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Bio::IdentifiableI(3) User Contributed Perl DocumentationBio::IdentifiableI(3)

NAME
       Bio::IdentifiableI - interface for objects with identifiers

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();
	   # Gets authority:namespace:object_id
	   $lsid = $obj->lsid_string();
	   # Gets namespace:object_id.version
	   $ns_string = $obj->namespace_string();

DESCRIPTION
       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

FEEDBACK
   Mailing Lists
       User feedback is an integral part of the evolution of this and other
       Bioperl modules. Send your comments and suggestions preferably to one
       of the Bioperl mailing lists.  Your participation is much appreciated.

	 bioperl-l@bioperl.org			- General discussion
	 http://bioperl.org/wiki/Mailing_lists	- About the mailing lists

   Support
       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 Bugs
       Report bugs to the Bioperl bug tracking system to help us keep track
       the bugs and their resolution.  Bug reports can be submitted via the
       web:

	 http://bugzilla.open-bio.org/

AUTHOR - Ewan Birney
       Email birney@ebi.ac.uk

Implementation Specific Functions
       These functions are the ones that a specific implementation must
       define.

   object_id
	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

   version
	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

   authority
	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

   namespace
	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

Implementation optional functions
       These functions are helper functions that are provided by the interface
       but can be overridden if so wished

   lsid_string
	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

   namespace_string
	Title	: namespace_string
	Usage	: $string   = $obj->namespace_string()
	Function: a string which gives the common notation of
		  namespace:object_id.version
	Returns : A scalar

perl v5.14.1			  2011-07-22		 Bio::IdentifiableI(3)
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