Bio::Ontology DocumentRegistry
SummaryIncluded librariesPackage variablesSynopsisDescriptionGeneral documentationMethods
Toolbar
WebCvs
Summary
Bio::Ontology::DocumentRegistry - Keep track of where to find ontologies.
Allows lookups by name.
Package variables
Privates (from "my" definitions)
$instance;
Included modules
Data::Dumper
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
BEGIN Code
new
No description
Code
get_instanceDescriptionCode
documentsDescriptionCode
Methods description
get_instancecode    nextTop
 Title   : get_instance
Usage : my $singleton = Bio::Ontology::DocumentRegistry->get_instance();
Function: constructor
Returns : The Bio::Ontology::DocumentRegistry singleton.
Args : None
Usage
documentscodeprevnextTop
 Title   : documents
Usage : my($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
BEGINTop
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__;
}
newdescriptionprevnextTop
sub new {
  return shift->get_instance(@_);
}
get_instancedescriptionprevnextTop
sub get_instance {
  return $instance;
}
documentsdescriptionprevnextTop
sub documents {
  my($self,$name) = @_;

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

1;
}
General documentation
FEEDBACKTop
Mailing ListsTop
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 Top
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 BugsTop
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 DayTop
Email allenday@ucla.edu
APPENDIXTop
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _