During a PhD or Master's, information management becomes increasingly challenging: more papers, notes scattered everywhere, and difficulty finding a specific concept when you need it. This article shares a practical approach to managing research notes using Notion and Obsidian together—not the most complex system, but one you can actually maintain long-term.
Why Combine Notion and Obsidian
Each tool excels in different areas:
- Notion: Great for project management, table tracking, and team sharing. You can build a literature tracking database, experiment progress table, and meeting note templates. It's visual and syncs across devices.
- Obsidian: Ideal for deep notes and knowledge networks. It uses local Markdown files, supports bidirectional links (
[[page name]]), and lets you visualize relationships between concepts and papers. Works offline, data stays local.
You don't need to sync data between them—just use each for its strengths.
Notion Side: Literature Tracking Database
Create a Literature Database
In Notion, create a new Database (Table view) with these fields:
- Title: Paper title
- Authors: Author names (text)
- Year: Publication year (number)
- Journal: Journal or conference name
- Status: To Read / Reading / Read / Important (Select or Multi-select)
- Tags: Methods, topic keywords (Multi-select)
- Relevance: Relevance to your research (1–5 star Rating)
- Notes: Brief summary (Text)
- DOI / Link: Direct link to the paper
This gives you a filterable literature manager by method, topic, or year. Use Zotero for storage and citations; this Notion table tracks reading status and categorization.
Experiment Logs and Project Progress
If you run experiments, create a Board view in Notion with stages like "Design → In Progress → Analysis → Complete". Each card can include the protocol, materials list, and links to raw data.
Obsidian Side: Concept and Understanding Knowledge Network
Build Your "Domain Map"
For each important paper you finish, create a note in Obsidian containing:
- What problem the paper solves
- Core method or conclusion (in your own words, not the abstract)
- Connection to your research
- Points you don't understand or question
- Links to related notes using
[[page name]]
The key is to write in your own words—that process itself deepens understanding. Copy-pasting abstracts adds little memory or thinking value.
The Power of Bidirectional Links
In Obsidian, when you write [[scRNA-seq]] in a note, that term becomes a clickable link, and the scRNA-seq page automatically shows this note in its "Linked mentions" section. As notes grow, you get a knowledge graph of interconnected concepts—your own domain map.
Suggested Folder Structure
Avoid deep folder hierarchies—they make finding things harder. Recommended structure:
00-Inbox/ ← New notes to organize 01-Literature/ ← Literature notes 02-Concepts/ ← Methods and concepts 03-Projects/ ← Research project notes 04-Meetings/ ← Group meeting and meeting minutes
Use tags instead of folders for more flexible categorization.
How They Work Together
Your daily workflow:
- Update paper status in Notion database (mark as "Read" when done)
- For important papers, write a detailed note in Obsidian
- When writing papers or reports, use Obsidian graph to review related concepts, and manage writing progress in Notion
Don't try to sync everything—each tool does its job. Avoid using one tool for everything.
Other Useful Tools
- Zotero (see related article on this site): PDF storage and citation management, complements the Notion literature database
- Excalidraw (Obsidian plugin): Draw hand-drawn style diagrams directly in Obsidian, great for experiment workflows and concept maps
- Templater (Obsidian plugin): Set note templates to auto-fill date, tags, etc. when creating new literature notes
Summary
Notion manages tasks (paper status, experiment progress, meeting notes), while Obsidian manages understanding (deep reading notes, concept networks). This combination is simple to start and low-cost to learn, but if you stick with it, you'll find everything you need when writing papers, preparing defenses, or reporting to your supervisor. The most important feature of a note system is not how many functions it has—it's whether you're willing to maintain it consistently.
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