Bio::Ontology::DocumentRegistry

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.

  [email protected]                  - General discussion
  http://bioperl.org/wiki/Mailing_lists  - About the mailing lists

Support

Please direct usage questions or support issues to the mailing list: [email protected] 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 [email protected]

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)'