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Bio::Ontology::DocumenUseriContributed Perl Bio::Ontology::DocumentRegistry(3)

NAME
       Bio::Ontology::DocumentRegistry - Keep track of where to	find
       ontologies.  Allows lookups by name.

SYNOPSIS
	 my $registry =	Bio::Ontology::DocumentRegistry->get_instance();
	 my($ont,$def,$fmt) = $registry->documents('Sequence Ontology');

	 my $io	= Bio::OntologyIO->new(-url => $ont,
				       -defs_url => $def,
				       -format => $fmt);
	 my $so	= $io->next_ontology();
	 #...

DESCRIPTION
       Do not use this directly, use Bio::Ontology::OntologyStore instead.
       Bio::Ontology::OntologyStore uses Bio::Ontology::DocumentRegistry to
       load and	cache ontologies as object graphs, you can just	ask it for
       what you	want by	name.  See Bio::Ontology::OntologyStore	for details.

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:

	 https://github.com/bioperl/bioperl-live/issues

AUTHOR - Allen Day
       Email allenday@ucla.edu

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

   get_instance
	Title	: get_instance
	Usage	: my $singleton	= Bio::Ontology::DocumentRegistry->get_instance();
	Function: constructor
	Returns	: The Bio::Ontology::DocumentRegistry singleton.
	Args	: None
	Usage

   documents
	Title	: documents
	Usage	: my($ontology_url, $definitions_url, $format) = $obj->documents('Sequence Ontology');
	Function: Maps an ontology name	to a list of (local or)	remote URIs where the
		  files	can be located.
	Returns	: A 3-item list:
		  (1) URI for the ontology file
		  (2) URI for the ontology definitions file
		  (3) format of	the files (dagedit, obo, etc)
	Args	: Name of an ontology, e.g. 'Sequence Ontology', or 'Cellular Component
		  (Gene	Ontology)'

perl v5.24.1			  2017-07-08Bio::Ontology::DocumentRegistry(3)

NAME | SYNOPSIS | DESCRIPTION | FEEDBACK | AUTHOR - Allen Day | APPENDIX

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