Put the API version into its own module:

  DESCRIPTION
    The module exports the software_version() subroutine which
    returns the release version of the Ensembl Core API.

modules/Bio/EnsEMBL/ApiVersion.pm

+=head1 LICENSE
+
+  Copyright (c) 1999-2010 The European Bioinformatics Institute and
+  Genome Research Limited.  All rights reserved.
+
+  This software is distributed under a modified Apache license.
+  For license details, please see
+
+    http://www.ensembl.org/info/about/code_licence.html
+
+=head1 CONTACT
+
+  Please email comments or questions to the public Ensembl
+  developers list at <ensembl-dev@ebi.ac.uk>.
+
+  Questions may also be sent to the Ensembl help desk at
+  <helpdesk@ensembl.org>.
+
+=cut
+
+=head1 NAME
+
+Bio::EnsEMBL::ApiVersion
+
+=head1 SYNOPSIS
+
+  use Bio::EnsEMBL::ApiVersion;
+
+  printf( "The API version used is %s\n", software_version() );
+
+=head1 DESCRIPTION
+
+The module exports the software_version() subroutine which returns the
+release version of the Ensembl Core API.
+
+=cut
+
+package Bio::EnsEMBL::ApiVersion;
+
+use strict;
+use warnings;
+
+use Exporter;
+
+use base qw( Exporter );
+
+our @EXPORT = qw( software_version );
+
+my $API_VERSION = 59;
+
+sub software_version { return $API_VERSION }
+
+1;