I'm in the process of turning many knowledge aspects of my life into a personal knowledge base inside org-mode. For books I'm reading, I find it invaluable to create org-mode items. One per concept. Sometimes I don't even bother filling the content. E.g. I just use a title like "Hadamard transform definition" and nothing else. It'd be to time consuming to write up the definition, and it's pointless as that's in the book anyway.
Then, org-drill brings up some of this cards according to the spaced-repetition algorithm. I answer them with pen and paper. Sometimes I need to prove a theorem, or recall a definition like in the example above. I then open up a book to check my reply is correct and grade myself accordingly. It's a great system to systematize learning.