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BioMapper

io.github.trentleslie/biomapper ยท version 1.6.3

Community listing. Not installed or verified by cosmic-mcp. Read the source and its permissions before you run it.

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

https://github.com/Phenome-Health/biomapper

Quick facts

  • Listing: Community
  • Published Nov 7, 00:17 UTC
  • Transport: stdio
  • Package: pypi biomapper 1.6.3
  • Listed by cosmic-mcp: Nov 9, 04:27 UTC

Memory and knowledge

Setup snippets

Generated from the registry entry. cosmic-mcp has not run or reviewed this server; values in angle brackets are yours to fill in.

Run it locally (pypi)

uvx 'biomapper==1.6.3'

Claude Desktop (claude_desktop_config.json)

{
  "mcpServers": {
    "biomapper": {
      "args": [
        "biomapper==1.6.3"
      ],
      "command": "uvx",
      "env": {
        "BIOMAPPER_API_KEY": "<your biomapper api key>",
        "BIOMAPPER_BASE_URL": "<your biomapper base url>",
        "BIOMAPPER_MCP_HOME": "<your biomapper mcp home>",
        "BIOMAPPER_MCP_ROOTS": "<your biomapper mcp roots>"
      }
    }
  }
}

Claude Code

claude mcp add 'biomapper' -- uvx 'biomapper==1.6.3'

Cursor (.cursor/mcp.json)

{
  "mcpServers": {
    "biomapper": {
      "args": [
        "biomapper==1.6.3"
      ],
      "command": "uvx",
      "env": {
        "BIOMAPPER_API_KEY": "<your biomapper api key>",
        "BIOMAPPER_BASE_URL": "<your biomapper base url>",
        "BIOMAPPER_MCP_HOME": "<your biomapper mcp home>",
        "BIOMAPPER_MCP_ROOTS": "<your biomapper mcp roots>"
      }
    }
  }
}

VS Code (.vscode/mcp.json)

{
  "servers": {
    "biomapper": {
      "args": [
        "biomapper==1.6.3"
      ],
      "command": "uvx",
      "env": {
        "BIOMAPPER_API_KEY": "<your biomapper api key>",
        "BIOMAPPER_BASE_URL": "<your biomapper base url>",
        "BIOMAPPER_MCP_HOME": "<your biomapper mcp home>",
        "BIOMAPPER_MCP_ROOTS": "<your biomapper mcp roots>"
      },
      "type": "stdio"
    }
  }
}

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