How to Use the Zenodo MCP in Claude

Q: How do I search for datasets using Zenodo with Claude Desktop?

You use the listrecords tool. Your AI client sends a query, and it returns a list of published record IDs you can then examine further in the chat.

Q: Can I create a deposition using Zenodo with Claude Desktop?

Absolutely. The createdeposition tool lets your agent establish a new deposition on Zenodo, giving you a place to upload and organize your data right away.

Q: What if I need to update metadata for my record using Zenodo with Claude Desktop?

You call updatedeposition or use the specific tools like editdeposition. Your agent makes sure the changes are applied correctly, keeping your research up-to-date.

Manage scientific datasets on Zenodo. Works perfectly with Claude Desktop.

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Connect Zenodo MCP to Claude Desktop

Create your Vinkius account to connect Zenodo to Claude Desktop and route execution through our secure gateway. The platform manages server hosting, runtime updates, and security layers. Configuration requires no manual server provisioning.

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Setup Zenodo with Claude Desktop

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Track and Modify Depositions

You can create a new Zenodo deposition using `create_deposition`. Need to adjust something? Use `edit_deposition` on published works, or modify an existing one with `update_deposition`. This lets you manage the life cycle of your research data directly from Claude Desktop. It's important to know that once you call `publish_deposition`, deletion isn't an option. However, if you messed up before publishing, you can always run `discard_deposition` to throw out unsaved changes.

Search and Retrieve Records

Get immediate access to published data using the `get_record` tool. You simply provide an ID, and your agent pulls the full Zenodo record details right into the chat. Checking existing works is fast; try running `list_records` first if you don't know which records exist. Need a whole list of available research? The `list_depositions` tool fetches all depositions associated with your account, giving you a clear overview before you select what to work on next.

Handle Files and Versions

Uploading data is straightforward; use `upload_deposition_file` to add text files to any deposition. If the dataset changes, don't worry—the `new_version_deposition` tool handles versioning automatically. You just run it, and Zenodo tracks the update. Want to see what files are already attached? Running `list_deposition_files` shows you everything in a specific deposition. Remember that deleting individual files is handled by `delete_deposition_file`.

Setup guide

Set up Zenodo MCP in Claude Web or Desktop

1

Open Claude Settings

Go to claude.ai, click your profile icon, then navigate to Customize → Connectors.
2

Add Custom Connector

Click the "+" button and select Add custom connector. Paste your Vinkius endpoint URL: https://edge.vinkius.com/[YOUR_TOKEN_HERE]/mcp Replace [YOUR_TOKEN_HERE] with your token from cloud.vinkius.com. For OAuth-protected servers, expand Advanced settings to add credentials.
3

Start a conversation

Open a new chat. The Zenodo MCP tools are available immediately — no restart needed.

Endpoint URL

https://edge.vinkius.com/[YOUR_TOKEN_HERE]/mcp

No configuration file needed — paste the URL directly in the Claude web interface.

Available on Free (1 connector), Pro, Max, Team, and Enterprise plans.

Prerequisites

Claude Desktop installed (macOS or Windows)
Active Vinkius subscription with a valid endpoint token

1

Open Claude Desktop Settings

Click the menu icon at the top-left corner, go to Settings → Developer → Edit Config. This opens claude_desktop_config.json in your default text editor.
2

Paste the Zenodo MCP configuration

Copy the JSON snippet on the right into the mcpServers object. Replace [YOUR_TOKEN_HERE] with your endpoint token from cloud.vinkius.com.
3

Restart Claude Desktop

Close and reopen the application. Claude needs a full restart to load new MCPs — refreshing a conversation is not enough.
4

Verify the connection

Open a new conversation. Click the 🔌 icon at the bottom of the message input. You should see tools listed under zenodo-mcp.

json

{
  "mcpServers": {
    "zenodo-mcp": {
      "url": "https://edge.vinkius.com/[YOUR_TOKEN_HERE]/mcp"
    }
  }
}

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Independent Platform Disclaimer: Vinkius is an independent platform and is not affiliated with, endorsed by, sponsored by, verified by, or otherwise authorized by Zenodo. All third-party trademarks, logos, and brand names are the property of their respective owners. Their use on this website is strictly for informational purposes to identify service compatibility and interoperability.

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Common questions about Zenodo MCP in Claude Desktop

You use the `list_records` tool. Your AI client sends a query, and it returns a list of published record IDs you can then examine further in the chat.

Absolutely. The `create_deposition` tool lets your agent establish a new deposition on Zenodo, giving you a place to upload and organize your data right away.

You call `update_deposition` or use the specific tools like `edit_deposition`. Your agent makes sure the changes are applied correctly, keeping your research up-to-date.

Yes. The Claude Desktop app allows your agent to reach your filesystem and local databases on localhost, making it great for developers who need to integrate local files into their workflows.

This MCP Server primarily touches deposition IDs, record IDs, metadata (like titles and descriptions), and file contents. Your agent manages these structured identifiers and text-based records.

Use it with your favorite AI tools

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