I refer you to this link Re: CGI to query other websites that I posted 7 years ago in 2010. I clicked on the links therein and although these links are obsolete, they do refer and forward to current PubMed pages.

The basic situation is that if your want to use PubMed in any serious way (which means bioinformatics), you should use the PubMed library of functions to access their site. They have programs and libraries that are compatible with Perl. This will be much more efficient for both your code and their server site.

I think what I said 7 years ago is still valid. I highly recommend that you look at the current PubMed tools. I am sure that they are even better in the last 7 years.

Update: ok, resolved PubMed link from above Monk Post: Entrez Programming Utilities Help
"The Entrez Programming Utilities (E-utilities) are a set of eight server-side programs that provide a stable interface into the Entrez query and database system at the National Center for Biotechnology Information (NCBI)". The part about "stable interface" sounds pretty good to me.