Keypoints is an upcoming Mac app which combines note-taking and PDF highlighting. It extracts the highlighted text into individual notes and automatically appends the correct source info.
Keypoints will help you to collect and organize quotations and thoughts during your reading, and allows you to build up your personal knowledge base while highlighting your PDFs.
The ideal annotation tool would allow notes to be associated with highlights. It would have the option to specify what is included with each highlight or note, including: a citekey, a hyperlink back to the source, and a tag tool for note tags.
Beyond keeping my PDFs together, I want to be able to extract important information from them. I don’t just want to visually tag different parts of the PDF, but I want to be able to actively work with those bits of information. The next key advancement is to add semantic information to the text (or image) snippets.