#!/usr/bin/perl

use strict;
use warnings;

$_ = <<'--';
gregarious foo gregarious foo
foo gregarious foo gregarious
gregarious foo gregarious foo
--

s/(gregarious)/\\underline{$1}/g &&
s/\\underline\{(gregarious)\}/\\footnote{$1}/;

print;
 
__END__
\footnote{gregarious} foo \underline{gregarious} foo
foo \underline{gregarious} foo \underline{gregarious}
\underline{gregarious} foo \underline{gregarious} foo
[download]

Abigail