Zenodo MCP Server for Claude DesktopGive Claude Desktop instant access to 14 tools to Create Deposition, Delete Deposition, Delete Deposition File, and more

Name: Zenodo
Price: 29 USD
Availability: InStock
Rating: 0.2 (1 reviews)
Author: Vinkius

GDPR Free for Subscribers

Claude Desktop is Anthropic's native application for interacting with Claude AI models on macOS and Windows. It was the first consumer application to ship with built-in MCP support, making it the reference implementation for the Model Context Protocol standard.

Ask AI about this MCP Server for Claude Desktop

Open in ChatGPT Open in Claude Open in Perplexity

The Zenodo MCP Server for Claude Desktop is a standout in the Knowledge Management category — giving your AI agent 14 tools to work with, ready to go from day one.

Built for AI Agents by Vinkius

Vinkius delivers Streamable HTTP and SSE to any MCP client

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ChatGPT

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JetBrains

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+ other MCP clients

Classic Setup·json

{
  "mcpServers": {
    "zenodo": {
      // Your Vinkius token. get it at cloud.vinkius.com
      "url": "https://edge.vinkius.com/[YOUR_TOKEN_HERE]/mcp"
    }
  }
}

RecommendedModern Approach — Zero Configuration

Vinkius Desktop App

The modern way to manage MCP Servers — no config files, no terminal commands. Install Zenodo and 4,000+ MCP Servers from a single visual interface.

Download Free Open SourceNo signup required

Fully ManagedVinkius Servers

60%Token savings

High SecurityEnterprise-grade

IAMAccess control

EU AI ActCompliant

DLPData protection

V8 IsolateSandboxed

Ed25519Audit chain

<40msKill switch

Stream every event to Splunk, Datadog, or your own webhook in real-time

* Every MCP server runs on Vinkius-managed infrastructure inside AWS - a purpose-built runtime with per-request V8 isolates, Ed25519 signed audit chains, and sub-40ms cold starts optimized for native MCP execution. See our infrastructure

About Zenodo MCP Server

Connect your Zenodo account to any AI agent to streamline your scientific research workflows and data management through natural conversation.

Claude Desktop is the definitive way to connect Zenodo to your AI workflow. Add Vinkius Edge URL to your config, restart the app, and Claude immediately exposes all 14 tools in the chat interface. ask a question, Claude calls the right tool, and you see the answer. Zero code, zero context switching.

What you can do

Deposition Management — Create new unpublished depositions, update metadata, and manage your research drafts directly from the AI.
Record Discovery — Search and list public records across the entire Zenodo database to find relevant research, software, or datasets.
File Inspection — List all files attached to specific depositions to understand the contents of a research package.
Metadata Control — Precisely update titles, creators, descriptions, licenses, and access rights for your unpublished work.
Version Tracking — Retrieve specific deposition details using unique IDs to monitor the status of your submissions.

The Zenodo MCP Server exposes 14 tools through the Vinkius. Connect it to Claude Desktop in under two minutes — credentials fully managed, no infrastructure to provision, no vendor lock-in. Your configuration, your data, your control.

All 14 Zenodo tools available for Claude Desktop

When Claude Desktop connects to Zenodo through Vinkius, your AI agent gets direct access to every tool listed below — spanning open-access, research-data, metadata-management, and more. Every call runs in a secure, isolated environment with full audit visibility. Beyond a simple connection, you get real-time monitoring of agent activity, enterprise governance, and optimized token usage.

create

Create deposition on Zenodo

You can optionally provide metadata. Create a new Zenodo deposition

delete

Delete deposition on Zenodo

Note: Only unpublished depositions can be deleted. Delete an unpublished Zenodo deposition

delete

Delete deposition file on Zenodo

Delete a file from a Zenodo deposition

discard

Discard deposition on Zenodo

Discard edits on a Zenodo deposition

edit

Edit deposition on Zenodo

Edit a published Zenodo deposition

get

Get deposition on Zenodo

Retrieve a Zenodo deposition by ID

get

Get record on Zenodo

Retrieve a published Zenodo record by ID

list

List deposition files on Zenodo

List files in a Zenodo deposition

list

List depositions on Zenodo

List Zenodo depositions

list

List records on Zenodo

Search published Zenodo records

new

New version deposition on Zenodo

Create a new version of a Zenodo deposition

publish

Publish deposition on Zenodo

WARNING: Once published, a deposition cannot be deleted. Publish a Zenodo deposition

update

Update deposition on Zenodo

Update a Zenodo deposition

upload

Upload deposition file on Zenodo

Upload a text file to a Zenodo deposition

Connect Zenodo to Claude Desktop via MCP

Follow these steps to wire Zenodo into Claude Desktop. The entire setup takes under two minutes — your credentials stay safe behind Vinkius.

Open Claude Desktop Settings

Go to Settings → Developer → Edit Config to open claude_desktop_config.json

Add the MCP Server

Paste the configuration above into the mcpServers section

Restart Claude Desktop

Close and reopen Claude Desktop to load the new server

Start using Zenodo

Look for the 🔌 icon in the chat. your 14 tools are now available

Why Use Claude Desktop with the Zenodo MCP Server

Claude Desktop by Anthropic provides unique advantages when paired with Zenodo through the Model Context Protocol.

Claude Desktop is the reference MCP client. it was designed alongside the protocol itself, ensuring the most complete and stable MCP implementation available

Zero-code configuration: add a server URL to a JSON file and Claude instantly discovers and exposes all available tools in the chat interface

Claude's extended thinking capability lets it reason through multi-step tool usage, chaining multiple API calls to answer complex questions

Enterprise-grade security with local config storage. your tokens never leave your machine, and connections go directly to Vinkius Edge network

Zenodo + Claude Desktop Use Cases

Practical scenarios where Claude Desktop combined with the Zenodo MCP Server delivers measurable value.

Interactive data exploration: ask Claude to query DNS records, look up WHOIS data, and cross-reference results in a single conversation

Ad-hoc security audits: type a domain name and let Claude enumerate subdomains, check DNS history, and flag configuration anomalies. all through natural language

Executive briefings: generate comprehensive domain intelligence reports by asking Claude to compile findings into a formatted summary

Learning and training: new team members can explore API capabilities conversationally without needing to read documentation

Example Prompts for Zenodo in Claude Desktop

Ready-to-use prompts you can give your Claude Desktop agent to start working with Zenodo immediately.

"Search for public Zenodo records related to 'machine learning in healthcare'."

"Create a new Zenodo deposition for a dataset titled 'Global Temperature Trends 2023'."

"List all files currently attached to my deposition with ID 987654."

Troubleshooting Zenodo MCP Server with Claude Desktop

Common issues when connecting Zenodo to Claude Desktop through Vinkius, and how to resolve them.

Server not appearing after restart

Ensure the JSON is valid (no trailing commas). Check the file path: ~/Library/Application Support/Claude/claude_desktop_config.json (macOS) or %APPDATA%\\Claude\\ (Windows).

Authentication error

Verify your Vinkius token is correct. Go to cloud.vinkius.com to regenerate it if needed.

Tools not showing in chat

Click the 🔌 icon at the bottom of the chat input. If it shows 0 tools, the server may still be connecting. wait a few seconds.

Zenodo + Claude Desktop FAQ

Common questions about integrating Zenodo MCP Server with Claude Desktop.

How does Claude Desktop discover MCP tools?

When Claude Desktop starts, it reads the claude_desktop_config.json file and connects to each configured MCP server. It calls the tools/list endpoint to fetch the schema for every available tool, then surfaces them as clickable options in the chat interface via the 🔌 icon.

What happens if the MCP server is temporarily unavailable?

Claude Desktop handles disconnections gracefully. if the server is unreachable at startup, the tools simply won't appear. Once the server becomes available again, restarting Claude Desktop will re-establish the connection. There is no timeout penalty or error loop.

Can I connect multiple MCP servers simultaneously?

Yes. You can add as many servers as you need in the mcpServers section of the config file. Each server appears as a separate tool provider, and Claude can use tools from multiple servers in a single conversation turn.

Is there a limit on the number of tools per server?

Claude Desktop can handle hundreds of tools per server. However, for optimal LLM performance, Vinkius servers are designed to expose focused, well-documented tool sets rather than overwhelming the model with too many options.

Does Claude Desktop support Streamable HTTP transport?

Yes. Claude Desktop supports both SSE (Server-Sent Events) and the newer Streamable HTTP transport that Vinkius uses. Simply provide the server URL. Claude auto-negotiates the transport protocol.