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Summary

Bio::Ontology::DocumentRegistry - Keep track of where to find ontologies.
Allows lookups by name.

Package variables

Included modules

Inherit

Bio::Root::Root

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.

Methods

Methods description

 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)'

Methods code

BEGIN {

$instance = {
   'Sequence Ontology' => {
	    ontology => "http://song.cvs.sourceforge.net/*checkout*/song/ontology/so.ontology?rev=HEAD",
        definitions => "http://song.cvs.sourceforge.net/*checkout*/song/ontology/so.definition?rev=HEAD",
        format => 'soflat',
                                    },
   'Sequence Ontology OBO' => {
	    ontology => "http://song.cvs.sourceforge.net/*checkout*/song/ontology/so.obo?rev=HEAD",
        definitions => "http://song.cvs.sourceforge.net/*checkout*/song/ontology/so.definition?rev=HEAD",
        format => 'obo',
                                    },
   
   #### TODO Server http://umn.dl.sourceforge.net/ does not respond, are there
   #### alternative sources? 
   'Sequence Ontology Feature Annotation' => {
        ontology => 'http://umn.dl.sourceforge.net/sourceforge/song/sofa.ontology',
        definitions =>'http://umn.dl.sourceforge.net/sourceforge/song/sofa.definition',
        format => 'soflat',
                                    },
    'Gene Ontology' => {
         ontology => [
							 'http://www.geneontology.org/ontology/function.ontology',
							 'http://www.geneontology.org/ontology/process.ontology',
							 'http://www.geneontology.org/ontology/component.ontology'
							],
			definitions => 'http://www.geneontology.org/ontology/GO.defs',
         format => 'soflat',
							  },
            };

#aliases
$instance->{Gene_Ontology} = $instance->{'Gene Ontology'};

bless $instance, __PACKAGE__;

}

sub new {

  return shift->get_instance(@_);

}

sub get_instance {

  return $instance;

}

sub documents {

  my($self,$name) = @_;

  if(defined($self->{$name})){
    return ($self->{$name}{ontology} , $self->{$name}{definitions}, $self->{$name}{format});
  } else {
    return ();
  }
}

1;

}

General documentation

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

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.

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://redmine.open-bio.org/projects/bioperl/

Email allenday@ucla.edu

The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _