Someone mentioned that tending to a zettelkasten seemed to be too much trouble. The “tending to” is not necessarily a bad thing. For instance, I take notes in margins and on Cornell-lined paper, then type those notes into my zettlekasten, put in links to valid references, and link other notes to the new note.
Using this method I have many opportunities to think about and integrate the information. Linking to and from other notes relates the new information to things I already know (scaffolding). Tagging can also be a mental exercise, asking yourself where does this apply? What is the focus? How will I search for this in the future? If using something like Tinderbox, TheBrain, LiquidText, Curio, one also builds and remembers spatial relationships in the material. This ties in nicely with The Method of Loci, also known as memory palaces.
The alternative is to efficiently highlight the pdf.
My (as well as others) thesis is that the perceived efficiency of highlighting is not efficient at all if your goal is mastery and retention of the information.