/ 
bioperl-1.2.3
/ Bio::IdentifiableI

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();

# 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

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://bio.perl.org/MailList.html           - About the mailing lists

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 email or the web:

bioperl-bugs@bio.perl.org
http://bugzilla.bioperl.org/

AUTHOR - Ewan Birney

Email birney@sanger.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