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Bio::IdentifiableI.3pm

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