Digital highlighting done right

Methods for annotating academic texts


Do you have any academic guilty pleasures? During my studies, I certainly did: highlighters. I absolutely loved marking up my readings with neon pink, yellow, and green markers. But I did feel guilty whenever I noticed that I hadn’t really understood the text but had instead been focusing on the process of highlighting. The text was reduced to a mere canvas. And digital highlighting wasn't any better, since then I had even more colors to choose from.

Fortunately, there are ways to highlight and annotate your academic texts in a much more useful way.

After you've performed a database search and found a few scholarly sources that could be relevant for your paper, you'll want to take a good look at their abstracts, tables of contents, and outlines. While doing this, you’ll also check to make sure that the  journal the article appeared in is legitimate. Using your information literacy skills, you'll also take into account additional criteria when evaluating the sources you found. Then, you can weed out the ones that are irrelevant to your research questions or that have dubious origins.

Now the fun begins! You can start reading and analyzing the articles. But what’s the best way to keep track of the most important ideas and passages as you read? Should you use highlighters like I did? Should you take notes as we suggested in this previous blog post?

Below I’ll discuss different highlighting and annotation methods and then present five different approaches you can use with the reference management program Citavi.

First things first: what should you annotate?

Why highlight or annotate at all? When you read a text for a paper, your end goal is to use its insights in your own work. So, you’ll want to keep track of what new ideas you glean from it and which sections might be important later on. Highlighting or underlining is one of the quickest and easiest ways to do this.

It can be tempting to highlight everything that strikes you as important while you read, but try to resist the impulse and limit yourself to highlighting around 10-20% of the text. Otherwise it will be more difficult for you to pick out the most important ideas later on.

Since academic texts are written for other academics, authors often assume that the core definitions, concepts and methodologies do not need to be re-stated. This can be difficult when you’re just starting out since you won’t yet be familiar with this background information and the technical language and jargon used can be confusing. It can be helpful to highlight terms for which you need to look up a definition, synonym or translation. You can also highlight text passages that you did not understand so that you can go back to them and try to parse their meaning later on. Doing so helps you broaden your knowledge of a field and build upon the insights of other scholars in your own work. Also highlight new ideas and important text passages to separate them from the surrounding text.

Reading can be thought of as having a conversation with the author of the work. Read with a critical eye, and you’ll likely encounter statements or arguments that you disagree with or that you have questions about. You can highlight these passages and add your thoughts as comments on the text. Or you can paraphrase or summarize the author’s statements in your own words.

Beyond these suggestions, there’s even more content you might want to highlight or underline. For example, you might want to highlight important definitions, cited sources that you want to locate, and important keywords.

Additional recommendations for annotating and commenting

In addition to simply highlighting text passages you can also use symbols or abbreviations to mark up your text. For example, you can use circles, stars, parentheses, exclamation points, and question marks or letters and abbreviations. Just be sure to create a legend with explanations so that you still know what everything means five months from now. That will also help you more easily find the passages you need later on when writing your paper. The University of Adelaide gives some examples of commonly used note-taking systems in this PDF document.

Traditionally, you would write your symbols and abbreviations in the margins of the physical text. If you borrow a book from the library, you can paperclip a narrow sheet of paper to the margin of each page and then use symbols. Alternatively, you can copy the most important parts of the book (making sure to respect fair use rules) and then highlight as usual.

If you’re working with digital texts, your annotations can be created with a click. For example, you can use icons, emojis or stamps. You can also assign a specific meaning to each highlighter color in your PDF reader. For example, definitions might always be blue and sources you want to locate could be red. These color assignments should also be saved in a legend. Your comments can be typed up or, if you’re working on a tablet, you can write them out by hand with a stylus.

To save longer comments, summaries or notes, you can use a separate document, for example a Word document, and just save your thoughts while reading there. To make sure you don’t lose the link to original work, add the citation information to the document and don't forget page numbers.

Evaluating PDFs with Citavi

It’s even easier with a software program or app designed for annotating academic texts, for example Zettelkasten or Weava. In the reference management program Citavi, there are many tools available to help you analyze PDFs. This guide explains the features in detail. Your notes and annotations are automatically linked with each text passage making it easier to find them again, bring them into an outline and cite them.

In Citavi every type of highlight has a certain color and type of knowledge item associated with it. This makes it easy for you to remember later on what color stands for what and it means that you shouldn’t need to create a legend. In addition, teamwork is easier since each team member knows that the color orange stands for a comment, for example. You also can hide the annotations and comments made by your colleagues if you ever need to look at a clean version of the PDF.

If you’re working on your own, you have a number of options for how you can annotate and comment on texts with Citavi. Below I’ve outlined a five different workflows that our team recommends and others that were recommended to us by our users.

1) Highlight first, then classify further

This workflow requires you to read the text at least twice. In your first reading, you will skim the text and highlight anything that jumps out at you as being important. Use the yellow highlighter to do this. This first step gives you a good overview of the text. Since scholarly articles usually have a similar structure, you can use that to orient yourself. For example, at the beginning you’ll almost always see an abstract which summarizes the work. At the end you’ll usually find a discussion section that places the author’s conclusions in a wider context. If you have to read a lot of articles, concentrate on these sections during your first reading. Just doing this can already help you identify and filter out articles that aren’t a good fit so that you don’t have to waste any additional time on them.

During your second round of reading, read the text closely but still focus most on the text passages you identified in your first go-through and make decisions about what you want to do with them:

  • Save definitions
    Change important highlighted terms to red highlights by right-clicking the yellow highlight and then clicking “Highlight in red”. These red highlights let you save the term in the Core statement field and then write the definition in the Text field. In this way you can build up a glossary of important terminology.
  • Plan additional steps
    If you highlighted sources that the author cited and that you want to look at yourself, right-click the highlight and change it to a task to remind yourself to order or check out the source.
  • Save quotations and comments
    Passages that you want to cite with their exact wording can be changed to a direct quotation by right-clicking the highlight and selecting “Add as quotation”. If you want to add your own comments to a highlighted section, for example to make connections to your pre-existing knowledge or to save questions you have, you can click the yellow highlight and then click the orange comment bubble in the toolbar to change the highlight to a comment. Add a short summary or a couple keywords in the Core statement field and then add your comment in the text field.

2) Direct quotations only

In this workflow your goal is to read the text one time only. To do this, you’ll need to be very concentrated to be able to pick out the most important sections as you go. However, this does not mean that you’ll need to read the text from beginning to end as you would a novel. Instead, you should zone in on the passages you expect to contain the most important ideas or findings. Only seminal or other important texts should be read in their entirety. Even when reading these texts, make sure to set a time limit for yourself so you don’t get lost in the details.

To keep yourself from having to read the text again, add all important text passages as direct quotations. Add a short summary of the text or a few keywords to the Core statement field. This will help you more easily remember and find the text passage later on. To keep from forgetting the context, add your own comments to the direct quotation. The advantage of saving everything as a direct quotation is that the text of the passage is added to Citavi and can be searched and easily viewed in the Word Add-In when writing your paper. You can then rephrase it in your own words, or you can click to insert it in your document, making sure to add quotation marks if you didn’t already do so in Citavi.

3) Use your own color system

This method isn’t one of the methods officially supported by Citavi and it is a bit of a workaround. However, many users work with Citavi in this way, so we thought we would still share the method with you.

In this workflow you continue using the highlighter colors the way you would in other PDF readers or on paper. You simply ignore all the other annotation options that Citavi offers and continue using the highlighter colors the way you otherwise would. For example, if you’ve always used purple highlights for definitions, you would just ignore the fact that purple highlights stand for indirect quotations in Citavi. With this method you leave the text fields for the knowledge items empty since you’re only interested in highlights. You also wouldn’t use the Knowledge Organizer at all. Instead, you would write your paper directly in Word, looking back at your highlighted PDFs in Citavi as necessary. Since some highlight colors aren’t visible unless you hover over them, it's a good idea to  export your highlights to the PDF file.

Alternatively, you can open the PDF file in the external PDF reader of your choice instead of in Citavi. However, this option is not available for cloud projects.

4) Ask questions

An additional method is to formulate questions to help guide your reading before you start. You can create a template for yourself with the following questions and save it in Citavi as a summary:

  • Which questions does the author answer?
  • Is there any conflict of interest? What’s the author’s background?
  • Which methodology was used and why?
  • Has the author’s initial research question been answered?
  • Etc.

You can copy the template for each text you read. With this method you would not highlight or annotate much, if at all. Instead, while you read you would leave the knowledge item open and answer the questions as you go. If the answers end up being too long you can alternatively create a knowledge item for each question.

5) The minimalist approach

The Summary knowledge item can also be used to summarize the text as a whole. With this approach you would hardly mark up the text at all. Instead, you would write a summary for the text as a whole. For tips on writing summaries, see this earlier blog post. If you tend to write long summaries, you can type them up in your word processor and then add the document to each reference as an attachment.

Despite the title of this blog post, there’s really no "right" or "wrong" when annotating and commenting on academic texts. Experiment and combine different methods to find the approach that works best for you. Hopefully you’ll even find one that makes you enjoy the reading process as much as I used to enjoy my highlighters, but minus the guilt.

Which of the workflows have you tried? Do you use another system not mentioned here? And what are some of your (academic) guilty pleasures? Continue the conversation with us on Facebook!


For further reading

Hermida, Julian (June 15, 2009): The importance of teaching academic reading skills in first-year university courses. In: SSRN Journal. DOI: 10.2139/ssrn.1419247.

Qayyum, Muhammad Asim (2008): Capturing the online academic reading process. In: Information Processing & Management 44 (2), S. 581–595. DOI: 10.1016/j.ipm.2007.05.005.


Created by: Jana Votteler – Published on: 6/2/2020
Tags: Reading tips

About Jana Votteler

Jana Behrendt, a librarian by training, is deeply interested in everything related to personal information management. However, she does not read as much as you would expect from a librarian. She loves hiking in the Swiss Alps – as long as she doesn’t have to look down.

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