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Biothings MCP Server

@longevity-genie

リポジトリ

基本情報

カテゴリ

その他

ライセンス

MIT

トランスポート

stdio

作者

longevity-genie

Biothings MCP Server について

MCP (Model Context Protocol) server for biothings

#bioinformatics#genetics#genetic-variants#biothings#mcp-server

Biothings MCP Server の設定

以下の設定を使って、このサーバーを MCP 対応クライアントに追加してください。

{
  "mcpServers": {
    "biothings-mcp": {
      "command": "uvx",
      "args": [
        "biothings-mcp"
      ]
    }
  }
}

Biothings MCP Server のツール

ツール一覧はまだありません

この掲載には表示できるツール一覧がまだありません。サーバーにツールがないという意味ではありません。対応機能はプロジェクトのドキュメントをご確認ください。

上のボタンで一時的なサンドボックスでこのサーバーを実行し、ツール一覧を取得できます。

概要

What is biothings-mcp?

biothings-mcp is a Model Context Protocol (MCP) server that provides a standardized interface for accessing and manipulating biomedical data from the BioThings platform, including gene annotation (mygene.info), variant annotation (myvariant.info), and chemical compound annotation (mychem.info). It is designed for AI assistants and agents that require specialized biomedical knowledge.

How to use biothings-mcp?

Install and run the server using uvx (no cloning required) or by cloning the repository. For STDIO mode, use uvx biothings-mcp; for HTTP streamable mode, use uvx --from biothings-mcp server run; for SSE mode, use uvx --from biothings-mcp sse. Optionally specify a custom output directory with --output-dir. Configure your MCP‑compatible AI client using the provided JSON configuration files (e.g., mcp-config.json for local servers, mcp-config-remote.json for the public hosted server).

Key features of biothings-mcp

  • Standard MCP interface for BioThings biomedical data
  • Supports gene, variant, chemical, taxon, and download tools
  • Local file saving with automatic directory creation and unique filenames
  • Supports STDIO, HTTP streamable, and SSE transport modes
  • Type safety via the biothings-typed-client library
  • Ready-to-use configuration for AI clients like Cursor and Claude Desktop

Use cases of biothings-mcp

  • AI assistants querying gene annotations from mygene.info
  • Analyzing genetic variants via myvariant.info
  • Chemical compound lookup from mychem.info
  • Downloading NCBI Entrez data (sequences, GenBank) for analysis
  • Integrating specialized biomedical knowledge into MCP-compatible AI clients

よくある質問

1

What biomedical data sources does biothings-mcp provide access to?

It supports mygene.info (gene annotation), myvariant.info (variant annotation), and mychem.info (chemical compound annotation), all accessed via BioThings REST APIs.

2

How do I run biothings-mcp?

You can run it with uvx without cloning: `uvx biothings-mcp` for STDIO mode, `uvx --from biothings-mcp server run` for HTTP streamable mode, or `uvx --from biothings-mcp sse` for

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