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Set Up Obsidian

Zotero stores the paper. Obsidian stores what you think about the paper.

Obsidian itself is free. You can synchronise your notes yourself using Git and a private repository on a service such as GitHub, or use the official Obsidian Sync service. Obsidian Sync currently starts at USD $4 per month when billed annually, or USD $5 when billed monthly. I pay for it, and for me it is worth the convenience, but you absolutely do not need it.

I recommend Obsidian because its notes are ordinary Markdown files. Markdown is straightforward, readable outside the app and flexible enough for headings, links, tables, images, equations and code. Obsidian also makes it easy to link notes together and see a visual graph of the ideas in your project.

If you already have a note-taking system that you genuinely use, you can keep it. Notion, OneNote or even good old pen and paper will also work.

1. Create one research vault

Install Obsidian from the official website, then create a vault for your research work.

You do not need an elaborate structure. This is enough to begin:

research-vault/
├── inbox/
├── literature/
├── concepts/
├── projects/
├── templates/
└── attachments/
  • inbox is for quick notes that you have not organised yet.
  • literature contains one note per useful paper.
  • concepts contains ideas that appear across papers, such as latency, presence or shared control.
  • projects contains your own questions, designs, experiments and decisions.
  • templates keeps reusable note structures.
  • attachments stores the images and small files embedded in notes.

Start there. Add more folders only when a repeated need appears.

Why are we organising notes like this?

This structure is loosely inspired by the Zettelkasten method, a note-taking approach built around capturing small ideas and gradually connecting them into a larger network of knowledge.

In our simplified version:

  • inbox notes are quick or fleeting notes that you have not processed yet;
  • literature notes record useful ideas and evidence from individual papers;
  • concept notes combine and connect ideas that appear across multiple papers; and
  • project notes turn those connected ideas into research questions, decisions and actual work.

You do not need to follow every rule of Zettelkasten or become obsessed with building the perfect "second brain". The useful idea is simply that notes should not remain as isolated summaries. Over time, they should connect with other papers, concepts and your own research.

2. Keep literature notes separate from project notes

A literature note records what you learned from someone else's work. A project note records your own work and reasoning.

That distinction matters. Six months later, you should be able to tell whether a statement came from a paper, from your own experiment or from an idea you have not tested yet.

A project decision can link to the papers that informed it:

We will compare point-cloud and video representations because both
[[Smith 2025 — Remote Teleoperation]] and [[Nguyen 2024 — XR Interfaces]]
report visibility limitations, but evaluate them under different tasks.

3. Use a simple paper-note template

Create a template like this in your templates folder:

---
citekey:
year:
status: to-read
topics: []
---

# <Paper title>

## Why I opened this

## Research question

## What they did

## What they found

## Important evidence

## Assumptions and limitations

## What I think

## Relevance to my project

## Related papers and concepts

## Questions to follow up

The citekey should match the citation key in Zotero. You can also paste a Zotero item link into the note so you can jump back to the reference and PDF.

Do not fill every heading just because it exists. A note should capture what is useful about that paper for your current question.

4. Build a map by linking ideas

Folders help you store notes. Links help you think across them.

When a recurring idea appears, give it a concept note and link to it using Obsidian's [[double bracket]] links. For example:

[[Network latency]]
[[Operator workload]]
[[Situational awareness]]
[[Point-cloud representation]]

The concept note can then collect:

  • papers that make a relevant claim;
  • methods used to measure the concept;
  • findings that agree or disagree;
  • your current understanding; and
  • questions that remain unresolved.

Obsidian's Graph view can show the network that develops. I treat it as a useful map of my notes, not as proof that the literature review is complete. A beautiful graph can still be built from shallow notes.

A small habit that makes this work

After reading a useful paper, spend five minutes turning highlights into your own words and adding two or three links. Do not leave all of the thinking trapped inside PDF annotations.

When you are ready, use this system while reading your first paper.