Obsidian Setup Guide

Intermediate · 45–60 min · Zotero account (Better BibTeX for full integration)

A research archive is only as useful as the connections you can draw through it.

Why use Obsidian?

You don't strictly need Obsidian, but it's the recommended environment for integrating AI tools into this workflow. It acts as a local, markdown-based knowledge management system that creates a web of interconnected notes.

Benefits for your research workflow:

• Markdown-based: Create a web of interconnected notes with markup that is easy for both humans and AI to read and write.
• Local data: Store everything in plain text files on your machine.
• Linking: Create connections between ideas, papers, and notes, mirroring how research actually happens.
• Extensible with plugins: Connect directly to Zotero and other tools to create a research pipeline.
• AI-accessible: The AI tools we use can read and help synthesize the knowledge in your research vault through a plugin, such as the Obsidian MCP server.

This guide covers the setup and integration of Obsidian as a personal research environment.

Step 1: install and configure Obsidian

1.1 download Obsidian

1. Visit obsidian.md
2. Download for your operating system
3. Install the application
4. Launch Obsidian

1.2 create your research vault

1. Click "Create new vault"
2. Name: Research
3. Location: Choose a folder on your computer
4. Click "Create"

1.3 enable community plugins

1. Settings (gear icon) → Community Plugins
2. Turn off "Restricted Mode"
3. Click "Browse" to access the plugin marketplace

1.4 essential Obsidian navigation

Other essential keys:

• Cmd/Ctrl+Click on links: Open in new tab
• Cmd/Ctrl+P: Command palette (search all features)
• Cmd/Ctrl+O: Quick switcher (find any note fast)

Step 2: essential folder structure

Create this structure in your vault:

/Research/
│
├── 00-Inbox/                    # Temporary notes, to be processed
├── 01-Literature-Notes/          # Individual research file notes from Zotero
│   ├── by-author/               # Optional: organize by first author
│   ├── by-year/                 # Optional: organize by publication year
│   └── by-topic/                # Optional: organize by research topic
├── 02-Permanent-Notes/           # Your synthesized insights
├── 03-AI-Conversations/          # Exported from AI tools
├── 04-Research-Projects/         # Project-specific notes
│   └── Research-2025/
├── 05-Daily-Notes/              # Research journal
├── 06-Maps-of-Content/          # Index/overview notes
├── Templates/                    # Note templates
└── Attachments/                  # Images, PDFs (if stored locally)

Create folders:

1. Right-click in file explorer → New Folder
2. Create each folder in the structure above

Step 3: Zotero integration options

Step 4: additional essential plugins

4.1 dataview (Required)

Create dynamic tables and queries from your notes.

Installation:

1. Community Plugins → Search "Dataview"
2. Install → Enable

Example Use:

TABLE
  authors AS "Authors",
  year AS "Year",
  rating AS "Rating"
FROM "01-Literature-Notes"
WHERE contains(tags, "#research")
SORT year DESC

4.2 templater (Highly recommended)

Advanced templates with dynamic content.

Installation:

1. Community Plugins → Search "Templater"
2. Install → Enable
3. Settings → Templater → Template Folder: Templates

4.3 citations plugin

Pandoc-style citations without full Zotero integration.

Installation:

1. Community Plugins → Search "Citations"
2. Install → Enable
3. Configure BibTeX export from Zotero

4.4 Obsidian MCP server (for AI access)

Allow Cherry Studio to read your vault.

Installation:

1. Download MCP server: GitHub - Obsidian MCP
2. Community Plugins → Search "Local REST API"
3. Install → Enable
4. Settings → Local REST API:
   • Enable server
   • Port: 27124
   • Enable: "Read access"

In Cherry Studio:

• Add MCP Server → Obsidian
• Vault path: Your vault location
• Port: 27124

Step 5: create templates

5.1 literature note template

Save as: Templates/literature-note-template.md

---
title: "{{title}}"
authors: [{{authors}}]
year: {{year}}
citekey: {{citekey}}
tags: [literature-note, {{tags}}]
date-created: {{date}}
date-modified: {{date}}
---

# {{title}}

## 📚 Metadata
- **Authors**: {{authors}}
- **Year**: {{year}}
- **Journal**: {{publicationTitle}}
- **DOI**: {{DOI}}
- **Zotero**: [Open](zotero://select/items/{{id}})
- **PDF**: [Open]({{pdfLink}})

## 🎯 Key Takeaways
-

## 📝 Summary
{{abstractNote}}

## 🔬 Methodology
- **Approach**:
- **Data**:
- **Analysis**:

## 💡 Main Findings
1.
2.
3.

## 🔗 Connections
- **Supports**:
- **Contradicts**:
- **Extends**:
- **Related**: [[]]

## 💭 Personal Thoughts
-

## 📌 Annotations
{{annotations}}

## ❓ Questions
-

## 📅 Reading Progress
- [ ] Abstract
- [ ] Introduction
- [ ] Methods
- [ ] Results
- [ ] Discussion
- [ ] Conclusion

5.2 daily note template

Save as: Templates/daily-note-template.md

---
date: {{date}}
tags: [daily-note]
---

# {{date:YYYY-MM-DD}}

## 📚 Reading Goals
- [ ]

## 🔬 Research Activities
-

## 💡 Insights
-

## 🤖 AI Conversations
-

## 📝 Notes
-

## 🔗 Created Notes
-

## 📅 Tomorrow
-

Step 6: configure settings

6.1 core settings

1. Settings → Options:
   • Default location for new notes: 00-Inbox
   • New link format: Shortest path
   • Use [[Wikilinks]]: Yes

6.2 files & links

1. Settings → Files & Links:
   • Deleted files: Move to Obsidian trash
   • Attachment folder: Attachments
   • Automatically update internal links: Yes

6.3 daily notes

1. Settings → Core Plugins → Daily Notes → Enable
2. Configure:
   • New file location: 05-Daily-Notes
   • Template: Templates/daily-note-template.md
   • Date format: YYYY-MM-DD

6.4 graph view

1. Settings → Core Plugins → Graph View → Enable
2. Use Cmd/Ctrl + G to view knowledge graph
3. Filter by tags or folders

Step 7: workflow integration

7.1 Zotero → Obsidian workflow

Adding new literature:

1. In Obsidian: Cmd/Ctrl + P → "Zotero Integration: Create Literature Note"
2. Search for a paper by title, author, or citekey
3. Select the paper. Obsidian creates a note with metadata.
4. Review and add your insights

Batch Import:

1. Select multiple items in Zotero
2. Right-click → Copy Better BibTeX Citation Key
3. In Obsidian: Create new note
4. Run command: "Zotero Integration: Insert Literature Notes"

7.2 Cherry Studio → Obsidian workflow

Export AI Conversations:

1. In Cherry Studio: Export → Markdown
2. Save to: 03-AI-Conversations/YYYY-MM-DD-topic.md
3. In Obsidian: Review and link to relevant notes

MCP Access:

1. Cherry Studio can read your vault via MCP
2. Ask: "What are my notes about [topic]?"
3. AI retrieves and synthesizes from your vault

7.3 Obsidian → synthesis workflow

Creating Permanent Notes:

1. Review literature notes
2. Identify recurring themes
3. Create a permanent note in 02-Permanent-Notes
4. Link to supporting literature notes
5. Add to relevant Map of Content

Maps of Content (MOCs):

1. Create an index note in 06-Maps-of-Content
2. List and organize related notes
3. Add brief descriptions
4. Update as collection grows