PhDs are notoriously laborious, but my experience was quite the opposite. I finished my PhD ahead of time, submitted four first-author papers, and built a business on the side while still having time for my friends and family. I think the key to that is how I structure and manage information. While most peers reread papers whenever they wrote their papers and thesis, my digital knowledge management system did all that for me, saving me weeks, if not months, on every publication. In this article, I would like to give you a 15-minute tutorial on how to get started with this to finish your PhD or master’s in record time.
Learn the foundational systems researchers are rarely taught: from powerful note-taking and knowledge management methods to modern lit review tools, ethical AI and productive research workflows.
Before we get into the details, understand why this is important and be motivated by this new way of managing information. The first months of doing this, of using the system, will not feel natural, and the more motivated you feel and the more you see why you’re doing this, the better the results will be.
Video Version of this article
Here is a quick run-through the article as a video if you prefer.
Why should academics use digital notes?
Most academics use pen-and-paper notes or annotations in Zotero. We typically love our notebooks for more than just their function. Here is my wonderful collection of Moleskines from a few years back.
The biggest problem is that you won’t remember what’s in your note collection. There is no way to search it and to retrieve information – you need to skim 100s of pages. Pen-and-paper notes help us remember, but they don’t scale.
Simply said: Your mind isn’t big enough to hold enough relevant information to get you through a PhD and a notebook isn’t the best tool to solve that issue.
A better solution is digital notes. The best tool for digital notes is Obsidian.
Here is an older presentation on digital notes, if you prefer video tutorials:
The video is a bit more conceptual in nature than this tutorial.
What is Obsidian, and why use it?
Obsidian is a text-only note-taking tool with 1000s of plugins to expand its functionality and is arguably better than Notion, the biggest note-taking app. In particular, for academics, Obsidian has a few advantages:
- Files are stored locally, making the app fast and your data private
- Obsidian can work with PDFs and connect to reference managers like Zotero.
- Obsidian can be used for project management
- …or to document code and databases
Additionally, Obsidian is AI-ready, as it stores information in a text-only format that AI Agents can use.
What is a knowledge management system?
Your files on your hard drive are organised in folders. Papers in your Zotero library may be using tags. There is always some organisational structure, but the biggest repository of human knowledge, Wikipedia, has barely any of it and instead uses a highly connected network of links to organise ideas. The way we create this network determines how useful it is for retrieving and synthesising information.
You have probably been on a “Wikipedia binge” where you start with one topic (nuclear physics) and, through a series of clicks, end up somewhere entirely different (cat breeds, e.g. through quantum physics and Schrodinger’s cat). Technically speaking, going from one concept to an unrelated other is creativity. If you can do it with your academic notes, generating novel research ideas will be easy, as well as many other benefits of digital notes.
Getting started with Obsidian in 12 minutes
Let’s set up our academic knowledge management system in under 15 minutes. The best analogy for understanding how Obsidian works is the browser. If the internet is a series of websites that your browser navigates primarily through links, Obsidian is a browser for local (text) files that it navigates through links in these files. It uses a slightly modified text format called Markdown, which allows placing links into your notes, adding headers and so on. You don’t need to learn Markdown formatting for this tutorial.
Step 1: Install Obsidian & create a “vault”
Go to Obsidian.md, download the tool and install it. When you launch it for the first time, it will ask you to create a vault.
What is a vault? Technically, it’s a folder on your hard drive where Obsidian stores its data.
Step 2: Create a folder for sources and one for notes
Papers, PDF, Websites and everything made by others will live in the sources folder. Every idea you extract from these sources will live in the notes folder.
You can delete the “Welcome” note and close both open tabs.
Step 3: Install the Editing Toolbar Plugin
If you can’t be bothered learning Markdown and prefer a more Microsoft Word/Notion-type experience, install the editing toolbar plugin:
After doing this, you will get a bar to add any kind of formatting by clicking the buttons, rather than using the somewhat cryptic markdown syntax (e.g. add ### to make something a header).
The only thing you must remember is that typing in two square brackets [[… creates a link. A pop-up will open and prompt you which note you want to link to. This, of course, only works once you have a few notes.
Step 4: First Sources – Import a paper, lecture or any other source
Everything has to start with sources, as your goal in academia is typically to learn, synthesise, and advance knowledge. The first step is to create a source note and add a PDF to it. Here I will use “Biology 101” presentation.
Benefits of using Source Notes:
- It serves as an anchor. Any information from this lecture can easily be linked to this source note.
- Because this note contains a PDF, you can always double-check yourself.
- This note is mostly a container for the PDF, but it can also include the date you attended the lecture, the author, or links to any associated homework.
The most important behavioural shift you need to master is that this source will not contain any information on the lecture at all. It is merely an anchor to link any findings back to their original source. More on that below.
Step 5: Add topic Notes to store your ideas
The big mindset shift is to store your notes on “Biology 101” not in the note for “Biology 101” but in dozens of concept notes linked with one another.
Note how every bit of information has a link to the source note. This is not very useful when you have one lecture, but once you have 300 papers in your vault, this will be the only way how you can check the sources your ideas came from. More importantly for academic work, you must be able to always cite a source paper; this link enables you to have that information.
Step 6: Create new notes for each concept you encounter
At first, this will increase the number of notes you have to manage. But there is a finite number of concepts in every domain, and this phase will not last long. After a while, you will not need to create any new concepts, but just take notes in different notes. Here is how this can look a little bit later:
Obsidian has a feature to visualise the connections as a graph, the button is located at the top left. You now have a network of connected ideas, which mirror how your brain works, rather than a summary of a lecture. Every note is short and bite-sized. All your knowledge is sorted by topics, and that’s how you can use it best.
Step 7: Keep going until you have ~50 notes.
Obsidian has thousands of plugins and ways to organise your information. For now, you don’t need any of them. Just two folders: Sources + Notes and linking. This setup will enable you to create very complex knowledge networks later. If you want to dive deeper, here are some starters:
But remember, none of that is important to start with. 2 folders + Links is all it takes. You will understand the system once you hit ~50 topic notes. This is the threshold at which your mind will start forgetting concepts, but the links in your notes will remind you of them. These 50 notes have to be on single, atomic concepts:
At this point, you will feel how the capacity of your mind to process information expands through digital notes. It is a magical feeling.
Why do you need a network of digital notes?
First, it saves you a lot of time as most sources repeat ideas, but your notes don’t have to. For instance, in a lecture on “Botany 101” you will learn the same definitions, but since your notes already captured the definition for the topic botany, you can skip writing it down – time saved!
Second, synthesising information and writing a literature review becomes much easier. A knowledge network can find contrasting or supporting opinions of your domain using links:
If you want to know what fossil fuel emissions do to the climate, you might start with a note on fossil fuels, which leads you through a series of links to the idea of sea level rise. The transition leads you from the note on climate change and melting ice sheets to sea level rise. These connections have meaning:
→ “Fossil Fuel emissions cause climate change, which leads to melting ice sheets, which leads to rising sea levels (Source A, Source B)”.
This statement is a synthesis of ideas presented in multiple sources and collected by you at different times without necessarily being presented in this order. That’s how you come up with new ideas for publications. And at the same time, you can use it for your academic writing, because you have linked the sources with every concept. You don’t have to think where an idea came from; it is already in your notes.
It’s magical.
Rules for your knowledge management system
To ensure that your knowledge network remains useful, you need to follow a few rules. It is similar to gardening, while plants grow mostly on their own, you need to plant them in the sun, water them and protect them from pests. Your notes also need a good environment to grow in – here are my hard-earned rules for note-taking.
Rule 1: No information in source notes
Don’t store any ideas within the source notes. This prevents them from being part of the knowledge network, because a source is treated as someone else’s property, and all you can do is link to it.
Rule 2: 3+ Links for every new note
When creating a new note, always make sure to have at least three links going in or out. This ensures that no node is disconnected, and from every single node you always have the option to go in different directions, which branches out your knowledge network and creates this useful connectivity.
Rule 3: Split up notes with 15+ links
If certain notes have too many links, they are not topical enough and aren’t useful for finding new ideas. Break those notes into smaller, more topical notes which are specialised. You can simply copy the parts of this bigger note into multiple smaller notes. But importantly, keep the larger note as a table of contents and add the links to these sub-notes. This ensures that any previous links to the big parent node still remain intact.
Rule 4: Every sentence in the notes folder needs a source link
Every part of your notes should always have a source associated with it. If they don’t have a source, treat it as your own personal opinion that you captured in a note. Simply adding a link to every statement makes source tracking easy.
Rule 5: Don’t rely on folders, use index notes instead
When your node collection grows, you will want to organise notes by folders, but folders don’t scale because of the parent problem: A file can only be located in one folder, but might belong to multiple folders. Here, note B is a tutorial on a specific topic, and it’s also a video. If you have a folder for tutorials and videos, you could place it in both.
A better option is an index note – a note containing mostly links to other notes. For example, create a note for tutorials and a note for videos.
Next steps in your Obsidian Journey
If you follow this advice until you have 50 notes, you will already become more advanced than 90% of your peers and start noticing compounding effects on your learning ability and your ability to synthesise information. But Obsidian can do so much more than that, as it allows it to be used for project management, source management, and many other areas of academic life, all under one system.
The next learning step from here is to master Obsidian’s basics, which make it better than Notion. Here are two tutorials: Using Obsidian Bases For Academic Note Taking and Discovering new Ideas Hidden in Your Notes with Obsidian Bases
Another incredible feature is the canvas, which helps you synthesise large, complex bodies of work more easily: Leverage Mind Mapping to Manage Large Research Projects
For more advanced academic work, learn how to connect Zotero to your note-taking system: Connecting Zotero and Obsidian with the ZotLit Plugin + Templates.
Join the note-taking course if you want step-by-step video guides on how you, as an academic or student, can benefit from Obsidian:
This course shows you how to build a system of connected notes and tools that generate research ideas on auto-pilot. Stay organized in big projects and access everything you ever read in seconds.
Summary
This short introduction to digital note-taking in Obsidian is the absolute minimal viable note-taking system. It relies on two folders:
- One for notes, where your findings go
- One for sources, where academic papers, lectures, and so on reside
Your main learning is that you take notes on concepts in brief, atomic sentences that each link back to the source where you learned them from. Complex bodies of work and learning almost anything at record speed
