Usage : Function: Get a previously instantiated and registered instance of this class by name or by identifier. One of the main purposes of this class is to enable TermI implementations to return their respective ontology without keeping a strong reference to the respective ontology object. Only objects previously registered objects can be retrieved. This is a class method, hence you can call it on the class name, without dereferencing an object. Example : Returns : a L<Bio::Ontology::OntologyI> implementing object, or undef if the query could not be satisfied Args : Named parameters specifying the query. The following parameters are recognized: -name query the store for an ontology with the given name -id query for an ontology with the given identifier If both are specified, an implicit AND logical operator is assumed.

register_ontology
Title : register_ontology Usage : Function: Registers the given Ontology object for later retrieval by name and identifier. Example : Returns : TRUE on success and FALSE otherwise Args : the L<Bio::Ontology::OntologyI> object(s) to register

remove_ontology
Title : remove_ontology Usage : Function: Remove the specified ontology from the store. Example : Returns : TRUE on success and FALSE otherwise Args : the L<Bio::Ontology::OntologyI> implementing object(s) to be removed from the store