Bio
IdentifiableI
Summary
Bio::IdentifiableI - interface for objects with identifiers
Package variables
No package variables defined.
Included modules
Inherit
Synopsis
# to test this is an identifiable object
$obj->isa("Bio::IdentifiableI") ||
$obj->throw("$obj does not implement the Bio::IdentifiableI interface");
# accessors
$object_id = $obj->object_id();
$namespace = $obj->namespace();
$authority = $obj->authority();
$version = $obj->version();
# utility function
$lsid = $obj->lsid_string(); # gives authority:namespace:object_id
$ns_string = $obj->namespace_string(); # gives namespace:object_id.version
Description
This interface describes methods expected on identifiable objects, ie
ones which have identifiers expected to make sense across a number of
instances and/or domains. This interface is modeled after pretty much
ubiquitous ideas for names in bioinformatics being
databasename:object_id.version
examples being
swissprot:P012334.2
or
GO:0007048
We also work well with LSID proposals which adds in the concept of an
authority, being the DNS name of the organisation assigning the namespace.
Helper functions are provided to make useful strings being
lsid_string - string complying to the LSID standard
namespace_string - string complying to the usual convention of
namespace:object_id.version
Methods
Methods description
Title : object_id
Usage : $string = $obj->object_id()
Function: a string which represents the stable primary identifier
in this namespace of this object. For DNA sequences this
is its accession_number, similarly for protein sequences
Returns : A scalar
Status : Virtual |
Title : version
Usage : $version = $obj->version()
Function: a number which differentiates between versions of
the same object. Higher numbers are considered to be
later and more relevant, but a single object described
the same identifier should represent the same concept
Returns : A number
Status : Virtual |
Title : authority
Usage : $authority = $obj->authority()
Function: a string which represents the organisation which
granted the namespace, written as the DNS name for
organisation (eg, wormbase.org)
Returns : A scalar
Status : Virtual |
Title : namespace
Usage : $string = $obj->namespace()
Function: A string representing the name space this identifier
is valid in, often the database name or the name
describing the collection
Returns : A scalar
Status : Virtual |
Title : lsid_string
Usage : $string = $obj->lsid_string()
Function: a string which gives the LSID standard
notation for the identifier of interest
Returns : A scalar |
Title : namespace_string
Usage : $string = $obj->namespace_string()
Function: a string which gives the common notation of
namespace:object_id.version
Returns : A scalar |
Methods code
sub object_id
{ my ($self) = @_;
$self->throw_not_implemented(); } | sub version
{ my ($self) = @_;
$self->throw_not_implemented(); } | sub authority
{ my ($self) = @_;
$self->throw_not_implemented(); } | sub namespace
{ my ($self) = @_;
$self->throw_not_implemented(); } | sub lsid_string
{ my ($self) = @_;
return $self->authority.":".$self->namespace.":".$self->object_id; } | sub namespace_string
{ my ($self) = @_;
return $self->namespace.":".$self->object_id .
(defined($self->version()) ? ".".$self->version : '');} | General documentation
User feedback is an integral part of the evolution of this and other
Bioperl modules. Send your comments and suggestions preferably to one
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| Implementation Specific Functions | Top |
These functions are the ones that a specific implementation must
define.
| Implementation optional functions | Top |
These functions are helper functions that are provided by
the interface but can be overridden if so wished