How to Use the Zenodo MCP in Cline

Q: How does Cline access and list Zenodo records?

You call listrecords. The MCP Server returns a full index of all published scientific research datasets. You can then loop through this list in your code to build out components.

Q: Can I version data using Cline and Zenodo for my project?

Absolutely. Use newversiondeposition followed by uploaddepositionfile. This sequence lets you track every iteration of your source material, which is crucial for reproducibility.

Q: What if I want to list all possible depositions? Does the MCP Server handle it?

Yes. The listdepositions tool lets you quickly check every single deposition associated with your account ID, giving you a manifest of everything stored.

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Create your Vinkius account to connect Zenodo to Cline 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 Cline

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Retrieve Dataset Metadata for Components

Need to write a dashboard that references external data? Use `get_record` or `list_records` to pull metadata directly into your component. You get the ID, and Cline knows how to pass that context. This makes it easy to mock API calls locally because you're pulling from an actual Zenodo MCP Server source.

Programmatic Dataset Creation

Start a new data project directly in your terminal environment. You can use `create_deposition` and optionally provide metadata right in the script. The agent handles the setup. After creating it, you immediately follow up with `upload_deposition_file` to populate the initial text file needed for testing.

Lifecycle Control via Scripting

If a feature breaks or needs refinement, don't worry. You can use `discard_deposition` to throw away bad edits before committing them. Alternatively, you might need to update the existing record using `update_deposition`. This level of control means your code always interacts with reliable, managed data sources.

Setup guide

Set up Zenodo MCP in Cline

Prerequisites

VS Code with Cline extension installed
Active Vinkius subscription with a valid endpoint token

1

Open Cline MCP settings

Click the Cline icon in the VS Code sidebar to open the Cline panel. Then click the MCP Servers icon (server stack) at the top-right corner of the panel.
2

Add a remote server

Click "Remote Servers" at the top, then click "Add Remote MCP". In the Name field, type zenodo-mcp. In the URL field, paste your Vinkius endpoint: https://edge.vinkius.com/[YOUR_TOKEN_HERE]/mcp. Get your token from cloud.vinkius.com.
3

Enable the server

After saving, the server appears in the Cline MCP panel. Toggle the switch to enable it. The status indicator turns green when the connection is live.
4

Start using tools

Return to the Cline chat and ask: "Check my latest Zenodo refund status." Cline will discover the available tools and request your approval before invoking each one — giving you full control over every action.

Cline MCP Settings

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

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Common questions about Zenodo MCP in Cline

You call `list_records`. The MCP Server returns a full index of all published scientific research datasets. You can then loop through this list in your code to build out components.

Absolutely. Use `new_version_deposition` followed by `upload_deposition_file`. This sequence lets you track every iteration of your source material, which is crucial for reproducibility.

Use it when you need to modify data that's already published but needs minor text changes. `edit_deposition` allows this without requiring a full re-upload, saving time in your development cycle.

Yes. The `list_depositions` tool lets you quickly check every single deposition associated with your account ID, giving you a manifest of everything stored.

The server manages scientific research datasets. This includes the core metadata, uploaded file contents, and versioning history for your academic work.

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