BioMapper

Local install

io.github.trentleslie/biomapperv1.6.2 GitHub verified

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

Health & Science

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Registry entry

Open in the registry

{
  "_meta": {
    "io.modelcontextprotocol.registry/official": {
      "status": "active",
      "isLatest": true,
      "updatedAt": "2026-11-04T22:57:17.958052Z",
      "publishedAt": "2026-11-04T22:57:17.958052Z",
      "statusChangedAt": "2026-11-04T22:57:17.958052Z"
    }
  },
  "server": {
    "name": "io.github.trentleslie/biomapper",
    "title": "BioMapper",
    "$schema": "https://static.modelcontextprotocol.io/schemas/2025-12-11/server.schema.json",
    "version": "1.6.2",
    "packages": [
      {
        "version": "1.6.2",
        "transport": {
          "type": "stdio"
        },
        "identifier": "biomapper",
        "runtimeHint": "uvx",
        "registryType": "pypi",
        "registryBaseUrl": "https://pypi.org",
        "environmentVariables": [
          {
            "name": "BIOMAPPER_MCP_ROOTS",
            "description": "Folders map_file may read and write, path-separated (needed when the client shares no roots)"
          },
          {
            "name": "BIOMAPPER_API_KEY",
            "isSecret": true,
            "description": "Optional API key; the hosted deployment is keyless"
          },
          {
            "name": "BIOMAPPER_BASE_URL",
            "description": "Override the API root (staging or a local engine)"
          },
          {
            "name": "BIOMAPPER_MCP_HOME",
            "description": "Where job state lives (default ~/.cache/biomapper/mcp)"
          }
        ]
      }
    ],
    "repository": {
      "url": "https://github.com/Phenome-Health/biomapper",
      "source": "github"
    },
    "websiteUrl": "https://github.com/Phenome-Health/biomapper#use-from-an-agent-mcp",
    "description": "Resolve metabolite, lipid, protein, gene and lab names to knowledge-graph IDs."
  }
}

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Try it

This server only runs locally, from a package. Install it with the instructions on this page to try it.

Install

Pick your client. Values in capitals, like YOUR_TOKEN, are yours to fill in.

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Run in a terminal

claude mcp add biomapper \
  -- uvx biomapper==1.6.2

Environment

BIOMAPPER_MCP_ROOTS (optional, not in the config above): Folders map_file may read and write, path-separated (needed when the client shares no roots)
BIOMAPPER_API_KEY (optional, not in the config above): Optional API key; the hosted deployment is keyless
BIOMAPPER_BASE_URL (optional, not in the config above): Override the API root (staging or a local engine)
BIOMAPPER_MCP_HOME (optional, not in the config above): Where job state lives (default ~/.cache/biomapper/mcp)

Tools

We don't run packages, so we can't list this server's tools.