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Bio::Ontology::OntologUserrContributed Perl DocBio::Ontology::OntologyStore(3)

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.

perl v5.14.1			  2011-07-22   Bio::Ontology::OntologyStore(3)
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