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
File::Spec::Functions
FileHandle
Inherit
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
Methods description
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 : |
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. |
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. |
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. |
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. |
Usage : my $ontology =
Bio::Ontology::OntologyStore->guess_ontology('GO:0000001');
Function: tries to guess which ontology a term identifier comes from,
loads it as necessary,
and returns it as a Bio::Ontology::Ontology object.
Example :
Returns : a Bio::Ontology::Ontology object, or warns and returns undef
Args : an ontology term identifier in XXXX:DDDDDDD format.
Guessing is based on the XXXX string before the colon. |
Methods code
sub new
{ return shift->get_instance(@_); } | sub get_instance
{ my ($self,@args) = @_;
if(! $instance) {
$instance = $self->SUPER::new(@args);
}
return $instance;} | sub get_ontology
{ my ($self,@args) = @_;
my $ont;
my ($name,$id) = $self->_rearrange([qw(NAME ID)], @args);
if($id) {
$ont = $ont_store_by_id{$id};
return unless $ont;
}
if($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 $ont;} | sub register_ontology
{ my ($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;} | 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");
delete $ont_store_by_id{$ont->identifier()};
delete $ont_store_by_name{$ont->name()} if $ont->name();
}
return 1;} | sub guess_ontology
{ my ($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
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
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:
http://bugzilla.open-bio.org/
Hilmar Lapp <hlapp@gmx.net>
Allen Day <allenday@ucla.edu>
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _