How to Use the KEGG MCP in Claude Code

Q: Can Claude Code use KEGG to map pathways?

Indeed. You can instruct Claude Code to use kegglink to find pathway associations and pipe that data into your own analysis scripts.

Claude Code runs KEGG queries in your terminal for automated genomic pipelines.

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Connect KEGG MCP to Claude Code

Create your Vinkius account to connect KEGG 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 KEGG with Claude Code

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Headless KEGG tool execution in Claude Code

Claude Code pipes `kegg_info` and `kegg_list` output directly into your shell scripts. It handles the data flow for your CI/CD pipelines without a GUI. You get raw, actionable data at the command line. Claude Code executes the queries, parses the results, and prepares them for your next deployment step.

Batch process ID conversions with Claude Code

Use `kegg_conv` to translate massive sets of genomic IDs in bulk. Claude Code runs these tasks headlessly to keep your build times low. It handles the API interaction reliably. Claude Code triggers the conversion, captures the response, and writes the translated IDs to your logs.

Automate drug-drug interaction lookups in Claude Code

Claude Code utilizes `kegg_ddi` to verify drug safety in your automated tests. It checks your compound lists against KEGG data before finishing the build. You maintain strict safety standards without manual review. Claude Code alerts you to interactions by failing the test suite if a dangerous combination is found.

Setup guide

Set up KEGG 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 kegg-mcp with a green status indicator.
3

Start using tools

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

Terminal

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

Get your connection token →

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

Get your connection token →

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Common questions about KEGG MCP in Claude Code

Use the tool execution command in your terminal. Tell Claude Code to run `kegg_find` with your search string to get immediate results in your shell output.

Indeed. You can instruct Claude Code to use `kegg_link` to find pathway associations and pipe that data into your own analysis scripts.

Only locally. Claude Code maintains a record of the commands it ran in your session history, keeping your interactions contained to your machine.

The server is managed by Vinkius. You just need to run the standard refresh command in your terminal to pull the latest tool definitions.

The server uses a zero-trust architecture. Your genomic IDs and query parameters are encrypted during transit to the KEGG API, ensuring no third party can intercept your research.

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