Obsidian Setup Guide

Beginner · Local notes first · Zotero and plugins optional

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

Why use Obsidian?

Obsidian keeps your research notes as local Markdown files. You can link sources, interpretations, and decisions, then work with an AI collaborator when the task calls for it. Another text editor also works.

Start by opening a vault and saving a note. You need no Zotero account, AI account, or community plugin for this first step.

If you downloaded the Student Vault, open its extracted folder below. It already contains the folders, templates, and worksheets for the practice exercise. The later sections offer additions for your own research; follow only the ones your task needs.

Step 1: install and configure Obsidian

1.1 download Obsidian

Download Obsidian for your operating system from obsidian.md (opens in a new tab), install it, and open the application.

1.2 open a starter or create an empty vault

For a downloaded Student Vault:

1. Extract the ZIP into a folder you can find again.
2. Open Obsidian's vault switcher. Next to Open folder as vault, select Open.
3. Select the extracted folder containing Home.md.
4. Open Home.md, then START-HERE.md. Follow its steps to duplicate the Session 2 worksheet, move it into notes, and reopen your copy.

For an empty research vault:

1. Select Create new vault.
2. Name it Research, choose a location, and select Create.
3. Create a note, type a short line, then open another note and return. Check that your text remains.

Obsidian saves edits automatically. Its vault guide (opens in a new tab) explains both opening an existing folder and creating an empty vault.

1.3 keep the first setup simple

Keep Restricted Mode on while you open, copy, and edit notes. The Student Vault's exercises need no community plugins. Once you can reopen a saved working note, continue with its START-HERE.md; you can stop this setup guide here.

Add a plugin later only for a task that needs it. In Settings → Community plugins, turn on community plugins, then browse for the one you chose. See Obsidian's plugin security guidance (opens in a new tab) before enabling third-party code.

1.4 essential Obsidian navigation

Press Cmd+E on Mac or Ctrl+E on Windows or Linux to switch between editing and reading a note. In editing view, change the text. In reading view, follow its links and check the formatted result.

Other shortcuts:

• Cmd/Ctrl+P: open the command palette
• Cmd/Ctrl+O: find a note with the quick switcher
• Cmd/Ctrl+Click: open a link in a new tab

Step 2: choose a folder structure

Keep the Student Vault’s folders if you started with that download. Its worksheet paths depend on them.

For an empty research vault, this is one possible structure. Create only the folders your work needs:

/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)

To add a folder, right-click in the file list and select New folder.

Step 3: Zotero integration options

Skip this section for the fictional practice exercise. Add an integration when you want to bring Zotero notes into your vault. Choose one route and follow its own import or sync instructions.

Step 4: optional plugins

These plugins serve different tasks. None is required to complete the Student Vault exercises.

4.1 Dataview (opens in a new tab) for queries

Create dynamic tables and queries from your notes.

In Community plugins, find Dataview, then install and enable it. For example:

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

4.2 Templater (opens in a new tab) for dynamic templates

Advanced templates with dynamic content.

In Community plugins, install and enable Templater. Set its template folder to Templates in the plugin settings.

4.3 citations plugin (opens in a new tab)

Pandoc-style citations without full Zotero integration.

In Community plugins, install and enable Citations. Configure a BibTeX export from Zotero for it to read.

4.4 Obsidian MCP server (for AI access)

Connect Cherry Studio through the Obsidian MCP server (opens in a new tab). It exposes write and delete tools as well as reads; review the available tools and your host's approval settings before connecting a research vault.

1. Install Python 3.11 or newer and uv.
2. In Obsidian, install and enable Local REST API (opens in a new tab) from Community plugins.
3. Enable its server and obtain the API key from the plugin settings.
4. In Cherry Studio, add a stdio MCP server with command uvx, argument mcp-obsidian, and environment variable OBSIDIAN_API_KEY set to that key. The default host is 127.0.0.1 and port is 27124.
5. Keep the key out of shared configuration and source control. Test on a disposable note before allowing changes to research material.

Step 5: create templates

The Student Vault already has plain Markdown templates you can copy without a plugin. The examples below are optional starting points for a separate research vault. Their placeholders need an appropriate template or import tool; copying the text alone does not fill them.

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

These settings refer to the optional folder structure in Step 2. Keep your existing paths if you are following the Student Vault exercise.

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

Follow the import or sync instructions for the integration you chose in Step 3. Plugin commands differ; installing ZotLit or Better Notes does not install the separate Zotero Integration plugin.

Start with one paper. Check the imported title, citation key, source link, and annotations before importing more. Keep your interpretation separate from the imported material.

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