🛡️ Academic Research Workflow Template (Obsidian + Zotero)

Welcome! This is a simple and powerful template to help you organize your academic research notes, reading lists, and coding projects in one place.

It connects Zotero (for saving and reading PDFs) with Obsidian (for taking notes and linking ideas), keeping everything neat and automatic.

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⚡ Quick Start (Setup Guide)

To get this automated system running, you need to install and configure two Obsidian plugins:

1. Dataview (to automatically create tables of your papers).
2. Zotero Integration (to sync notes and highlights from Zotero).

👉 Click here to open the step-by-step Setup Guide to configure these plugins easily.

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📂 1. Folder Structure Explained Simply

Here is what each folder and file is used for:

• README.md: This guide.
• Workflow-Plugins-Setup-Guide.md: Step-by-step instructions to set up the plugins and Git.
• 00-Templates/: Contains pre-made layouts (templates) for paper notes and project overviews.
• 01-Reading-Queue.md: Your dashboard. It automatically lists all the papers you are reading.
• 02-Papers/: The folder where all your individual paper notes are stored.
• 03-Research-Gaps.md: A central page to write down unsolved research questions and ideas.
• 04-Topics.md: A page to map out themes, keywords, and fields of interest.
• Projects/: The directory for your code and experiments. Each project folder here is kept separate.

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🔄 2. Simple Daily Workflow (How to use it)

Here is the step-by-step process of using this setup:

graph TD
    A[New Paper PDF] -->|Drop into| B(Zotero App)
    B -->|Read, highlight & comment| B
    B -->|Obsidian: Ctrl+P -> Import Paper| C(02-Papers/ folder)
    C -->|Automatically appears in| D(01-Reading-Queue.md)
    C -->|Write new ideas in| E(03-Research-Gaps.md)
    E -->|Start coding in| F(Projects/ folder)

Step 2.1: Add & Read in Zotero

1. Drag and drop your paper PDF into Zotero.
2. Double-click the PDF inside Zotero to open it.
3. Highlight important sentences and write notes/comments on the PDF.

Step 2.2: Sync to Obsidian

1. Open Obsidian. Press Ctrl + P to open the command search.
2. Type Zotero Integration: Import Paper and press Enter.
3. Type the name of the paper or author, select it, and press Enter.
4. Obsidian will automatically create a neat summary file in 02-Papers/ containing all your highlights and comments!

Step 2.3: Check Your Reading Queue

• Open 01-Reading-Queue.md and switch to Reading View (Ctrl + E).
• Your paper will automatically show up in the table, sorted by publication year.

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🚦 3. Paper Reading Status

You can change the reading status of any paper by editing the status field in the metadata block at the top of the paper note:

• status: "❣️todo" : Unread paper waiting in the queue.
• status: "📖reading" : Currently reading.
• status: "🟢read" : Completed reading and note taking.

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🐙 4. Git Architecture (Managing Notes & Code Separately)

To prevent errors like "Git inside Git" and keep your personal notes secure, this template uses a Decoupled Git Architecture:

1. Your Research Notes (Vault Root):
   • The main folder is a Git repository for your notes, templates, and reading lists.
   • The root .gitignore is pre-configured to ignore the Projects/ folder.
   • You can push your notes to a private GitHub repository safely.
2. Your Coding Projects (Projects/):
   • Each folder inside Projects/ (e.g., Projects/Project1/) can be an independent Git repository.
   • You can initialize Git inside each project folder separately and push the code to a separate public or private GitHub repository.
   • Since the root Git ignores Projects/, there will be no conflicts or leaked configurations.