#!/usr/bin/env perl
use warnings;
use strict;

my $filename = "uniprotfile";
open my $ufh, "<", $filename
	or die "open $filename: $!";

while (<$ufh>) {
	chomp;
	my ($id,$content) = /^(AC|OS|OX|ID|GN)\s+(.*)/
		or next;
	if ($id eq 'AC') {
		my ($first) = $content=~/^([^;]+)/
			or die "couldn't parse '$content'";
		print "AC: $first\n";
		...
	}
	elsif ($id eq 'OS') {
		...
	}
	...
}