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();
DESCRIPTIONDo 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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AUTHOR - Allen DayEmail [email protected]
APPENDIXThe 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)'