The first argument to split() needs to be a regular expression matching the string that delimits the fields in your data. In your case, the fields in your line are separated by a '|', so the code could look like this:

#!/usr/bin/perl

use strict;

my $data = 'gi|12345678|ref|NP_001234.1|';
my @data = split /\|/, $data;
my $number = $data[1];
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Or more concisely:

#!/usr/bin/perl

use strict;

my $data = 'gi|12345678|ref|NP_001234.1|';
my $number = (split(/\|/, $data))[1];
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-Matt