branch-1-6/Bio/Ontology/DocumentRegistry.pm

   1 # $Id$
   2 #
   3 # BioPerl module for Bio::Ontology::DocumentRegistry
   4 #
   5 # Please direct questions and support issues to <bioperl-l@bioperl.org>
   6 #
   7 # Cared for by Allen Day <allenday@ucla.edu>
   8 #
   9 # Copyright Allen Day
  10 #
  11 # You may distribute this module under the same terms as perl itself
  12
  13 # POD documentation - main docs before the code
  14
  15 =head1 NAME
  16
  17 Bio::Ontology::DocumentRegistry - Keep track of where to find ontologies.
  18 Allows lookups by name.
  19
  20 =head1 SYNOPSIS
  21
  22   my $registry = Bio::Ontology::DocumentRegistry->get_instance();
  23   my($ont,$def,$fmt) = $registry->documents('Sequence Ontology');
  24
  25   my $io = Bio::OntologyIO->new(-url => $ont,
  26                                 -defs_url => $def,
  27                                 -format => $fmt);
  28   my $so = $io->next_ontology();
  29   #...
  30
  31 =head1 DESCRIPTION
  32
  33 Do not use this directly, use Bio::Ontology::OntologyStore instead.
  34 Bio::Ontology::OntologyStore uses Bio::Ontology::DocumentRegistry to
  35 load and cache ontologies as object graphs, you can just ask it for
  36 what you want by name.  See L<Bio::Ontology::OntologyStore> for
  37 details.
  38
  39 =head1 FEEDBACK
  40
  41 =head2 Mailing Lists
  42
  43 User feedback is an integral part of the evolution of this and other
  44 Bioperl modules. Send your comments and suggestions preferably to
  45 the Bioperl mailing list.  Your participation is much appreciated.
  46
  47   bioperl-l@bioperl.org                  - General discussion
  48   http://bioperl.org/wiki/Mailing_lists  - About the mailing lists
  49
  50 =head2 Support
  51
  52 Please direct usage questions or support issues to the mailing list:
  53
  54 I<bioperl-l@bioperl.org>
  55
  56 rather than to the module maintainer directly. Many experienced and
  57 reponsive experts will be able look at the problem and quickly
  58 address it. Please include a thorough description of the problem
  59 with code and data examples if at all possible.
  60
  61 =head2 Reporting Bugs
  62
  63 Report bugs to the Bioperl bug tracking system to help us keep track
  64 of the bugs and their resolution. Bug reports can be submitted via
  65 the web:
  66
  67   http://bugzilla.open-bio.org/
  68
  69 =head1 AUTHOR - Allen Day
  70
  71 Email allenday@ucla.edu
  72
  73 =head1 APPENDIX
  74
  75 The rest of the documentation details each of the object methods.
  76 Internal methods are usually preceded with a _
  77
  78 =cut
  79
  80
  81 # Let the code begin...
  82
  83 package Bio::Ontology::DocumentRegistry;
  84 use strict;
  85 use base qw(Bio::Root::Root);
  86 use Data::Dumper;
  87
  88 my $instance;
  89
  90 BEGIN {
  91 $instance = {
  92    'Sequence Ontology' => {
  93             ontology => "http://song.cvs.sourceforge.net/*checkout*/song/ontology/so.ontology?rev=HEAD",
  94         definitions => "http://song.cvs.sourceforge.net/*checkout*/song/ontology/so.definition?rev=HEAD",
  95         format => 'soflat',
  96                                     },
  97    'Sequence Ontology OBO' => {
  98             ontology => "http://song.cvs.sourceforge.net/*checkout*/song/ontology/so.obo?rev=HEAD",
  99         definitions => "http://song.cvs.sourceforge.net/*checkout*/song/ontology/so.definition?rev=HEAD",
 100         format => 'obo',
 101                                     },
 102
 103    #### TODO Server http://umn.dl.sourceforge.net/ does not respond, are there
 104    #### alternative sources?
 105    'Sequence Ontology Feature Annotation' => {
 106         ontology => 'http://umn.dl.sourceforge.net/sourceforge/song/sofa.ontology',
 107         definitions =>'http://umn.dl.sourceforge.net/sourceforge/song/sofa.definition',
 108         format => 'soflat',
 109                                     },
 110     'Gene Ontology' => {
 111          ontology => [
 112                                                          'http://www.geneontology.org/ontology/function.ontology',
 113                                                          'http://www.geneontology.org/ontology/process.ontology',
 114                                                          'http://www.geneontology.org/ontology/component.ontology'
 115                                                         ],
 116                         definitions => 'http://www.geneontology.org/ontology/GO.defs',
 117          format => 'soflat',
 118                                                           },
 119             };
 120
 121 #aliases
 122 $instance->{Gene_Ontology} = $instance->{'Gene Ontology'};
 123
 124 bless $instance, __PACKAGE__;
 125 }
 126
 127
 128 sub new {
 129   return shift->get_instance(@_);
 130 }
 131
 132 =head2 get_instance
 133
 134  Title   : get_instance
 135  Usage   : my $singleton = Bio::Ontology::DocumentRegistry->get_instance();
 136  Function: constructor
 137  Returns : The Bio::Ontology::DocumentRegistry singleton.
 138  Args    : None
 139  Usage
 140
 141 =cut
 142
 143 sub get_instance {
 144   return $instance;
 145 }
 146
 147 =head2 documents
 148
 149  Title   : documents
 150  Usage   : my($ontology_url, $definitions_url, $format) = $obj->documents('Sequence Ontology');
 151  Function: Maps an ontology name to a list of (local or) remote URIs where the
 152            files can be located.
 153  Returns : A 3-item list:
 154            (1) URI for the ontology file
 155            (2) URI for the ontology definitions file
 156            (3) format of the files (dagedit, obo, etc)
 157  Args    : Name of an ontology, e.g. 'Sequence Ontology', or 'Cellular Component
 158            (Gene Ontology)'
 159
 160 =cut
 161
 162
 163 sub documents {
 164   my($self,$name) = @_;
 165
 166   if(defined($self->{$name})){
 167     return ($self->{$name}{ontology} , $self->{$name}{definitions}, $self->{$name}{format});
 168   } else {
 169     return ();
 170   }
 171 }
 172
 173 1;