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)'