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Bio::Ontology::OntologyStore.3pm

NAME

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

SYNOPSIS

   #----------
   #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' intance...
   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');
 
 

DESCRIPTION

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.

FEEDBACK

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/wiki/Mailing_lists  - About the mailing lists
 
 

Support

Please direct usage questions or support issues to the mailing list:

bioperl-l@bioperl.org

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.

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.open-bio.org/
 
 

AUTHOR - Hilmar Lapp

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

APPENDIX

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

new

  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    :
 
 

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
            Bio::Root::Root.
 
 

See 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 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.
 
 

See Bio::Ontology::OntologyI.

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

See Bio::Ontology::OntologyI.

remove_ontology

  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.

guess_ontology()

  Usage   : my $ontology = 
            Bio::Ontology::OntologyStore->guess_ontology('GO:0000001');
  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.