From Chaos to Knowledge: Organizing Your Research Notes with Obsidian, Zotero, and Git#

Speaker: Rohan Rahatgaonkar • Date: 24-10-2025

When / Where#

Friday 24th, October at 11:30 am • Sala Seminario

Abstract#

Your research brain is overflowing—dozens of papers read, hundreds of notes scattered across files, key insights buried and forgotten. Finding that one critical result from three months ago? Impossible. Managing versions of your evolving understanding? Chaotic. In this session, I’ll show you how to build an organized, interconnected research knowledge base using Obsidian for note-taking, Zotero for reference management, and Git for version control. By integrating these tools, you can seamlessly import annotated papers, synthesize observations into interconnected notes, and track how your ideas evolve over time. Whether you’re connecting stellar physics across multiple simulations, tracking conflicting theoretical explanations, or synthesizing survey data into coherent arguments, this workflow transforms your scattered research notes into a coherent, searchable knowledge graph. I’ll demonstrate practical setups for literature management, note organization, and collaborative research.

Git + Obsidian#

Committing to Git Advice:#

  • Commit Frequently: It’s a good practice to commit your changes often, even if they are small. This helps track the history of changes and makes it easier to roll back if needed.

  • Write Descriptive Commit Messages: Ensure your commit messages clearly describe the changes made. This is especially important for tracking your progress or when collaborating with others. Use messages like:

    • “Updated README with Obsidian setup instructions”

    • “Added meeting notes for 10/15/2024”

    • “Initial commit of thesis project folder structure”

  • Use Git Push Regularly: After committing, don’t forget to push your changes to GitHub. This ensures your work is backed up remotely.

Steps to Set Up GitHub for Obsidian Vault:#

  1. Create a GitHub Repository:

    • Go to GitHub, click on the + in the top right, and choose New Repository.

    • Name your repository Thesis-Project-Vault.

    • Add an optional description.

    • Choose Private.

    • Do not initialize with a README if you already have one in your Obsidian vault.

    • Click Create repository.

  2. Initialize Git in Your Local Vault:

    • Open the terminal in the folder where your Obsidian vault is stored.

    • Initialize a Git repository: bash git init

    • Add your GitHub remote:

  3. Stage and Commit Your Files:

    • Add and commit your files: bash git add . git commit -m “Initial commit”

  4. Push to GitHub:

    • Push your commit to the GitHub repository: bash git push -u origin master

Using a Personal Access Token (PAT) for Authentication:#

  1. Generate a Token:

    • Go to GitHub and navigate to Settings > Developer Settings > Personal Access Tokens.

    • Click Generate new token, and give it appropriate scopes (repo for repository access).

    • Copy the generated token.

  2. Set Git to Use HTTPS and Store Credentials:

    • If using HTTPS, set the remote URL: bash git remote set-url origin username/Thesis-Project-Vault.git

    • When prompted for a username and password, use your GitHub username and the Personal Access Token as the password.

  3. Store Credentials Locally:

    • To store the token so Git doesn’t ask every time: bash git config –global credential.helper store

Installing and Configuring the Obsidian Git Plugin:#

  1. Install the Plugin:

    • Open Obsidian.

    • Go to Settings > Community Plugins > Browse and search for Obsidian Git.

    • Install and enable the plugin.

  2. Configure the Plugin:

    • In *Settings, scroll down to *Obsidian Git.

    • Set the Auto pull and Auto push intervals if you want automatic syncing.

    • Test the configuration by using the command palette (Ctrl + P or Cmd + P) and searching for:

      • Git: Commit all changes

      • Git: Push

      • Git: Pull

Testing and Verifying Setup:#

  1. Verify on GitHub:

    • After performing a push, check your GitHub repository to ensure the files have been successfully uploaded.

  2. Sync with Git in Obsidian:

    • Use the Command Palette in Obsidian to manually commit, push, or pull changes as needed.

  3. Optional: Developer Console for Logs:

    • Open Developer Tools (Ctrl + Shift + I) in Obsidian to check for any errors or logs related to Git operations.

Conclusion:#

By following these steps, you have successfully configured your Obsidian vault with Git and GitHub for version control. Regular commits and pushes will ensure that your work is backed up and easy to track over time.

Files#