Bio/Ontology/DocumentRegistry.pm

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