Bio::Ontology::DocumentRegistry - Keep track of where to find ontologies.

BioPerl documentation Contained in the BioPerl distribution.

Index

Code Index:

NAME

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

SYNOPSIS

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  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

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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

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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:

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

AUTHOR - Allen Day

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Email allenday@ucla.edu

APPENDIX

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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)'
BioPerl documentation Contained in the BioPerl distribution. 
#
# BioPerl module for Bio::Ontology::DocumentRegistry
#
# Please direct questions and support issues to <bioperl-l@bioperl.org> 
#
# Cared for by Allen Day <allenday@ucla.edu>
#
# Copyright Allen Day
#
# You may distribute this module under the same terms as perl itself

# POD documentation - main docs before the code



# Let the code begin...

package Bio::Ontology::DocumentRegistry;
use strict;
use base qw(Bio::Root::Root);
use Data::Dumper;

my $instance;

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;