# Obsidian Setup Guide

URL: https://research-memex.org/docs/implementation/foundational-setup/obsidian-setup-guide
Description: Obsidian gives research notes a local, linked structure that AI tools can read and help synthesize.



<GuideMeta>
  Intermediate · 45–60 min · Zotero account (Better BibTeX for full integration)
</GuideMeta>

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

## Why use Obsidian? [#why-use-obsidian]

<Aside label="Writing the paper?">
  [Zettlr](/docs/implementation/foundational-setup/zettlr-setup-guide) shares Better BibTeX keys with Obsidian and exports to Word or PDF.
</Aside>

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 [#step-1-install-and-configure-obsidian]

### 1.1 download Obsidian [#11-download-obsidian]

1. Visit [obsidian.md](https://obsidian.md)
2. Download for your operating system
3. Install the application
4. Launch Obsidian

### 1.2 create your research vault [#12-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 [#13-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 [#14-essential-obsidian-navigation]

<Card title="Edit vs. Preview Mode" icon="toggle-right">
  * Edit Mode (Cmd/Ctrl+E): See raw markdown syntax, edit text directly.
  * Preview Mode (Cmd/Ctrl+E again): See beautifully formatted output with styled callouts, tables, and links.
  * Toggle between modes to edit or read the same note.
  * These callout boxes, like this one, are easiest to read in Preview mode.
  * Tip: Use Preview mode when reading, Edit mode when writing.
</Card>

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 [#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-3-zotero-integration-options]

<Tabs>
  <Tab title="Option A: ZotLit">
    Useful for power users who want faster, direct database access and more customization.

    Installation:

    1. Download from [zotlit.aidenlx.top](https://zotlit.aidenlx.top/)
    2. Settings → Community Plugins → Install from file
    3. Select downloaded `.zip` file → Enable

    Configuration:

    1. Settings → ZotLit
    2. Point to your Zotero Data Directory
    3. Use JavaScript-enhanced templates for notes

    Features:

    * Faster performance (direct database access)
    * Real-time annotation sync
  </Tab>

  <Tab title="Option B: Better Notes (Two-Way Sync)">
    Useful for researchers who want synchronized, editable notes in both Zotero and Obsidian.

    Installation:

    1. In Zotero: Download from [GitHub - Better Notes](https://github.com/windingwind/zotero-better-notes)
    2. In Zotero: Tools → Add-ons → Install Add-on From File

    Configuration:

    1. In Zotero: Tools → Better Notes → Preferences
    2. Set sync folder to your Obsidian vault location

    Features:

    * True two-way synchronization of notes
    * Automatically syncs changes from either application
  </Tab>
</Tabs>

## Step 4: additional essential plugins [#step-4-additional-essential-plugins]

### 4.1 [dataview](https://github.com/blacksmithgu/obsidian-dataview) (Required) [#41-dataview-required]

Create dynamic tables and queries from your notes.

Installation:

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

Example Use:

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

### 4.2 [templater](https://github.com/SilentVoid13/Templater) (Highly recommended) [#42-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](https://github.com/hans/obsidian-citation-plugin) [#43-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) [#44-obsidian-mcp-server-for-ai-access]

Allow Cherry Studio to read your vault.

Installation:

1. Download MCP server: [GitHub - Obsidian MCP](https://github.com/MarkusPfundstein/mcp-obsidian)
2. Community Plugins → Search "[Local REST API](https://github.com/coddingtonbear/obsidian-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 [#step-5-create-templates]

### 5.1 literature note template [#51-literature-note-template]

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

```markdown
---
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 [#52-daily-note-template]

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

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

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

## 📚 Reading Goals
- [ ]

## 🔬 Research Activities
-

## 💡 Insights
-

## 🤖 AI Conversations
-

## 📝 Notes
-

## 🔗 Created Notes
-

## 📅 Tomorrow
-
```

## Step 6: configure settings [#step-6-configure-settings]

### 6.1 core settings [#61-core-settings]

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

### 6.2 files & links [#62-files--links]

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

### 6.3 daily notes [#63-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 [#64-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 [#step-7-workflow-integration]

### 7.1 Zotero → Obsidian workflow [#71-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 [#72-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 [#73-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