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BioMapper

io.github.trentleslie/biomapper ยท v1.8.0

Resolve metabolite, lipid, protein, gene and lab names to knowledge-graph IDs.

Website Source code Set it up

Connect Runs on your machine

Terminal
claude mcp add biomapper -e BIOMAPPER_MCP_ROOTS=<BIOMAPPER_MCP_ROOTS> -e BIOMAPPER_API_KEY=<BIOMAPPER_API_KEY> -e BIOMAPPER_BASE_URL=<BIOMAPPER_BASE_URL> -e BIOMAPPER_MCP_HOME=<BIOMAPPER_MCP_HOME> -- uvx biomapper==1.8.0
claude_desktop_config.json
{
  "mcpServers": {
    "biomapper": {
      "command": "uvx",
      "args": [
        "biomapper==1.8.0"
      ],
      "env": {
        "BIOMAPPER_MCP_ROOTS": "<BIOMAPPER_MCP_ROOTS>",
        "BIOMAPPER_API_KEY": "<BIOMAPPER_API_KEY>",
        "BIOMAPPER_BASE_URL": "<BIOMAPPER_BASE_URL>",
        "BIOMAPPER_MCP_HOME": "<BIOMAPPER_MCP_HOME>"
      }
    }
  }
}
~/.cursor/mcp.json
{
  "mcpServers": {
    "biomapper": {
      "command": "uvx",
      "args": [
        "biomapper==1.8.0"
      ],
      "env": {
        "BIOMAPPER_MCP_ROOTS": "<BIOMAPPER_MCP_ROOTS>",
        "BIOMAPPER_API_KEY": "<BIOMAPPER_API_KEY>",
        "BIOMAPPER_BASE_URL": "<BIOMAPPER_BASE_URL>",
        "BIOMAPPER_MCP_HOME": "<BIOMAPPER_MCP_HOME>"
      }
    }
  }
}
.vscode/mcp.json
{
  "servers": {
    "biomapper": {
      "type": "stdio",
      "command": "uvx",
      "args": [
        "biomapper==1.8.0"
      ],
      "env": {
        "BIOMAPPER_MCP_ROOTS": "<BIOMAPPER_MCP_ROOTS>",
        "BIOMAPPER_API_KEY": "<BIOMAPPER_API_KEY>",
        "BIOMAPPER_BASE_URL": "<BIOMAPPER_BASE_URL>",
        "BIOMAPPER_MCP_HOME": "<BIOMAPPER_MCP_HOME>"
      }
    }
  }
}

Replace the values in angle brackets with your own. Keys stay on your machine; we never see them.

Tools

This server runs locally, so its tools are listed by your MCP client once it starts.

Environment variables

NameDescription
BIOMAPPER_MCP_ROOTS
Optional		Folders map_file may read and write, path-separated (needed when the client shares no roots)
BIOMAPPER_API_KEY
Optional, secret		Optional API key; the hosted deployment is keyless
BIOMAPPER_BASE_URL
Optional		Override the API root (staging or a local engine)
BIOMAPPER_MCP_HOME
Optional		Where job state lives (default ~/.cache/biomapper/mcp)

Details

Package[email protected] (PYPI, stdio)
First published10 Nov 2026
Last updated10 Nov 2026
Registry nameio.github.trentleslie/biomapper

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