Capturing and visualizing research knowledge is personally an exciting space. I feel that deep reading and absorbing content continues to be challenging, due to the ever-increasing amount of published research, rudimentary reading apps (Google PDF reader finally addressing issue with easily looking up references), and due to somewhat disconnected tools for reading and note-taking. Similar to the readers piggy-backing on the PDFjs library, I've developed an app that helps me capture and organize personal research knowledge [1]. Additionally, visualizations and customizable contexts for notes help to recall and link information.
[1] https://www.knowledgegarden.io/