How to Use the KEGG MCP in VS Code Copilot
Give your entire VS Code Copilot team direct access to KEGG genomic records and drug interaction data via a shared config.
Works with every AI agent you already use
…and any MCP-compatible client
Connect KEGG MCP to VS Code Copilot
Create your Vinkius account to connect KEGG 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.
Shared KEGG Access in VS Code Copilot
The `kegg_get` tool retrieves flat-file genomic database entries directly into your team's Copilot Chat. Because you configure this MCP Server in a shared `.vscode/mcp.json` file, every developer on the repo can pull the exact same human gene records. It standardizes how your engineering team accesses biological data. Before running complex scripts, `kegg_info` verifies the current database release. Your entire organization stays aligned on the same data version. Nobody wastes time debugging a parser that broke due to an unseen schema update.
Resolve Genomic ID Conflicts
The `kegg_conv` tool translates outside identifiers into native KEGG formats right inside your editor. When a developer asks Copilot to map NCBI IDs from a legacy database, it handles the translation instantly using this MCP setup. You stop writing custom regex to clean up mismatched biological names. Next, `kegg_link` finds related entries using those newly mapped IDs. Copilot can trace a specific compound to all its linked pathways and generate the corresponding SQL or API calls. Your team builds cross-referencing features much faster.
Build Safer Interaction Apps
The `kegg_ddi` tool finds adverse drug-drug interactions while you build healthcare applications. You can prompt Copilot to test your alert logic by fetching real metabolic conflicts from the database. The AI writes test cases based on actual clinical data, not mocked strings. To populate dropdowns or search bars in your app, `kegg_list` grabs the full list of organisms or pathways. If you need a specific subset, `kegg_find` searches by keyword or chemical data. The agent writes the exact frontend components needed to display these lists.
Set up KEGG 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.jsonin your workspace. - 2
Add the KEGG 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 KEGG tools listed. Try asking: "List my recent KEGG transactions" and Copilot will invoke them automatically.
{
"mcpServers": {
"kegg-mcp": {
"url": "https://edge.vinkius.com/[YOUR_TOKEN_HERE]/mcp"
}
}
}Independent Platform Disclaimer: Vinkius is an independent platform and is not affiliated with, endorsed by, sponsored by, verified by, or otherwise authorized by KEGG. 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 KEGG MCP in VS Code Copilot
Use it with your favorite AI tools
Connect this server to Cursor, Claude, VS Code, and more.
Start using the KEGG MCP today
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