Bio::Ontology OntologyStore
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Summary
Bio::Ontology::OntologyStore - A repository of ontologies
Package variables
Privates (from "my" definitions)
%ont_store_by_name = ()
%ont_aliases = ( 'Gene Ontology' => 'Gene_Ontology' )
$instance = undef
%ont_store_by_id = ()
Included modules
Bio::Ontology::DocumentRegistry
Bio::OntologyIO
File::Spec::Functions
FileHandle
Inherit
Bio::Root::Root
Synopsis
  #----------
#SCENARIO 1
#----------
#make an ontology object manually. via OntologyIO my $io = Bio::OntologyIO->new( #params to fetch Cell Ontology here ); my $cell_ontology = $io->next_ontology; #this is a singleton that caches the fact that you've created #a 'Cell Ontology' intance... my $store = Bio::Ontology::OntologyStore->get_instance(); #...and it can hand you back a copy of it at any time. my $cell_ontology_copy = $store->get_ontology('Cell Ontology'); #---------- #SCENARIO 2 #---------- my $store = Bio::Ontology::OntologyStore->get_instance(); #this use case allows the construction of an ontology on #demand just by supplying the name. my $ontology = $store->get_ontology('Sequence Ontology');
Description
The primary purpose of this module is that of a singleton repository
of Bio::Ontology::OntologyI instances from which an Ontology
instance can be retrieved by name or identifier. This enables TermI
implementations to return their corresponding OntologyI through using
this singleton store instead of storing a direct reference to the
Ontology object. The latter would almost inevitably lead to memory
cycles, and would therefore potentially blow up an application.
Methods
newDescriptionCode
get_instanceDescriptionCode
get_ontologyDescriptionCode
register_ontologyDescriptionCode
remove_ontologyDescriptionCode
guess_ontologyDescriptionCode
Methods description
newcode    nextTop
 Title   : new
Usage : my $obj = Bio::Ontology::OntologyStore->new();
Function: Returns the Bio::Ontology::OntologyStore object.
Unlike usual implementations of new, this implementation will try to return a previously instantiated store, if there is any. It is just a synonym for get_instance. In order to avoid ambiguities in your code, you may rather want to call rather get_instance explicitly, which also usually is better associated with this kind of behaviour. Returns : an instance of Bio::Ontology::OntologyStore Args :
get_instancecodeprevnextTop
 Title   : get_instance
Usage :
Function: Get an instance of this class for perusal.
Since by design this class is meant to be used as a singleton, the implementation will return a previously instantianted store if there is one, and instantiate a new one otherwise. In order to use this class by means of an instance, call this method for added code clarity, not new(). Example : Returns : an instance of this class Args : named parameters, if any (currently, there are no class-specific parameters other than those accepted by Bio::Root::Root.
See Bio::Root::Root.
get_ontologycodeprevnextTop
 Title   : get_ontology
Usage :
Function: Get a previously instantiated and registered instance of
this class by name or by identifier.
One of the main purposes of this class is to enable TermI implementations to return their respective ontology without keeping a strong reference to the respective ontology object. Only objects previously registered objects can be retrieved. This is a class method, hence you can call it on the class name, without dereferencing an object. Example : Returns : a Bio::Ontology::OntologyI implementing object, or undef if the query could not be satisfied Args : Named parameters specifying the query. The following parameters are recognized: -name query the store for an ontology with the given name -id query for an ontology with the given identifier If both are specified, an implicit AND logical operator is assumed.
See Bio::Ontology::OntologyI.
register_ontologycodeprevnextTop
 Title   : register_ontology
Usage :
Function: Registers the given Ontology object for later retrieval
by name and identifier.
Example : Returns : TRUE on success and FALSE otherwise Args : the Bio::Ontology::OntologyI object(s) to register
See Bio::Ontology::OntologyI.
remove_ontologycodeprevnextTop
 Title   : remove_ontology
Usage :
Function: Remove the specified ontology from the store.
Example :
Returns : TRUE on success and FALSE otherwise
Args : the Bio::Ontology::OntologyI implementing object(s)
to be removed from the store
See Bio::Ontology::OntologyI.
guess_ontology()codeprevnextTop
 Usage   : my $ontology = 
Bio::Ontology::OntologyStore->guess_ontology('GO:0000001');
Function: tries to guess which ontology a term identifier comes from,
loads it as necessary,
and returns it as a Bio::Ontology::Ontology object.
Example :
Returns : a Bio::Ontology::Ontology object, or warns and returns undef
Args : an ontology term identifier in XXXX:DDDDDDD format.
Guessing is based on the XXXX string before the colon.
Methods code
newdescriptionprevnextTop
sub new {
    return shift->get_instance(@_);
}
get_instancedescriptionprevnextTop
sub get_instance {
   my ($self,@args) = @_;

   if(! $instance) {
       $instance = $self->SUPER::new(@args);
   }
   return $instance;
}
get_ontologydescriptionprevnextTop
sub get_ontology {
  my ($self,@args) = @_;
  my $ont;

  my ($name,$id) = $self->_rearrange([qw(NAME ID)], @args);
  if($id) {
    $ont = $ont_store_by_id{$id};
    return unless $ont; # no AND can be satisfied in this case
} if($name) { my $o = $ont_store_by_name{$name}; if(!$o){ my $doc_registry = Bio::Ontology::DocumentRegistry->get_instance(); my($url,$def,$fmt) = $doc_registry->documents($name); if(ref($url) eq 'ARRAY'){ my $io = Bio::OntologyIO->new(-url => $url, -defs_url => $def, -format => $fmt, ); $o = $io->next_ontology(); $ont_store_by_name{$name} = $o; } elsif($url){ my $io = Bio::OntologyIO->new(-url => $url, -defs_url => $def, -format => $fmt, ); $o = $io->next_ontology; $ont_store_by_name{$name} = $o; } } if((! $ont) || ($ont->identifier() eq $o->identifier())) { $ont = $o; } else { $ont = undef; } } return $ont;
}
register_ontologydescriptionprevnextTop
sub register_ontology {
  my ($self,@args) = @_;
  my $ret = 1;
  foreach my $ont (@args) {
    if(ref($ont) && $ont->isa('Bio::Ontology::OntologyI')){
      $ont_store_by_name{$ont->name()} = $ont if $ont->name;
      next;
    }

	if(! (ref($ont) && $ont->isa("Bio::Ontology::OntologyI"))) {
      $self->throw((ref($ont) ? ref($ont) : $ont)." does not implement ".
                   "Bio::Ontology::OntologyI or is not an object");
	}
	if($self->get_ontology(-name => $ont->name())) {
      $self->warn("ontology with name\" ".$ont->name().
                  "\" already exists in the store, ignoring new one");
      $ret = 0;
      next;
	}
	if($self->get_ontology(-id => $ont->identifier())) {
      $self->warn("ontology with id\" ".$ont->identifier().
                  "\" already exists in the store, ignoring new one");
      $ret = 0;
      next;
	}
	$ont_store_by_name{$ont->name()} = $ont;
	$ont_store_by_id{$ont->identifier()} = $ont;
  }
  return $ret;
}
remove_ontologydescriptionprevnextTop
sub remove_ontology {
    my $self = shift;
    my $ret = 1;

    foreach my $ont (@_) {
	$self->throw(ref($ont)." does not implement Bio::Ontology::OntologyI")
	    unless $ont && ref($ont) && $ont->isa("Bio::Ontology::OntologyI");
	# remove it from both the id hash and the name hash
delete $ont_store_by_id{$ont->identifier()}; delete $ont_store_by_name{$ont->name()} if $ont->name(); } return 1;
}
guess_ontologydescriptionprevnextTop
sub guess_ontology {
  my ($self,$id) = @_;

  my($prefix) = $id =~ /^(.+?):.+$/;

  my %prefix = (
                SO => 'Sequence Ontology',
                SOFA => 'Sequence Ontology Feature Annotation',
                GO => 'Gene Ontology',
               );

  return $prefix{$prefix} || undef;
}

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 - Hilmar LappTop
  Hilmar Lapp <hlapp@gmx.net>
Allen Day <allenday@ucla.edu>
APPENDIXTop
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _