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

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Claude Code is Anthropic's agentic CLI for terminal-first development. Add Zenodo as an MCP server in one command and Claude Code will discover every tool at runtime. ideal for automation pipelines, CI/CD integration, and headless workflows via Vinkius.

Ask AI about this MCP Server for Claude Code

The Zenodo MCP Server for Claude Code 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

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Classic Setup·bash
# Your Vinkius token. get it at cloud.vinkius.com
claude mcp add zenodo --transport http "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.

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Fully ManagedVinkius Servers
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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 Code registers Zenodo as an MCP server in a single terminal command. Once connected, Claude Code discovers all 14 tools at runtime and can call them headlessly. ideal for CI/CD pipelines, cron jobs, and automated workflows where Zenodo data drives decisions without human intervention.

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  • Deposition Management — Create new unpublished depositions, update metadata, and manage your research drafts directly from the AI.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 Code 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 Code

When Claude Code 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 Code via MCP

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

01

Install Claude Code

Run npm install -g @anthropic-ai/claude-code if not already installed
02

Add the MCP Server

Run the command above in your terminal
03

Verify the connection

Run claude mcp to list connected servers, or type /mcp inside a session
04

Start using Zenodo

Ask Claude: "Using Zenodo, show me...". 14 tools are ready

Why Use Claude Code with the Zenodo MCP Server

Claude Code provides unique advantages when paired with Zenodo through the Model Context Protocol.

01

Single-command setup: `claude mcp add` registers the server instantly. no config files to edit or applications to restart

02

Terminal-native workflow means MCP tools integrate seamlessly into shell scripts, CI/CD pipelines, and automated DevOps tasks

03

Claude Code runs headlessly, enabling unattended batch processing using Zenodo tools in cron jobs or deployment scripts

04

Built by the same team that created the MCP protocol, ensuring first-class compatibility and the fastest adoption of new protocol features

Zenodo + Claude Code Use Cases

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

01

CI/CD integration: embed Zenodo tool calls in your deployment pipeline to validate configurations or fetch secrets before shipping

02

Headless batch processing: schedule Claude Code to query Zenodo nightly and generate reports without human intervention

03

Shell scripting: pipe Zenodo outputs into other CLI tools for data transformation, filtering, and aggregation

04

Infrastructure monitoring: run Claude Code in a cron job to query Zenodo status endpoints and alert on anomalies

Example Prompts for Zenodo in Claude Code

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

01

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

02

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

03

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

Troubleshooting Zenodo MCP Server with Claude Code

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

01

Command not found: claude

Ensure Claude Code is installed globally: npm install -g @anthropic-ai/claude-code
02

Connection timeout

Check your internet connection and verify the Edge URL is reachable

Zenodo + Claude Code FAQ

Common questions about integrating Zenodo MCP Server with Claude Code.

01

How do I add an MCP server to Claude Code?

Run claude mcp add --transport http "" in your terminal. Claude Code registers the server and discovers all tools immediately.
02

Can Claude Code run MCP tools in headless mode?

Yes. Claude Code supports non-interactive execution, making it ideal for scripts, cron jobs, and CI/CD pipelines that need MCP tool access.
03

How do I list all connected MCP servers?

Run claude mcp in your terminal to see all registered servers and their status, or type /mcp inside an active Claude Code session.

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