Reference

Bio::IdentifiableI(3pm)

interface for objects with identifiers

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.

  [email protected]                  - General discussion
  http://bioperl.org/wiki/Mailing_lists  - About the mailing lists

Support

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

[email protected]

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:

  https://github.com/bioperl/bioperl-live/issues

AUTHOR - Ewan Birney

Email [email protected]

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

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