Bio::Ontology::DocumentRegistry - Keep track of where to find ontologies. Allows lookups by name.
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(); #...
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.
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.
firstname.lastname@example.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists
Please direct usage questions or support issues to the mailing list:
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.
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:
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
Title : get_instance Usage : my $singleton = Bio::Ontology::DocumentRegistry->get_instance(); Function: constructor Returns : The Bio::Ontology::DocumentRegistry singleton. Args : None Usage
Title : documents Usage : my($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)'