Provided by: libbio-perl-perl_1.7.2-2_all bug


       Bio::Ontology::OntologyStore - A repository of ontologies


         #SCENARIO 1

         #make an ontology object manually. via OntologyIO
         my $io = Bio::OntologyIO->new(
                                       #params to fetch Cell Ontology here
         my $cell_ontology = $io->next_ontology;

         #this is a singleton that caches the fact that you've created
         #a 'Cell Ontology' instance...
         my $store = Bio::Ontology::OntologyStore->get_instance();

         #...and it can hand you back a copy of it at any time.
         my $cell_ontology_copy = $store->get_ontology('Cell Ontology');

         #SCENARIO 2

         my $store = Bio::Ontology::OntologyStore->get_instance();
         #this use case allows the construction of an ontology on
         #demand just by supplying the name.
         my $ontology = $store->get_ontology('Sequence Ontology');


       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.


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AUTHOR - Hilmar Lapp

         Hilmar Lapp E<lt>hlapp@gmx.netE<gt>
         Allen Day E<lt>allenday@ucla.eduE<gt>


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

        Title   : new
        Usage   : my $obj = Bio::Ontology::OntologyStore->new();
        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    :

        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

        Example :
        Returns : an instance of this class
        Args    : named parameters, if any (currently, there are no
                  class-specific parameters other than those accepted by

       See Bio::Root::Root.

        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

                  This is a class method, hence you can call it on the class
                  name, without dereferencing an object.

        Example :
        Returns : a 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

       See Bio::Ontology::OntologyI.

        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 Bio::Ontology::OntologyI object(s) to register

       See Bio::Ontology::OntologyI.

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

       See Bio::Ontology::OntologyI.

        Usage   : my $ontology =
        Function: tries to guess which ontology a term identifier comes from,
                  loads it as necessary,
                  and returns it as a Bio::Ontology::Ontology object.
        Example :
        Returns : a Bio::Ontology::Ontology object, or warns and returns undef
        Args    : an ontology term identifier in XXXX:DDDDDDD format.
                  Guessing is based on the XXXX string before the colon.