Bio::IdentifiableI - interface for objects with identifiers
# 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();
# Gets authority:namespace:object_id
$lsid = $obj->lsid_string();
# Gets namespace:object_id.version
$ns_string = $obj->namespace_string();
This interface describes methods expected on identifiable objects, i.e. 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
Example:
swissprot:P012334.2
or:
GO:0007048
The object will also work with LSID proposals which adds the concept of an
authority, being the DNS name of the organisation assigning the namespace. See
<
http://lsid.sourceforge.net/>.
Helper functions are provided to make useful strings:
lsid_string - string complying to the LSID standard
namespace_string - string complying to the usual convention of
namespace:object_id.version
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These functions are the ones that a specific implementation must define.
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
These functions are helper functions that are provided by the interface but can
be overridden if so wished
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