How to Use the Zenodo MCP in Claude Code

Q: How do I script finding all existing records using Zenodo and Claude Code?

Run listrecords. The output provides a JSON array of IDs for every published record. Your shell script can then iterate over this list to process each dataset individually.

Q: What's the best way to check deposition status using Zenodo and Claude Code?

Just use getdeposition with a known ID. This command pulls all current metadata, showing whether it's published or if edits are pending for your scientific research datasets.

Q: Can I manage file uploads in a script using Zenodo and Claude Code?

Yes, use uploaddepositionfile. This is perfect for CI/CD because it accepts the content as standard input (STDIN), making it easy to pipe data into the MCP Server.

Q: Does this MCP Server support listing all available depositions?

Yup. listdepositions gives you a machine-readable manifest of every deposition, letting your script build a complete inventory quickly.

Automate Scientific Data Tasks in CI/CD with Claude Code and Zenodo MCP Server.

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Connect Zenodo MCP to Claude Code

Create your Vinkius account to connect Zenodo to Claude Code 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 Code

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Batch Search Across All Deposition Records

Running a nightly cron job? Use `list_records` to get an exhaustive list of all available scientific research datasets. Your script processes this list, extracting necessary IDs for downstream tasks. This is ideal for CI/CD pipelines that need to validate against multiple external data sources.

Programmatic State Transitions

Need to deploy a dataset only after passing all tests? Use `publish_deposition` in your pipeline script. The MCP Server handles the state change, making the data accessible only when specified. You can check its current status using `get_deposition` before attempting deployment.

Versioned File Deployment

When a dependency file changes, your script needs to update it. Use `upload_deposition_file` to push the new text file. Then, immediately call `new_version_deposition` to tag the change. This ensures that every run of your pipeline uses a verifiable and version-controlled input.

Setup guide

Set up Zenodo MCP in Claude Code

Prerequisites

Claude Code CLI installed (npm install -g @anthropic-ai/claude-code)
Active Vinkius subscription with a valid endpoint token

1

Run the add command

Open your terminal and run the command shown on the right. Replace [YOUR_TOKEN_HERE] with your endpoint token from cloud.vinkius.com. Use --scope user to make it available across all projects.
2

Verify the connection

Start a Claude Code session and type /mcp to list connected servers. You should see zenodo-mcp with a green status indicator.
3

Start using tools

Ask Claude Code something like "Check my latest Zenodo transactions." It will automatically discover and invoke the available Zenodo tools.

Terminal

claude mcp add --transport http zenodo-mcp https://edge.vinkius.com/[YOUR_TOKEN_HERE]/mcp

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Prerequisites

Claude Code CLI installed
Active Vinkius subscription with a valid endpoint token

1

Open the config file

Create or edit .mcp.json in your project root for project-level scope, or ~/.claude.json for user-level scope.
2

Add the Zenodo MCP

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

Restart Claude Code

Start a new Claude Code session. Type /mcp to confirm the server is connected. The tools will be automatically available in your conversation.

.mcp.json

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

Get your connection token →

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Common questions about Zenodo MCP in Claude Code

Run `list_records`. The output provides a JSON array of IDs for every published record. Your shell script can then iterate over this list to process each dataset individually.

Just use `get_deposition` with a known ID. This command pulls all current metadata, showing whether it's published or if edits are pending for your scientific research datasets.

Yes, use `upload_deposition_file`. This is perfect for CI/CD because it accepts the content as standard input (STDIN), making it easy to pipe data into the MCP Server.

Yup. `list_depositions` gives you a machine-readable manifest of every deposition, letting your script build a complete inventory quickly.

The server handles scientific research datasets. This includes the metadata, version history, and file contents for all deposited academic work.

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Connect this server to Cursor, Claude, VS Code, and more.

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