Obsidian Setup Guide

​

Why Use Obsidian?

• Markdown-based: Create a web of interconnected notes with a simple, powerful markup language that is easy to read and write for both humans and AI.
• You Own Your Data: Everything is stored in plain text files on your local machine.
• Powerful 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 seamless research pipeline.
• AI-Accessible: Through a specific plugin, the AI tools we use can directly read and help you synthesize the knowledge in your research vault (e.g., the Obsidian MCP server).

​

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 in 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 plugin marketplace

​

1.4 Essential Obsidian Navigation

• 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

/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)

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)

1. Community Plugins → Search “Dataview”
2. Install → Enable

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)

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

​

4.3 Citations Plugin

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

​

4.4 Obsidian MCP Server (For AI Access)

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”

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

​

Step 5: Create Templates

​

5.1 Literature Note Template

---
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

---
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

1. In Obsidian: Cmd/Ctrl + P → “Zotero Integration: Create Literature Note”
2. Search for paper by title/author/citekey
3. Select paper → Creates note with metadata
4. Review and add your insights

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

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

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

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

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