Annotating PDF lecture notes: the method and the tools

Highlighting feels like work. Yet the review by Dunlosky et al. (2013) of learning techniques ranks it among the least useful methods when used on its own. Rereading your highlights is closer to recognition than to recall.

What works better is testing yourself: trying to recall the answer before seeing it. This is the testing effect (Roediger and Karpicke, 2006). So annotation keeps all its value, as long as it prepares that test rather than replacing it.

Three simple rules make all the difference.

• Highlight little. One sentence per paragraph at most, often none. If everything is important, nothing is.
• Keep a stable color code, the same in every subject. For example: yellow for definitions, green for numbers and dates, pink for what often comes up on exams, blue for mechanisms, orange for what you don't understand yet.
• Turn a highlight into a question. Every marked passage should become a card or an MCQ question. If not, ask yourself why you highlighted it.

An example in pharmacology: rather than highlighting "NSAIDs inhibit cyclooxygenases", write the card "What is the mechanism of action of NSAIDs?". Our tips on how to make good flashcards cover this step in detail.

Each tool has its strengths. This table compares the principles, not the details of each version.

If you mostly fill handwritten notebooks from scratch, GoodNotes is more complete. If you work on your university handouts, with a highlighter, a mouse or an Apple Pencil, and want to review what you mark, Mnemesia will save you a lot of back and forth.

In Mnemesia, each handout opens in the subject where it's filed. The annotation tools:

• A highlighter in six colors, to stick to your color code.
• A pen for writing and drawing freehand on the page, with your finger or an Apple Pencil, and an eraser.
• Notes attached to a passage, written in the margin, and sticky notes placed on the page.
• Text recognition for scanned handouts: a photocopied past exam paper becomes searchable, selectable and highlightable, without sending anything over the internet.
• Image cropping: select a diagram and it becomes a card, for example an image occlusion card with its labels hidden.
• A "notes and mistakes" deck specific to each handout, to record what you get wrong.
• Opening the course in a second window, to keep the handout in view while you write your cards.

The annotated PDF is stored next to the original handout, in your course folder. You can open it with any other reader, print it or send it.

• During or right after class: an active reading, with few highlights and your questions as comments.
• That same evening: each highlight becomes a front and back card, a cloze deletion or an image occlusion.
• Over the following days: spaced repetition brings these cards back at the right time.
• Before the exam: MCQ practice checks that you can apply the material, not just recite it.

The annotated handout then becomes an index: when a card gives you trouble, you go back to the original passage to understand it, instead of rereading everything.

• Highlighting on the first read, before you understand the structure of the course. Read first, mark afterwards.
• Changing your color code from one subject to another: after a month, nobody knows what green means anymore.
• Copying the course into your comments. A useful comment is a question, a link to another chapter or a mistake not to repeat.
• Saving annotations for "later": if they don't become cards within the week, they won't be of any use.
• Rereading your highlights the night before the exam instead of practicing. Testing yourself, with cards or MCQs, is far better.

Self-testing explains why searching for the answer helps you remember better than rereading it.

Mnemesia runs on Mac, iPad, Windows, Linux and Android tablets. On iPad, your courses are real files visible in the Files app.

On the App Store Mac and iPad, turn on iCloud in Settings: a handout annotated on the iPad shows up annotated on the Mac. With Windows, Linux or an Android tablet, there is no sync: choose one main device for your courses, and back up its folder regularly.