GRASP
Is your notetaking system letting you down?
April 15th, 2026, by
If you are well into your research project, you already know that notetaking is central to everything you do. But there’s a difference between taking notes and having a system that actually works for you.
How often have you had a great idea, written it down, and six months later, couldn’t find it? Or sat down to write, only to spend hours sifting through notes trying to reconstruct connections you know you made somewhere? Perhaps you’ve lost track of which sources support which arguments, or found yourself re-reading articles you’d already covered.
If this sounds familiar, you’ve probably created a notetaking method that isn’t built for the kind of work you’re doing. In this post, I’ll suggest a different way of thinking about out notetaking, and discuss some of the features of Obsidian, a free notetaking app that you may want to consider using if you are looking to improve your system for organising your notes.
Why our usual system breaks down
Most of us organise our notes the same way we organise all the documents in our file manager, as a hierarchy of folders and subfolders with each note sitting in one location. It feels workable until we see that an idea could belong in three places at once, or we’d like to connect two notes from different folders that relate to each other.
Often our notes become archives we never revisit. We find it difficult to remember where particular notes were stored, or in which note a particular idea was captured. We write things down and move on, and over time our notes become a graveyard of forgotten ideas.
A different way of thinking - linking notes to each other
An alternative approach is to see that the connections we make between our notes are just as valuable as the notes themselves.
The act of linking notes together encourages us to ask, “how does this connect to what I already know?”. This is a small but powerful habit that can deepen our understanding and brings to light connections we might never have found by browsing our folders.
The concept of a “second brain”, popularised by Tiago Forte, is a useful metaphor for understanding how connecting ideas together can turn out isolated notes into a web of thinking. Forte argues that while your brain is great at generating ideas, it is not great at storing them. Instead, a well-designed digital system can take over the storage and retrieval work, freeing your mind to focus on thinking and making meaning.
The key shift is moving from a warehouse model (organisation by category) to a network model (organisation by connection). Rather than asking “where does this note go”, we ask “what does this note connect to?” Over time, the system starts to reflect the way we actually think rather than just exist as a storage facility.
Another metaphor that might resonate with you is the idea of a “digital garden”. A garden is something you tend over time. You plant seeds - getting fleeting ideas down before they disappear. You water and fertilise - returning to notes to develop them. You lay paths - linking notes together so you can move fluidly between related ideas. And every so often, you prune and weed - clearing out or updating notes, so your garden not only stays alive, but thrives.
Good research notetaking and thinking is not a storage exercise, but a slow, iterative cultivation of ideas over the course of your research project.
Why Obsidian works well for this
Obsidian is a free notetaking app designed to link ideas and notes. A few things make it stand out:
Plain text files. Your notes are stored as simple, lightweight, Markdown files on your own device — not locked inside a proprietary platform. They’ll be readable by any text editor, on any operating system, for as long as you need them.
You own your data. Nothing is held on a company’s server. Your notes are yours, completely.
Wiki-style linking. You can connect notes using [[double brackets]], building a web of related ideas that mirrors how you actually think. So a note on [[constructivism]] might link to [[research methodology]], which links to [[Chapter 3 argument]]. Connections you create become navigable hyperlinks within Obsidian that you can easily follow.
Graph view. Obsidian visualises your notes as a network, so you can literally see how your knowledge clusters and connects, as well and spot the gaps.
A rich plugin ecosystem. The large Obsidian community offers hundreds of free plugins to extend the app’s functionality.
Beyond these core features, Obsidian also offers full-text search across all your notes, template creation so you can maintain consistency in how you capture different types of information (meeting notes, reading notes, daily journals), and extensive customisation options to make the workspace suit the way you think and work. In addition to the plain text files, you can also include and link to pdfs and image files in the app. Moreover, making backups is easy and fast.
One important note: Obsidian is not a reference manager and isn’t meant to replace Zotero or Endnote. It sits alongside those tools, as the place where you think through and connect what you’re reading.
Using Obsidian for HDR research
HDR study presents a particular notetaking challenge: you’re not just capturing information, you’re building an argument over several years, across hundreds of sources, while your thinking constantly evolves. That’s very different from everyday notetaking, and the kind of complex ideas-processing that Obsidian is built for.
Some ways HDR students can use it:
- Research journal / daily notes — a running log of what you worked on, what questions emerged, and what you were thinking. Invaluable for reviewing your progress, or simply remembering what you were thinking six months ago.
- Brainstorming - getting thoughts, ideas, anything, out of your brain and onto the page, however scrappy or rambling, is beneficial for overcoming writing blocks and exploring ideas without the usual self-censorship
- Literature notes — linking source notes to the arguments, themes and ideas they support, creating and using templates for a standardised approach to journal article notes
- Thesis planning — mapping chapter arguments, linking supporting sources to each section, and tracking what still needs to be written or read.
- Meeting and conference notes — notes from supervisor meetings, conferences or research group discussions can all be linked back to relevant project notes
Tending your garden: tips for getting started
Like any tool, Obsidian has a learning curve, particularly if you want to take advantage of the functionality which make it so useful.
It’s worth resisting the urge to transfer all your existing files over and recreate your old folder system (something I did myself for the first couple of years, entirely missing the point).
The investment of time to learn and familiarise yourself with the app, and patience to build it slowly, is definitely worth it!
A few principles that help:
Start small and grow it gradually. You don’t need a perfect system before you begin. Plant a few seeds, make a few links, and let the structure emerge from use rather than trying to design it all upfront.
Create small notes. A note containing one or two key ideas, points from one journal article, or a single brainstorm, makes your system very versatile for linking ideas and related concepts or sources together.
Get ideas from others, but make it your own. There’s no shortage of Obsidian setups shared online, and browsing them is useful — but what works for others may not work for your research workflow. Take what’s useful and leave the rest.
Let it evolve. Your system at year one will look different from your system at year three, and that’s a good sign. A garden that never changes isn’t growing.
Use it regularly — daily if you can. The value of a connected notetaking system compounds over time, but only if you’re consistently adding to it and revisiting it. Just five minutes of notes after a reading session, or a recap of progress each day, is enough to keep your digital garden alive.
Final thoughts
Good notetaking for research isn’t about capturing everything — it’s about building a system that encourages you to be selective and create meaningful connections between ideas. Obsidian won’t write your thesis for you, but it can give you a place where your ideas are linked, findable, and alive. Whether you think of it as a second brain or a digital garden, small, consistent effort over time is the secret to success. If your current system isn’t working for you, it might be time to try something different.
Useful resources
Obsidian.md. Download and documentation
Obisidian Help vault. A guide to all the functions.
Markdown cheatsheet. Indispensable.
Nick Milo, Linking Your Thinking Obsidian YouTube channel For getting started, see Milo’s excellent set of YouTube tutorials for beginners.
Nicole van der Hoeven Another excellent Obsidian Youtuber with a useful video for getting started with Obsidian.
Ingur Mewburn (Thesis Whisperer Blog).
Building a second brain for writing – with Obsidian
Using Zotero and Obsidian: How I Use Obsidian MD and Zotero For Academic Research and (885) How to Connect Zotero and Obsidian for the Ultimate PhD Workflow
Please make any anonymous comments/ feedback, or suggestions for further posts at this link. If you would like to get in touch, or write a post for the Ideas Hub blog, please email karen.miller@curtin.edu.au
Photo by Hasan Hasanzadeh on Unsplash