When studying a printed book, note taking has its problems. Teachers frown on writing in their books and even when this is OK, the margins are really much to small. But, if we write our notes on paper, they are decontextualized. A digital copy of a book stored in a word processor can be reformated with wide spaces for writing notes. Also, some processors allow audio notes as well.
Students can also insert small graphics, either from clip art, or that they draw themselves.
Remember, you never just have one copy of a digital text, you have as many as you want. Repaginate a copy of the text by inserting page breaks at conceptually turning points. Break sentences apart by replacing the spaces between words with carriage returns. Now you have a comprehensive vocabulary list. These markings point out special parts of the text, making them distinct and findable.