Notes from an aspiring academic

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Digital note-taking for research

Sep 01, 2023, 7 min read

Ever since starting the psychology programme in 2011, I have been taking my notes in a digital format. To me the benefits have been clear from the beginning: no lost papers and the ability to easily include images, links and other media have been tremendously useful. But the notes from different courses have been living in isolated folders unable to refer to one another, and when I have written things it has been hard to find relevant notes to use. This is until I started using linked note-taking in Obsidian.

Key to the change is using Wiki-style links (in this case double-brackets [[like so]]) to create bidirectional links between two separate notes. So now, when I read something which reminds me of another idea/article/conversation, I can create a link between the notes and there is now a connection. Your ideas and thoughts become connected and start to interact with one another.

Here’s an example. In September last year, I watched the documentary about AlphaGo, an artificial intelligende algorithm trained to play the Chinese game of Go. I won’t go into more details here, but one thing I reflected on while watching the movie was that that the AI came up with new and original strategies which a human would not have used. Why? Because the AI only cared about winning, even if it was by the smallest margin, and chose moves that gave the highest probability of winning in the end. A human, on the other hand, typically wants to win with a secure margin. A few days later I was listening to a podcast about the electoral system in the US and how the “winner takes all” structure gives rise to insidious tactics like Gerrymandering. Winning by the smallest possible margin is ideal, because anything beyond 50.1% is “wasted” because you have already won. AlphaGo and Gerrymanderin are two separate contexts, but to me it was an interesting connection nonetheless. In a traditional folders-based note-taking archive, this connection would have been lost as soon as my mind wandered elsewhere, but thanks to linked note-taking I was able to establish the connection.

Linked notes in research

I have seen the biggest gains of linked note-taking while reading and creating draft outlines for research projects. My process is very much a work in progress but it goes something like this:

  1. Each paper gets its own note
  2. If the paper is related to a topic I work on, it gets linked. For example [[OCD]]
  3. Topics I currently write about or are interested in get their own “map of content (MOC)” note. This concept is from Nick Milo
  4. As new writing projects emerge, I scan one or multiple MOCs for papers to use and add them to a new note to start writing with a few key references already in place. I can also create a new MOC and start to build a tentative outline from scratch.

1. Each paper gets its own note

I use a template to quickly add some basic information about the paper. The note is named after the Zotero citekey (lastnameYYYY) and then the paper title. The screenshot below shows a typical paper note for an article I read about obsessive-compulsive disorder (OCD).

There are more advanced and automated strategies than mine (see “More reading” section below) but this strategy is easy to work with and suits me at the moment.

So pretty simple. The example citation can go straight into a draft if I don’t have anything else to add, but I can link to the note directly if I want to dive deeper or add more context from the paper.

The example paper is directly related to OCD, so I have added a link to the Map of Content for OCD. At this point nothing else is needed, if I open up the note for OCD I will see the link and can quickly browse papers related to the topic. But because I do research on OCD I want to have more granularity about the relevance.

3. Maps of Content for topics I am interested in or write about

Since I am reading quite a lot of papers about OCD I have created a loose outline with papers from various topics. The blue links indicate specific papers that I have added to the note, and the example paper shown above is added to the “Prevalence, comorbidity, and natural course” subheading. I have been a bit sloppy and not properly contextualized every note, but it’s a work in progress after all!

The panel on the right-hand side is super useful. I see a list of both linked and unlinked mentions (i.e., no formal link with brackets but mention of OCD somewhere in the file). I can also use the “local graph” at the top it to navigate my collection of notes by clicking on a specific note and see the local graph of that note, exploring other potential connections.

4. New writing projects use MOCs as a starting point

In a very idea-driven note-taking system like a Zettelkasten, new writing projects can emerge organically just from the sheer clustering of notes. Let’s imagine I took more notes on the peculiarity of “winner takes all” contexts with binary outcomes, perhaps after a while I would see an interesting cluster and have something to write about. However, the type of research I am involved in is a bit more planned than that and there’s usually a pretty clear idea about the output when we start a randomized clinical trial, for example. But the linked notes can still be useful for developing your ideas.

As I am reaching the end of my PhD studies I have started to think more about the possible next steps and new directions my research could take. I’ve started talking to a potential post-doc advisor about doing some studies on a related topic. I then created a MOC (blue dot) for that topic and linked a few papers that I had read previously. As I started to read more papers (yellow dots) I could see some key references that were linked both to my PhD topic (big blue dot on the left) and the planned post-doc topic (blue dot on the right). These were a great starting point to figure out some potential studies of my own, but I expect that the blue dot on the right will continue to sprawl out in other directions.

Conclusion: Linked notes increases the value of my reading and enhances my creativity

This method is still fairly new to me but I can already see how the added functionality of linking notes together helps me contextualize individual papers I read. They are no longer just sitting in an isolated document somewhere, gradually forgotten, but can now be used and re-used for various purposes.

Using maps of content is a very playful approach and truly feels like a digital sketch pad. I can link disparate ideas together and think about the possible connections, or create fairly structured outlines related to a specific research project.

More reading

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