Knowledge Hub: Obsidian Setup

Download Obsidian

Visit obsidian.md and download the installer for your operating system:

• macOS: Download DMG, drag to Applications
• Windows: Download installer, run setup
• Linux: Download AppImage or use package manager

No account required to start using Obsidian.

Create Research Vault Directory

Open your terminal and create the vault folder structure:

# Create main vault directory
mkdir ~/ResearchVault
cd ~/ResearchVault

# Create essential subfolders
mkdir "Literature Notes" Templates Projects

Expected directory structure:

ResearchVault/
├── Literature Notes/    # Paper notes from Zotero
├── Templates/          # Note templates
└── Projects/           # Research project folders

Initialize Vault in Obsidian

Launch Obsidian application.

At the vault selection screen:

1. Click "Open folder as vault"
2. Navigate to ~/ResearchVault
3. Click "Open"

Obsidian creates a hidden .obsidian folder for settings. The vault is now ready.

Enable Community Plugins

Navigate to Settings:

1. Click Settings icon (gear in bottom-left)
2. Go to Community Plugins section
3. Click "Turn on community plugins"
4. Confirm safety warning

Community plugins are now available for installation.

Install Zotero Integration Plugin

This plugin bridges Zotero and Obsidian for seamless literature notes.

Installation:

1. Settings → Community Plugins → Browse
2. Search: "Zotero Integration"
3. Install plugin by mgmeyers (22,000+ downloads)
4. Click Enable after installation

Configuration:

Navigate to Settings → Zotero Integration and configure:

Citation Export Path: ~/Documents/library.bib
Literature Note Folder: Literature Notes/
Citation Format: Pandoc
Template File: Templates/literature-note.md

Create Literature Note Template:

Save this template to Templates/literature-note.md:

---
title: {{title}}
authors: {{authors}}
year: {{year}}
doi: {{DOI}}
tags: [literature, unread]
status: unread
---

# {{title}}

**Authors**: {{authors}}
**Year**: {{year}}
**DOI**: [{{DOI}}](https://doi.org/{{DOI}})
**Citation**: `@{{citekey}}`

[Open in Zotero]({{zoteroSelectURI}})

## Summary

(What is the main argument or finding?)

## Key Points

-
-
-

## Methodology

(How did they conduct the research?)

## Relevance to My Research

(Why does this paper matter for my work?)

## Questions & Critiques

-
-

## Related Papers

-

Usage:

Right-click any item in Zotero → "Create Literature Note" → Note appears in Obsidian.

Install Dataview Plugin

Dataview lets you query your notes like a database.

Installation:

1. Settings → Community Plugins → Browse
2. Search: "Dataview"
3. Install by blacksmithgu
4. Enable plugin

Example Query 1: Track Unread Papers

Create a note called Reading Dashboard.md:

# Reading Dashboard

## Unread Papers

```dataview
TABLE status, authors, year
FROM "Literature Notes"
WHERE status = "unread"
SORT year DESC
```

This displays all unread papers with authors and publication year.

Example Query 2: Papers by Research Theme

## Machine Learning Papers

```dataview
LIST
FROM "Literature Notes"
WHERE contains(tags, "#machine-learning")
GROUP BY authors
SORT year DESC
```

Groups all machine learning papers by author.

Example Query 3: Recent Notes

## Last 7 Days

```dataview
TABLE file.ctime as "Created", status
FROM "Literature Notes"
WHERE file.ctime >= date(today) - dur(7 days)
SORT file.ctime DESC
```

Shows notes created in the past week.

Install Templater Plugin (Optional)

Templater provides advanced template automation with dynamic variables.

Installation:

1. Settings → Community Plugins → Browse
2. Search: "Templater"
3. Install by SilentVoid
4. Enable plugin

Configuration:

Settings → Templater:

Template folder location: Templates
Trigger Templater on new file creation: ON

Example: Daily Research Log Template

Create Templates/daily-log.md:

---
date: <% tp.date.now("YYYY-MM-DD") %>
type: daily-log
---

# Research Log - <% tp.date.now("dddd, MMMM DD, YYYY") %>

## Papers Read Today

<% tp.system.prompt("How many papers did you read?") %> papers

## Key Insights

-

## Tasks Completed

- [ ]

## Tomorrow's Goals

- [ ]

## Notes

Usage:

Use keyboard shortcut or command palette: "Templater: Insert Template" → Select daily-log.md