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Ensembl API MCP Server

@effieklimi

代码仓库

基本信息

分类

开发工具

许可证

MIT license

传输方式

stdio

作者

effieklimi

关于 Ensembl API MCP Server

A full-featured Model Context Protocol (MCP) server that exposes Ensembl’s REST API. Built using the TypeScript MCP SDK

#science#bioinformatics#biology#mcp#ai-agents#bioinformatics-tool#model-context-protocol#mcp-server

Ensembl API MCP Server 配置

使用下面的配置,将此服务器添加到你的 MCP 客户端。

{
  "mcpServers": {
    "ensembl-mcp-server": {
      "command": "npx",
      "args": [
        "-y",
        "@smithery/cli@latest",
        "install",
        "@effieklimi/ensembl-mcp-server",
        "--client",
        "claude",
        "--key",
        "your-smithery-secret-key"
      ]
    }
  }
}

Ensembl API MCP Server 工具

工具列表暂未提供

当前收录暂时没有可展示的工具列表，不代表服务没有工具。请查阅项目文档了解支持的能力。

点击上方按钮,在临时沙箱中运行此服务器并实时获取工具列表。

概览

What is 🧬 Ensembl API MCP Server?

A full-featured Model Context Protocol (MCP) server that exposes Ensembl’s REST API through 10 biologically grouped tools. Built with the TypeScript MCP SDK, it offers comprehensive coverage of Ensembl endpoints (genes, variants, sequences, comparative genomics, and more) in a production‑ready, biologist‑friendly interface.

How to use 🧬 Ensembl API MCP Server?

Install via Smithery (e.g. npx -y @smithery/cli install @effieklimi/ensembl-mcp-server --client claude) or clone the repository, run npm install, then configure your MCP client (e.g. Claude Desktop) to point to the server’s start command. For development, use npm run dev for hot reload. No API key is required.

Key features of 🧬 Ensembl API MCP Server

  • 10 tools covering nearly the entire Ensembl REST API
  • Built‑in rate limiting to stay within Ensembl quotas
  • Support for every species available in Ensembl
  • Biologist‑friendly grouping by biological task
  • Production‑ready TypeScript with robust error handling
  • Cross‑references to external databases (UniProt, etc.)

Use cases of 🧬 Ensembl API MCP Server

  • Fetch gene details by ID or symbol across any species
  • Retrieve DNA, RNA, or protein sequences for genomic regions
  • Explore variants and their annotations (VEP, LD, phenotypes)
  • Map coordinates between genome, cDNA, CDS, and protein
  • Find orthologs, build gene trees, and pull comparative alignments

常见问题

1

How is this different from calling the Ensembl REST API directly?

The server groups over 100 raw endpoints into 10 logical tools based on biological tasks, includes built‑in rate limiting, and handles error responses in a consistent way—making it easier for biologists and AI agents to query Ensembl.

2

What are the runtime dependencies?

Node.js and npm must be installed on the machine running the server. The server uses

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