Provided by: libbio-perl-perl_1.6.923-1_all bug


       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






       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

       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


   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.
                  - General discussion  - About the mailing lists

       Please direct usage questions or support issues to the mailing list:

       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:

AUTHOR - Ewan Birney


Implementation Specific Functions

       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,
        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

Implementation optional functions

       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
        Returns : A scalar