Zotero Obsidian Research Workflow

An academic workflow for collecting, annotating, and synthesizing research

Combining Zotero for reference management with Obsidian for knowledge synthesis creates a powerful research system.

Why This Combination?

Benefits of Markdown-Based Writing

• Durable, standardized file format
• No program-specific lock-in
• Lighter and faster than traditional word processors
• Stays connected to your notes

The Workflow

1. Collect in Zotero

• Use browser connector to save articles, books, web pages
• Organize into collections by project or theme
• Read and annotate PDFs directly in Zotero
• Highlight key passages and add notes

2. Sync to Obsidian

Use the Zotero Integration plugin to:

• Import literature notes automatically
• Pull annotations and highlights
• Maintain citation keys for later export

3. Synthesize in Obsidian

• Create literature notes for each source
• Build concept notes that synthesize across sources
• Use backlinks to connect related ideas
• Develop arguments through linked notes

4. Write and Cite

• Draft manuscripts in Obsidian using markdown
• Use Pandoc to convert to Word/PDF with formatted citations
• Export bibliography from Zotero

Key Plugins

For Obsidian

For Zotero

Literature Note Template

---
title: "{{title}}"
authors: {{authors}}
year: {{year}}
citekey: {{citekey}}
tags:
  - literature-note
  - reading/in-progress
---

# {{title}}

## Summary
[Your summary of the main argument]

## Key Points
-

## Annotations
{{annotations}}

## Connections
- Related to [[concept note]]
- Contradicts [[other source]]

## Questions
-

Adding Local AI (Optional)

For RAG (Retrieval-Augmented Generation) with your vault:

Option 1: LLM Workspace Plugin

• Install from Community Plugins
• Configure to use local model (Ollama)
• Query your notes in natural language

Option 2: AnythingLLM

• Index your Obsidian vault
• Query with local AI model
• Keep data private and local

Option 3: Smart Connections

• Semantic search across your vault
• Find related notes automatically
• AI-powered synthesis

Tips for Success

1. Process regularly — Don't let unprocessed sources pile up
2. Write in your own words — Summaries beat highlights for retention
3. Connect aggressively — Link to existing notes as you read
4. Review periodically — Revisit old literature notes
5. Start writing early — Synthesis happens through writing

Related

• Building a Digital Commonplace Book — The broader PKM system
• Digital Self-determination — Owning your knowledge tools

The goal is seamless flow from reading to synthesis to writing.