What does this tutorial cover?

Academic work entails the tasks of gathering, reading, and annotating resources, writing manuscripts, and citing references.

Synthesizing the wealth of information you’ve gathered, making connections, and expanding on scattered ideas can be challenging.

This tutorial will walk you through the process of integrating Obsidian and Zotero, allowing you to create a personalized knowledge management flow (=Zettelkasten)!

Zotero and Obsidian?

Zotero is a free, open-source reference management software. Below are the features that I found most useful:

  • Zotero allows users to automatically retrieve metadata of references
  • Zotero has web browser extension, enabling users to save references directly from websites.
  • Zotero allows users to highlight and annotate PDFs directly within the application.

Obsidian is a popular note-taking and knowledge management tool that allows users to create and link notes while also formatting content using the markdown system. Below are the features that I found most useful:

  • Obsidian emphasizes bidirectional linking, meaning that if you link one note to another, the linked note automatically links back to the original. This helps in creating a web of interconnected thoughts and ideas.
  • Obsidian provides a graph view that visually represents the connections between different notes, allowing users to see the relationships in their knowledge base.

Workflow

(A short demo in class; a short video will be uploaded later!)

On Zotero:

  1. Collect references (e.g. drag and drop PDF file, web browser extension)
  2. Read PDFs (e.g. leave notes, highlight, capture figures, etc.)

→ You want to link and synthesize the annotated notes.

On Obsidian:

  1. Load literature note from Zotero
  2. Skim through the loaded note and reorganize it
  3. Link your note as you write!

How can we build this work flow?

Step 1. Set up Zotero

  1. Download Zotero and Chrome Connector

  2. Install Better BibTeX plugin for Zotero

    Click It looks like this on Zotero...

    • If you click the button Open Better BibTeX preferences...

    - citation key formula: authors(n=1,etal=EtAl)+year

Step 2. Set up Obsidian

  1. Download Obsidian

  2. Create a new vault

    Click

    1. Set your vault name and path

    2. Click Create and now you’re in!

  3. Create folders

    • We need (1) a separate folder for storing literature notes loaded from Zotero, and (2) another separate folder to store all the meta information such as images and templates.
    • e.g. Folder structure
      • 50 Literature Notes
      • 80 Meta
        • 81 Attachments
        • 82 Templates
    • Create a template file in the folder 82 Templates

  4. Install community plug-ins

    Click
    1. Click settings (gear icon in the bottom left)
    2. Community plugins » Turn on community plugins
    3. Browse
    4. Search for Zotero Integration and click Install
    5. In this way, install the following community plugins: Pandoc Plugin,Pandoc Reference List,Citations, Dataview, and Admonition

    6. Enable installed plugins
    7. Now, scroll down in the left panel (community plugins) and click Zotero Integration !

  5. Set up Zotero Integration

    Click
    1. Note import loaction: 50 Literature Notes/
    2. Import Formats: Click Add Import Format and put in information
      • Name: Create Literature Note
      • Output path: 50 Literature Notes/@{{citekey}}.md
      • Image output path: 80 Meta/81 Attachments/{{citekey}}/
      • Template file: put your template file here
      • Bibliography style: pick one

  6. Set up hotkeys for loading notes from Zotero

    Click
    • Press Hotkeys in the left panel » Set hotkeys for Create Literature Note

Step 3. Additional settings

Zotero

  1. Export My Library

    Click
    1. Right-click on My Library folder and click Export Library
    2. You will see the following screen:
      • Must click Export Notes and Keep updated » OK » Select path

  2. Better BibTeX settings

    Click

    1. Settings » Cite : You will see the following screen:

    2. Click Style Editor » choose your CSL(=citation style language) and click save as

    3. Settings » Open Better BibTeX preferences » Automatic export

    • Set path where My Library file is in!

Obsidian community plugin settings

  • Zotero Integration

    Click
    • Click Add citation format and add different formats as below

  • Pandoc References List

    Click

    • Fallback path to pandoc: click 🔍 and install if needed.

    • Path to bibliography file: folder where you stored My Library file exported from Zotero

  • Citations

    Click
    • Citation database format: BibLaTeX (or other if you choose different one)
    • Citation database path: the same folder (My Library file)
    • Literature note folder: 50 Literature Notes/
    • Literature note template: Put content of your template (e.g. templates.md )

Now we are all set! 👍

Step 4. Synthesize knowledge (=write!!!) on Obsidian

Useful to have: header!

---
category: paper
tags:
  - 
status: writing
---

To cite

  • [[@citekey]]: Link to the literature note
  • [@citekey]: Inline citation

Step 5. Export the Draft

To export the draft, you need the following information:

  • Path to the file that you want to export (#1)
  • Path to the csl file (#2)
  • Path where you want to store exported file (#3)
  • Title and format of your exported file (e.g. Title.docx)

In terminal, you should put the following (in a single line) and enter!

pandoc "#1" --bibliography "#2" --citeproc --csl "#3" -o "#3/Title.docx"

Note

  • A short video will be uploaded here (after the class) for revisiting!

Dataview

 TABLE  
 title as Title,  
 FirstAuthor as "First Author",  
 Year as Year,  
 itemType as Item,  
 Citekey as Citekey,  
 Contribution as Contribution  
 FROM "50 Literature Notes"

References