If you want to automate your queries to Ensembl using BioMart perl API you will face the problem of server overloading, thus an alternative is to use webservice, this script solved my problem, hope it helps, Cheers.

query-ensembl.pl

# an example script demonstrating the use of BioMart webservice
use strict;
use LWP::UserAgent;

open (FH,$ARGV[0]) || die ("\nUsage: perl getFromEnsembl.pl Query.xml\n\n");

my $xml;
while (<FH>){
    $xml .= $_;
}
close(FH);

my $path="http://www.biomart.org/biomart/martservice?";
my $request = HTTP::Request->new("POST",$path,HTTP::Headers->new(),'query='.$xml."\n");
my $ua = LWP::UserAgent->new;

my $response;

$ua->request($request,
	     sub{
		 my($data, $response) = @_;
		 if ($response->is_success) {
		     print "$data";
		 }
		 else {
		     warn ("Problems with the web server: ".$response->status_line);
		 }
	     },1000);