You could join all the search terms into one big regexp:

then fetch all the abstracts for each of your keys and run the regexp against each of them. Take care to precompile it with $re = qr/$re/. If you'd like the terms to only be found as whole words, something like $re = qr/\b(?:$re)\b/ should do.

With that many terms, it's probably well worth using Regexp::Trie:

use Regexp::Trie;
my $rt = Regexp::Trie->new;
while(<FILE2>) {
  $rt->add($_);
}
$rt = $rt->regexp;
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You can still add the word boundary stuff as above then.