How to Use the Zenodo MCP in VS Code Copilot

Q: How do I integrate Zenodo data into my codebase using VS Code Copilot?

You commit the configuration to .vscode/mcp.json. This makes the tools available to every developer on your team, ensuring consistent access to the scientific records.

Q: Can I list all existing depositions using Zenodo with VS Code Copilot?

Yes, run listdepositions through the agent. This tool fetches a complete inventory of every deposition associated with the configured account, useful for auditing.

Q: What is the process for publishing data using Zenodo with VS Code Copilot?

The team uses publishdeposition when the dataset is finalized. Because this is a shared tool, it's crucial to coordinate timing; once published, you can't delete it.

Q: Does Zenodo support local file access in VS Code Copilot?

While focused on repository-level sharing via .vscode/mcp.json, the structured nature of the configuration makes it ideal for team development that includes local data sources.

Standardize scientific data access across the team with Zenodo for VS Code Copilot.

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Connect Zenodo MCP to VS Code Copilot

Create your Vinkius account to connect Zenodo to VS Code Copilot 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 VS Code Copilot

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Manage Dataset Context

The `create_deposition` tool allows you to define a new deposition context, which gets committed to the repo's MCP configuration. Team members can use this shared resource knowing the data source is standardized. Developers can then use `edit_deposition` or `update_deposition` via Copilot Chat Agent mode. This ensures every engineer on the team works with the same, current dataset information.

Fetch and Reference Records

You get live data by calling `get_record`. When an engineer asks a question in Copilot Chat, it uses this tool to pull the required Zenodo record details. The result is instantly available for code generation. Need to see all possible records? Running `list_records` provides a comprehensive list of IDs and titles that can be used as inputs across multiple team projects.

Version Control and File Handling

Adding data is easy with `upload_deposition_file`. For versioning, the `new_version_deposition` tool handles tracking changes automatically. This builds an auditable trail of every dataset update right in your repository. If you need to know what files belong where, running `list_deposition_files` gives a clear inventory that can inform file handling functions across the team.

Setup guide

Set up Zenodo MCP in VS Code Copilot

Prerequisites

VS Code 1.99 or later with GitHub Copilot extension
Active Vinkius subscription with a valid endpoint token

1

Open MCP configuration

Open the Command Palette (Cmd+Shift+P / Ctrl+Shift+P) and run "MCP: Add Server". Select HTTP (Streamable) as the server type. VS Code will create .vscode/mcp.json in your workspace.
2

Add the Zenodo MCP

Paste the JSON snippet shown on the right into your .vscode/mcp.json. Replace [YOUR_TOKEN_HERE] with your endpoint token from cloud.vinkius.com.
3

Switch to Agent mode

Open Copilot Chat (Cmd+Shift+I / Ctrl+Shift+I) and switch to Agent mode using the dropdown. MCP tools are only available in Agent mode — they do not appear in Edit or Ask modes.
4

Verify the connection

In the Copilot Chat input, type # to list available tools. You should see the Zenodo tools listed. Try asking: "List my recent Zenodo transactions" and Copilot will invoke them automatically.

.vscode/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 VS Code Copilot

You commit the configuration to `.vscode/mcp.json`. This makes the tools available to every developer on your team, ensuring consistent access to the scientific records.

Yes, run `list_depositions` through the agent. This tool fetches a complete inventory of every deposition associated with the configured account, useful for auditing.

The team uses `publish_deposition` when the dataset is finalized. Because this is a shared tool, it's crucial to coordinate timing; once published, you can't delete it.

While focused on repository-level sharing via `.vscode/mcp.json`, the structured nature of the configuration makes it ideal for team development that includes local data sources.

This MCP Server handles deposition IDs, record IDs, metadata, and file contents. The tool manages these identifiers and text files within a controlled team environment.

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