EBI Bioinformatics Tools

This is a Model Context Protocol (MCP) server. It lets MCP clients (Claude Desktop, Claude Code, Continue, etc.) query the upstream Ebi Tools API in natural language. It is one of 100+ servers in the Bio MCP monorepo.

Connect

The server is deployed and ready at:

https://ebi-tools-mcp-server.quentincody.workers.dev/mcp

Add it to your MCP client (Claude Desktop → Settings → Developer → Edit Config):

{
  "mcpServers": {
    "ebi-tools": {
      "command": "npx",
      "args": ["mcp-remote", "https://ebi-tools-mcp-server.quentincody.workers.dev/mcp"]
    }
  }
}

For local development the server runs at http://localhost:8842/mcp (start it with ./scripts/dev-servers.sh ebi-tools):

{
  "mcpServers": {
    "ebi-tools-local": {
      "command": "npx",
      "args": ["mcp-remote", "http://localhost:8842/mcp"]
    }
  }
}

Tools

• ebi_tools_search — discover available API operations (Code Mode catalog search, 18 endpoints)
• ebi_tools_execute — Code Mode: write JavaScript in a V8 isolate (api.get() / api.post() / searchSpec()) instead of issuing tool calls one by one
• ebi_tools_query_data — run SQL over large responses auto-staged into a per-session SQLite database
• ebi_tools_get_schema — inspect the inferred schema of a staged dataset
• ebi_tools_job_result
• ebi_tools_job_status
• ebi_tools_list_tools
• ebi_tools_submit_job

Large responses (>30KB) are auto-staged into a queryable SQLite database; the tools return a data_access_id you can query with SQL.

Every tool returns both a human-readable content summary and a structured structuredContent payload.

Development

./scripts/dev-servers.sh ebi-tools            # run locally (port 8842)
pnpm --filter ebi-tools-mcp-server run deploy   # deploy to Cloudflare Workers

See docs/adding-mcp-servers.md and the root README for the full architecture (Code Mode, staging, portals).

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Auto-generated baseline README — refine with server-specific detail as needed.