Bio::Ontology::DocumenUseriContributed Perl Bio::Ontology::DocumentRegistry(3)NAMEBio::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:
http://bugzilla.open-bio.org/
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)'
perl v5.14.12011-07-22Bio::Ontology::DocumentRegistry(3)
