As Marshall pointed out, you should use the Entrez Programming Utilities.

Entrez offers a so-called SOAP webservice. You will find lots of resources out there that use the SOAP protocol. The other type of service that you will frequently encounter is REST. It is well worth learning a bit about those two techniques - SOAP comes with a bit of a learning curve wheres REST is more intuitive.

For SOAP, you should have a look at SOAP::Lite. To use a SOAP service, you need a description of what information you can send and retrieve and in what form, this is known as a "WSDL" (see below). To query REST services, you usually use something like LWP::Simple.

A very useful resource for your purposes is http://www.biocatalogue.org, which lists available webservices and tells you something about the APIs they use and gives you links to the WSDLs. That would be a good place to search for relevant sources of information for your web tool.