An efficient workflow for annotating PDFs, extracting highlights and comments, and filing them is essential for research, writing, and studying. Ideally highlights and comments should contain back-links that take you right back to the correct page in the PDF source document.
Adobe’s Acrobat Reader DC, PDF-XChange Editor, and various other PDF readers allow you to annotate PDF files. But, you don’t want these annotations to remain “imprisoned” in your PDF. Your highlights and comments become a lot more useful if you can extract them, aggregate markups from several documents, and re-find them when you need them. Unsurprisingly, the free version of Acrobat Reader doesn’t allow the export of annotations as a word or text file.
To accomplish this in an elegant way, I recommend that you manage your PDF documents in Zotero, a free, open-source research document management system created and maintained by the Roy Rosenzweig Center for History and New Media (George Mason University). With Zotero, you can collect and organize a large variety of document types, including PDF documents and web pages with the click of a few buttons.
To extract and manage PDF annotations in Zotero, you additionally need the free add-on Zotfile from zotfile.com. Zotfile was created by Joscha Legewie, a professor at New York University. A big thank you to Dr. Legewie for programming and maintaining this excellent cannot-live-without add-on!