I am doing PhD in biophysics and I ended up developing my own app for doing literature reviews, so this is going to be somewhat of a plug. I basically wanted an app that could translate between PDF annotations (highlighting, notes and images selections) and Markdown which I use for all other types of note taking. The app basically reads a PDF and extracts the annotations. It can fetch metadata using DOIs and embed it in the PDF attributes. You can add PDF annotations and have them extracted in real-time. The comments you add in Markdown are saved back to comments in the PDF. In addition, you can have it look up references in the PDF by underlining them so you can easily go through the bibliography. Unlike how most reference managers deal with PDFs, there is no "PDF annotation lock-in" and you can export your notes to plain Markdown and HTML or directly to Evernote and DEVONthink.
The app is called Highlights (highlightsapp.net) and is available on the Mac App Store now
The app is called Highlights (highlightsapp.net) and is available on the Mac App Store now