gcMeta-MCP

An MCP (Model Context Protocol) server that provides LLMs with access to the gcMeta (Global Catalogue of Metagenomics) platform.

English | 中文

📋 Table of Contents

• Overview

• Background

• Features

• Prerequisites

• Installation

• Configuration

• Usage

  • Claude Desktop

  • Other MCP Clients

  • Direct Execution

• Available Tools

• Development

• Project Structure

• Documentation

• Contributing

• License

• Citation

• Acknowledgements

Related MCP server: geo-mcp

Overview

gcMeta-MCP is a Model Context Protocol (MCP) server that bridges Large Language Models (LLMs) with the gcMeta — the Global Catalogue of Metagenomics platform maintained by WDCM / NMDC.

By exposing gcMeta's rich metagenomics data as MCP tools, this server enables LLM-powered assistants to search, retrieve, and analyze metagenomics data — including BioProjects, BioSamples, sequencing Runs, Metagenome-Assembled Genomes (MAGs), Biome Catalogues, Taxonomy Abundance, and Functional Annotations — all through natural language queries.

Background

gcMeta is a global repository of metagenome-assembled genomes (MAGs) enabling cross-ecosystem microbial discovery and function research. As of 2026, it hosts:

The platform organizes MAGs into 50+ Biome Catalogues spanning diverse ecosystems:

• Human: Gut, Skin, Vaginal

• Animals: Chicken, Pig, Cattle, Mouse, Cat, Dog, Horse, Goat, Sheep, etc.

• Marine: Seawater, Sediment

• Freshwater: Lake Water, Riverine, Sediment

• Environments: Agricultural Soil, Hot Spring, Permafrost, Wastewater, etc.

• Extreme Environments: Acid, Cold, Hot, Pressure, Saline-alkaline Habitats

• Plant Rhizosphere: Rice, Wheat, Arabidopsis, Bean

• Wild Animals: Bear, Deer, Elephant, Giant Panda, Koala, Vulture, etc.

gcMeta also provides functional annotation across several categories: Antibiotics Resistance Genes (ARGs), KEGG Pathways, Virulence Factors (VFs), Carbohydrate-Active enZYmes (CAZy), Biosynthetic Gene Clusters (BGCs), Mobile Genetic Elements (MGEs), and Defense Systems.

Features

• 🔌 MCP Protocol Support — Full compatibility with the Model Context Protocol specification.

• 🧬 13 Tools — Search and retrieve BioProjects, BioSamples, Runs, MAGs, Biome Catalogues, Taxonomy Abundance, Functional Annotations, and platform statistics.

• 🌐 Type-safe — Written in TypeScript with Zod schema validation for all inputs.

• ⚡ Lightweight — Minimal dependencies, stdio-based transport, no external server required.

• 🔧 Configurable — Custom base URL, authentication token, and timeout settings.

• 📦 Zero-config — Works out of the box with npx or direct installation.

Prerequisites

• Node.js >= 18.0.0

• An MCP-compatible client (e.g., Claude Desktop, Cursor, or any MCP client)

Installation

Option 1: Using npx (recommended — no installation needed)

npx gcmeta-mcp

Option 2: Global installation

npm install -g gcmeta-mcp
gcmeta-mcp

Option 3: Local development

git clone https://github.com/zengzichao/gcMeta-MCP.git
cd gcMeta-MCP
npm install
npm run build
npm start

Configuration

The server reads configuration from environment variables:

Copy .env.example to .env and adjust as needed:

cp .env.example .env

Usage

Claude Desktop

Add the following to your Claude Desktop configuration file:

• macOS: ~/Library/Application Support/Claude/claude_desktop_config.json

• Windows: %APPDATA%\Claude\claude_desktop_config.json

{
  "mcpServers": {
    "gcmeta": {
      "command": "npx",
      "args": ["-y", "gcmeta-mcp"]
    }
  }
}

For local development:

{
  "mcpServers": {
    "gcmeta": {
      "command": "node",
      "args": ["/path/to/gcMeta-MCP/dist/index.js"]
    }
  }
}

Other MCP Clients

This server uses stdio transport, making it compatible with any MCP-compliant client. Simply configure your client to run npx -y gcmeta-mcp as the server command.

Direct Execution

# After installation or building from source
node dist/index.js

# With custom base URL
GCMETA_BASE_URL=https://gcmeta.wdcm.org node dist/index.js

Available Tools

The server exposes 13 tools:

See the API Reference for detailed input/output specifications of each tool.

Development

# Install dependencies
npm install

# Build
npm run build

# Watch mode
npm run dev

# Lint
npm run lint

# Format
npm run format

Project Structure

gcMeta-MCP/
├── src/
│   ├── index.ts            # Server entry point
│   ├── gcmeta-client.ts    # gcMeta HTTP API client
│   ├── tools.ts            # MCP tool definitions
│   └── types.ts            # TypeScript type definitions
├── docs/
│   ├── en/                 # English documentation
│   │   ├── INSTALLATION.md
│   │   ├── API.md
│   │   └── CONFIGURATION.md
│   └── zh/                 # Chinese documentation
│       ├── 安装指南.md
│       ├── API文档.md
│       └── 配置说明.md
├── examples/
│   └── claude-desktop-config.json
├── package.json
├── tsconfig.json
├── eslint.config.js
├── .prettierrc
├── .editorconfig
├── .env.example
├── .gitignore
├── LICENSE
├── README.md               # English (this file)
├── README_zh.md            # Chinese
├── CHANGELOG.md
├── CONTRIBUTING.md
└── CONTRIBUTING_zh.md

Documentation

• Installation Guide (EN) | 安装指南 (中文)

• API Reference (EN) | API 文档 (中文)

• Configuration (EN) | 配置说明 (中文)

• Changelog

• Contributing (EN) | 贡献指南 (中文)

Contributing

Contributions are welcome! Please read the Contributing Guide (中文: 贡献指南) for details on how to submit pull requests, report issues, and suggest features.

License

This project is licensed under the MIT License.

Citation

If you use gcMeta-MCP in your research, please cite both the tool and the gcMeta platform:

@software{gcmeta-mcp,
  title  = {gcMeta-MCP: An MCP Server for the Global Catalogue of Metagenomics},
  author = {Zeng, Zichao},
  year   = {2026},
  version = {0.1.0},
  url    = {https://github.com/zengzichao/gcMeta-MCP}
}

Acknowledgements

• gcMeta — Global Catalogue of Metagenomics, maintained by WDCM / NMDC

• Model Context Protocol — The protocol specification

• WDCM — World Data Centre for Microorganisms

• NMDC — National Microbiology Data Center