I believe that \b seems to already do what you want with dashes, and you should be able to reduce your regex down to just: $annotation =~ /\b$term\b/i

See below.

#!/usr/bin/perl
use strict;
use warnings;
my @words=qw(one);
my $text=<<END;
This is one (will match)
This is onething (won't match)
This is one-thing. (will match)
This is a thing-one (will match)
This is a -one (will match)
This is a _one (won't match)
END
foreach my $line (split(/\n/,$text)) {
   foreach my $word (@words) {
       if ($line =~ /\b$word\b/) {
          print "matched [$line]\n";
       } else {
          print "not matched [$line]\n";
       }
   }
}
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