Bio/Ontology/DocumentRegistry.pm

   1 #
   2 # BioPerl module for Bio::Ontology::DocumentRegistry
   3 #
   4 # Please direct questions and support issues to <bioperl-l@bioperl.org>
   5 #
   6 # Cared for by Allen Day <allenday@ucla.edu>
   7 #
   8 # Copyright Allen Day
   9 #
  10 # You may distribute this module under the same terms as perl itself
  11
  12 # POD documentation - main docs before the code
  13
  14 =head1 NAME
  15
  16 Bio::Ontology::DocumentRegistry - Keep track of where to find ontologies.
  17 Allows lookups by name.
  18
  19 =head1 SYNOPSIS
  20
  21   my $registry = Bio::Ontology::DocumentRegistry->get_instance();
  22   my($ont,$def,$fmt) = $registry->documents('Sequence Ontology');
  23
  24   my $io = Bio::OntologyIO->new(-url => $ont,
  25                                 -defs_url => $def,
  26                                 -format => $fmt);
  27   my $so = $io->next_ontology();
  28   #...
  29
  30 =head1 DESCRIPTION
  31
  32 Do not use this directly, use Bio::Ontology::OntologyStore instead.
  33 Bio::Ontology::OntologyStore uses Bio::Ontology::DocumentRegistry to
  34 load and cache ontologies as object graphs, you can just ask it for
  35 what you want by name.  See L<Bio::Ontology::OntologyStore> for
  36 details.
  37
  38 =head1 FEEDBACK
  39
  40 =head2 Mailing Lists
  41
  42 User feedback is an integral part of the evolution of this and other
  43 Bioperl modules. Send your comments and suggestions preferably to
  44 the Bioperl mailing list.  Your participation is much appreciated.
  45
  46   bioperl-l@bioperl.org                  - General discussion
  47   http://bioperl.org/wiki/Mailing_lists  - About the mailing lists
  48
  49 =head2 Support
  50
  51 Please direct usage questions or support issues to the mailing list:
  52
  53 I<bioperl-l@bioperl.org>
  54
  55 rather than to the module maintainer directly. Many experienced and
  56 reponsive experts will be able look at the problem and quickly
  57 address it. Please include a thorough description of the problem
  58 with code and data examples if at all possible.
  59
  60 =head2 Reporting Bugs
  61
  62 Report bugs to the Bioperl bug tracking system to help us keep track
  63 of the bugs and their resolution. Bug reports can be submitted via
  64 the web:
  65
  66   https://github.com/bioperl/bioperl-live/issues
  67
  68 =head1 AUTHOR - Allen Day
  69
  70 Email allenday@ucla.edu
  71
  72 =head1 APPENDIX
  73
  74 The rest of the documentation details each of the object methods.
  75 Internal methods are usually preceded with a _
  76
  77 =cut
  78
  79
  80 # Let the code begin...
  81
  82 package Bio::Ontology::DocumentRegistry;
  83 use strict;
  84 use base qw(Bio::Root::Root);
  85 use Data::Dumper;
  86
  87 my $instance;
  88
  89 BEGIN {
  90 $instance = {
  91    'Sequence Ontology' => {
  92             ontology => "http://song.cvs.sourceforge.net/*checkout*/song/ontology/so.ontology?rev=HEAD",
  93         definitions => "http://song.cvs.sourceforge.net/*checkout*/song/ontology/so.definition?rev=HEAD",
  94         format => 'soflat',
  95                                     },
  96    'Sequence Ontology OBO' => {
  97             ontology => "http://song.cvs.sourceforge.net/*checkout*/song/ontology/so.obo?rev=HEAD",
  98         definitions => "http://song.cvs.sourceforge.net/*checkout*/song/ontology/so.definition?rev=HEAD",
  99         format => 'obo',
 100                                     },
 101
 102    #### TODO Server http://umn.dl.sourceforge.net/ does not respond, are there
 103    #### alternative sources?
 104    'Sequence Ontology Feature Annotation' => {
 105         ontology => 'http://umn.dl.sourceforge.net/sourceforge/song/sofa.ontology',
 106         definitions =>'http://umn.dl.sourceforge.net/sourceforge/song/sofa.definition',
 107         format => 'soflat',
 108                                     },
 109     'Gene Ontology' => {
 110          ontology => [
 111                                                          'http://www.geneontology.org/ontology/function.ontology',
 112                                                          'http://www.geneontology.org/ontology/process.ontology',
 113                                                          'http://www.geneontology.org/ontology/component.ontology'
 114                                                         ],
 115                         definitions => 'http://www.geneontology.org/ontology/GO.defs',
 116          format => 'soflat',
 117                                                           },
 118             };
 119
 120 #aliases
 121 $instance->{Gene_Ontology} = $instance->{'Gene Ontology'};
 122
 123 bless $instance, __PACKAGE__;
 124 }
 125
 126
 127 sub new {
 128   return shift->get_instance(@_);
 129 }
 130
 131 =head2 get_instance
 132
 133  Title   : get_instance
 134  Usage   : my $singleton = Bio::Ontology::DocumentRegistry->get_instance();
 135  Function: constructor
 136  Returns : The Bio::Ontology::DocumentRegistry singleton.
 137  Args    : None
 138  Usage
 139
 140 =cut
 141
 142 sub get_instance {
 143   return $instance;
 144 }
 145
 146 =head2 documents
 147
 148  Title   : documents
 149  Usage   : my($ontology_url, $definitions_url, $format) = $obj->documents('Sequence Ontology');
 150  Function: Maps an ontology name to a list of (local or) remote URIs where the
 151            files can be located.
 152  Returns : A 3-item list:
 153            (1) URI for the ontology file
 154            (2) URI for the ontology definitions file
 155            (3) format of the files (dagedit, obo, etc)
 156  Args    : Name of an ontology, e.g. 'Sequence Ontology', or 'Cellular Component
 157            (Gene Ontology)'
 158
 159 =cut
 160
 161
 162 sub documents {
 163   my($self,$name) = @_;
 164
 165   if(defined($self->{$name})){
 166     return ($self->{$name}{ontology} , $self->{$name}{definitions}, $self->{$name}{format});
 167   } else {
 168     return ();
 169   }
 170 }
 171
 172 1;