How I read, annotate, & organize research papers using Zotero + Notion
A post for researchers who read a LOT of papers
For researchers, it is essential to keep up on your field’s current literature (e.g., articles and reviews) and organize them for easy access. When you need a citation for a paper or a grant, you’ll be glad to have all your papers and notes stored in one place.
This method was inspired by a few people, including David Vanoni, but most recently Maya Gosztyla who has an amazing Twitter thread, Notion template, and Nature article on this very topic. She is a current grad student at UCSD, and you can follow her on Twitter here.
I hope this method and my added insights/screenshots will help people who want a better paper organization system. It has helped me create an entire database of relevant papers to my field of study (neuroscience).
My two main tools are Zotero and Notion.
What is Zotero?
Zotero advertises itself as “your personal research assistant.” In other words, it’s a reference manager where you can collect, organize, and annotate your research.
Why is Zotero the best reference manager?
- It’s free.
- You can use it with MS Word, LibreOffice, and Google Docs.
- There’s a browser plugin for Google Chrome (Zotero Connector), so that you can download any paper (along with its PDF) into Zotero.
- You can collaborate for free with as many people as you want.
- It’s open source and developed by a nonprofit organization. Being open source means that anyone can create a plugin (e.g., Notero) to make your life better. More on this later.
What is Notion?
Notion is a powerful, customizable workspace where you can write, plan, and organize just about anything. According to their website:
We’re more than a doc. Or a table. Customize Notion to work the way you do.
You can creates pages of content in Notion and then organize them into databases that can be sorted and filtered anyway you’d like to.
- Page = a fresh “canvas” for content
- Database = collection of pages
My Four-Step Paper Organization System
- Download a new paper to Zotero using Zotero Connector (a Google Chrome extension).
- Annotate and highlight article in Zotero.
- Automatically sync papers to Notion using the Notero plugin created by David Vanoni (This stores all the papers in an organized database with 0 effort).
- For important papers, take detailed notes in Notion (Notion Pro is free for all students and educators).
Step 1: Download a new paper to Zotero
When I find a paper that I want to read, I use Zotero Connector—a Google Chrome plugin for Zotero. I simply click the extension button (pink box) and it automatically downloads all the important information for the article and a copy of the PDF to Zotero (red oval).
- Note: it will only download the PDF if you have access to it (e.g., open-access, university access, or personal access).
Step 2: Annotate and highlight article in Zotero
Double click any paper in Zotero and the PDF will show up in a new tab ready for you to highlight and make comments on.
Step 3: Sync papers to Notion database
To sync papers automatically into Notion, I use an amazing plugin called Notero. A complete guide to setting Notero up is available on GitHub. Follow the instructions carefully, and it should work great.
Now, when I download a paper to Zotero using my Google Chrome extension, important information about the paper instantly syncs into a Notion database. In my screenshot below, you can see some of this information. I originally used one of the templates on Github for this.
- Synced information includes: full citation, keywords, DOI, authors’ names, etc. All of this information is available on the specific page for the paper.
I have columns for Status (Need to Read, Skimmed, Annotated, Didn’t Read), Type (Manuscript, Review, Method, Resource), Interesting (1 star, 2 star, 3 star), Action Items (urgent, very urgent, completed), and Relevant Projects. This was based on a template from Maya Gosztyla that you can find here.
Step 4: Take detailed notes in Notion
When the paper was synced into Notion it automatically creates a “page” for the paper. You can click on the paper name and it will open up to a page where you can take detailed notes. I like to include important definitions and screenshots of figures.
Conclusion
The result of all of this is a Notion database with every paper I have skimmed, annotated, or read along with papers I want to read. All papers can be sorted or filtered by any property (relevant project, completion status, etc.). This method also allows me to have papers organized in Zotero to easily create bibliographies and citations.
This system has worked very well for me, but ultimately make sure to do what’s best for you.
Please comment with any questions, and happy reading!
August 22, 2022 edit:
For more detailed instructions on how to set this up, I recommend Holly Jane’s YouTube tutorial. I also published a Medium article that may help: A technical guide to setting up Notero (Zotero + Notion plugin)
Anna Everett earned her B.S. in Neuroscience in 2022. She is a researcher, mental health educator, and advocate for women and other marginalized groups. She writes about life, productivity, the brain, human behavior, & health.
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