Christopher Fields > BioPerl > Bio::IdentifiableI



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Module Version: 1.006924   Source   Latest Release: BioPerl-1.007000_005


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


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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
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