I have collections of references Pubmed which have free PDFs in pubmed central. It would be nice to access the collection and import the references and the PDFs at the same time.
It’s actually against PubMed Central policy to allow automatic retrieval of the full-text content beyond their open access articles.
Non-open-access content is copyrighted so PubMed Central has to abide by agreements with the content publishers to protect that copyright. The agreement allows them to display the content for individual use, but any kind of systematic retrieval has to be blocked.
There’s information about it on their copyright page. EndNote counts as an “automated process”:
http://www.ncbi.nlm.nih.gov/pmc/about/copyright.html
Restrictions on Systematic Downloading of Articles
Crawlers and other automated processes may NOT be used to systematically retrieve batches of articles from the PMC web site. Bulk downloading of articles from the main PMC web site, in any way, is prohibited because of copyright restrictions.