Smart Notes, Smarter Research: How I Built My Writing System for Research

← back to writing · Feb 19, 2025 · 3 min read

Smart Notes, Smarter Research: How I Built My Writing System for Research

Without a system, writing feels like running a marathon with no training plan — exhausting, painful, and nearly impossible to finish.

Photo by Unseen Studio on Unsplash

Systems matter

I believe in the power of systems over willpower. Long-term success doesn’t rely solely on willpower. It requires effective systems. Success depends on a smart system, not just a smart mind. As willpower depletes over time, what keeps you going is a well-structured system. I learned that from the book How to Take Smart Notes by Sönke Ahrens.

To do my research effectively, I develop my own research system. Once you have a system in place, you can identify which stage needs to improve.

Writing, reading, thinking, literature review, data analysis, and presenting results — do you have a system for each skill? I’ve learned to build them.

Let’s start with writing. All researchers need writing skills, regardless of their fields. So, what is an effective system for research writing?

Previously, I took notes in a Word file. I created a single document, named Research Notebooks, for each project I work on. My Research Notebooks helped me track my daily research activities, including reading and writing. I also extracted key papers into an Excel file for literature review notes.

These approaches, however, had limitations. First, each paper was tied to a specific project, making them isolated points, while some of my projects had the same topic. Second, it was difficult to recall previous readings or compare them to build arguments for my manuscript.

Enter the Zettelkasten Method

The Zettelkasten note-taking system solved these problems. I learned about it also from How to Take Smart Notes by Sönke Ahrens. (I wrote a book review blog — Book Review: “How to Take Smart Notes” — How It Improved My Writing.) The concept of “linking your thinking” was exactly what I needed. But instead of using paper, as Niklas Luhmann — Zettelkasten ‘s father — did, I wanted a digital version.

I explored Obsidian, a tool that fits my needs perfectly. I had used Obsidian before, but I didn’t use it consistently because I thought note-taking was too time-consuming. My ignorance. The truth is, writing notes takes extra time, but reading without writing is a waste of time for learning.

Develop Zettelkasten for Research in Obsidian

I built my research writing system in Obsidian with the following main folders:

  • Templates
    – Literature Template
    – Permanent Template
    – Web Page Template
  • Fleeting Notes
    – Daily Notes
    – COVID-19 Inbox (my research topic is COVID-19)
  • MOCs (Maps of Contents)
  • Literature Notes
  • Permanent Notes
  • Project COVID-19
    – Manuscript COVID-19

I separated the Literature Template from the Web Page Template because note-taking from web pages is simpler than summarizing academic articles.

In the original Zettelkasten method, literature notes are brief — just two or three sentences in your own words. I struggled with this, so I modified it to fit my needs.

Here’s my Literature Note Template:

Title:
Author:
Year:
Journal:
[Link]()
Type: #Article
# Summary
- Objective:
- Setting:
- Method:
- Results:
- Key findings:
# Interesting Points
# Tags

Since my research is in health sciences, I found that this structure works best for me.

After using Obsidian for about three months, I feel more confident in recalling and linking information. The scattered information I once struggled with has transformed into knowledge and ideas writing.

A system is never static — it evolves, and so do you. Start building your own research system. As it grows, your research will grow, and so will you.

© 2026 Khanh Duong · made with care in Ho Chi Minh City Scholar · ORCID · Email