Bio::Ontology::DocumentRegistry(3) Keep track of where to find ontologies.


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.


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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


 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)'