Notetaking with Obsidian and Zotero

Intro

What attracted me to the note taking app Obsidian was that it was a plain text (markdown) approach that was agnostic about file storage- It’s just accessible, readable files in a folder (if you want to view it on multiple devices, whatever cloud host you use works fine, well… iCloud kind of sucks).

There are lots of YouTube tutorials about how to do notetaking digitally based off the ideas in How to Take Smart Notes. I found early that Obsidian can be as simple and as complex as you make it and it’s best to evolve your own system based on how you work rather than adopt someone else’s. Like most design problems you should start at minimum viable and then iterate to adapt to your actual workflow.

Whether or not you use Obsidian or some other app (Notion, etc.) for your notes, or even paper, I recommend you use Zotero for your bibliographies. Zotero will make your life immeasurably easier, especially if you add the Better BibTeX plugin, but more about that in a moment.

🎒 Zotero

Zotero serves as the foundation for collecting and managing research materials. It handles all PDFs and citations and has a browser extension to easily save sources from the web as well. The built-in PDF reader enables highlighting and annotation, while the Better BibTeX plugin manages citations effectively, especially when sharing with other tools. There’s both desktop and mobile versions, if you have an account you can sync your library between them. There’s plugins for Office and for Google Docs for adding live linked citations and autogenerating bibliographies, or you can export bibliographies in whatever format directly from Zotero. Zotero also does a pretty good job of automatically detecting bibliography metadata from pdfs, but it can also pull it up from a DOI or ISBN. If you have professors who haven’t figured out how (or are too lazy) to OCR (text detection) the pdf’s of readings they give you in this year 2025, you can OCR it in the horrible Adobe Acrobat app that you hopefully have access to as a student.

Key features:

Browser extension for saving sources
PDF reader with annotation tools
Citation management
Collections and tagging system

🪁 Obsidian

Obsidian functions as a knowledge management hub where ideas develop and connect. Through its Zotero integration plugin, annotations and highlights flow directly into the note-taking system. The ability to link between notes creates a growing network of knowledge that reveals unexpected connections through the graph view.

Obsidian is simple in its base configuration but can get really complex the more you configure it. Add plugins one at a time and make sure you actually need them/ understsnd them or else you’ll forget how your own setup works. I recommend turning on “unique note creator” in core plugins and browsing and installing the “obsidian zotero integration” plugin in community plugins as a start. You can organize your notes however you like, but as a base system I have a templates folder, a unique notes folder and a literature notes folder. a lot of people also keep a daily note folder for a journal thats separate from their unique concept notes. I also just name these folders with emojis because they’re easy for me to type and recognize (I use 🧩,🗳️,📙,📆).

Workflow

The research process flows through several stages, from initial collection to final writing. Each stage builds upon the previous one while maintaining connections back to source materials.

1. Source Collection and Organization

In Zotero, sources are organized using a simple system of three main folders: Inbox for new items, Next for upcoming reading, and Reading for active materials. Tags help group readings by course or project, making it easy to generate specific bibliographies when needed.

2. Reading and Annotation

When reading PDFs in Zotero, I highlight key passages and add comments that connect ideas to my work. These annotations become the raw material for more developed literature notes later. The PDF reader makes it easy to mark up texts while maintaining citation connections.

When I was an undergrad I took notes faster on paper than on the iPad or a laptop, and I used the Cornell note taking system, where you write down all the facts from the lecture in outline form in the main body of the page, questions in a margin alongside them, and then summaries at the bottom of each page. this is still a useful for this system, as the summaries can be re-copied and polished as unique concept notes in section 4.

3. 📙 Literature Notes

Using Obsidian’s Zotero plugin, highlights and annotations are imported into literature notes. The zotero plugin has a command called “create literature note” that will import notes, highlights and bibliographic metadata into an Obsidian note using whatever template you choose. I recommend you keep it pretty simple and don’t spend too much time going down the rabbit hole of different templates and workflows of academics online. Start simple and add stuff as you need it. Here’s a good starting template, which I keep in a templates folder “🧩” in Obsidian and choose in the Zotero integration plugin settings:

---
tags: 📥️/📚️
aliases: 
  - 
---

## {{title}}

### Formatted Bibliography

{{bibliography}}
{% if abstractNote %}
### Abstract

{{abstractNote}}
{% endif %}

{% for annotation in annotations -%}
 {%- if annotation.annotatedText -%}
  - "{{annotation.annotatedText | escape}}" [Page {{annotation.page}}](zotero://open-pdf/library/items/{{annotation.attachment.itemKey}}?page={{annotation.page}}&annotation={annoation.id})
 {%- endif %}
 {%- if annotation.imageRelativePath -%}
 {%- endif %}
{% if annotation.comment %}
 - {{annotation.comment}}
{% endif %}
{% endfor -%}

4. 🗳️ Unique Concept Notes

Zettelkasten is an analog method of creating a knowledge database that has been adapted over time for hypermedia. Imagine you had to create a small wikipedia for yourself with topics that have to fit onto notecards. Each card has a unique name (for mine I use the date and topic name), a summary, a list of other cards that it connects to, and a list of literature notes that are sources you can refer to. There are a million different variations on this method and you’ll find them packaged up in various ways by different productivity gurus. Just come up with a version that works for you! I’ll show you mine.

The goal isn’t to make as many of these as possible, it’s to have a curated list of ideas that connect to one another. These cards aren’t attached to any specific class or project, they’re topics that you refine and reuse over time, editing them, renaming them, reconnecting them as your ideas about things change. You’ll be able to use them not just for writing, but for theorizing artwork.

Here’s one of my permanent notes, this is about as long as I let them get:

---
202302051611 Game Modes
aliases:
  - mode
tags:
  - 📥️/👾
---

A Mode of game, in my usage, is a lens for understanding both the formal qualities and contexts of games, encompassing features of gameplay, creation, and player associations, distinct from traditional genre classifications. We might also be reminded of Modes in literature, Play modes as described by games themselves (Creative Mode, Survival Mode, etc) and Marxian modes of production.

- Multiple modes can exist for a single game
- Includes both player experience and game creation context
- Each mode has:
    - An imagined architecture
    - An imagined game-self
    - Relationship between self and architecture reveals implicit attitudes in both the player and designer, power relations, etc
    - Historical and cultural contexts from both the player and the designer
    
---
## Connections:

- [[The Dungeon Mode]]
- [[The Arcology Mode]]
- [[The Frontier Mode]]

## Sources:

- Sicart's Holistic game theory- [[@sicartProcedurality2011]]
- Rautzenberg says "Mode of game apprehension" [[@rautzenbergFramingUncertaintyComputer2020]]
- "THE FANTASTIC AS A MODE" in [[@jacksonFantasyLiteratureSubversion2008]]
- Yuk Hai's uses 'mode' constantly in [The Existence of Digital Objects](@huiExistenceDigitalObjects2016)

When you first start building up your network of concept notes it may be mostly ideas from lectures or readings, but over time your concept notes should start being mostly your own ideas, supported by existing sources. This is a long process of ‘grooming’ your notes and finding new connections between them that will give you lots of excellent fodder for writing, talks and artwork. Another important part of grooming your notes is noticing which ones have few or no connections to other notes. In my experience its best to either get rid of these notes or archive them in a separate folder. Think of your notes as a neural net, you want to find as many connections between nodes as possible, as they’ll become more memorable, stable and useful the more connected they become.

6. Writing Process

Writing emerges from following paths through connected notes. Starting from relevant concept cards, I can follow links to related ideas and supporting evidence. The network of connections often reveals unexpected relationships and arguments. Literature notes provide quick access to relevant quotes while maintaining proper citations.

Tips for Success

Successful use of this system depends on a few key practices. You can’t possibly read every book that you will be recommended by your thesis committee and peers. Skim and search PDFs in Zotero (on OSX you can also search the contents of PDF files within in a folder) before deep reading to find relevant sections quickly. Create concept notes while reading rather than letting highlights accumulate without processing. Review and link notes regularly to build connections. Most importantly, maintain citation connections throughout the process to make writing easier later.

why?

I’m doing this not because I am a super organized productivity nerd, but because my brain is a long-abused piece of sh*t and I require some external information scaffolding to synthesize ideas and carry out logical and creative thinking. I’d already kind of been doing it with my website and my goal is to make the website the published iceberg tip of an organized and reusable personal research database and idea factory.

Documents: