gcType-MCP

Version: 0.1.0

An MCP (Model Context Protocol) server for the gcType Type Strains Genome Database, providing AI assistants with seamless access to microbial type strain genome data, species information, 16S rDNA sequences, functional annotations, and more.

English | 中文

Table of Contents

• Overview

• Features

• Quick Start

• Installation

• Configuration

• Available Tools

• Usage Examples

• Project Structure

• Development

• Contributing

• License

• Acknowledgments

Related MCP server: GTDB-MCP

Overview

gcType-MCP is a Model Context Protocol (MCP) server that bridges AI assistants with the gcType Type Strains Genome Database. The gcType database, operated by the World Data Centre for Microorganisms (WDCM) and the National Microbiology Data Center (NMDC), is a comprehensive genomic database for microbial type strains, covering bacteria, archaea, and fungi.

By using this MCP server, AI assistants (such as Claude) can:

• Search type strains by species name, strain number, or genome accession

• Browse data across multiple categories (valid published species, type strain genomes, 16S rDNA sequences, etc.)

• Query functional annotations (core genome, prophage, defense systems, antibiotic resistance, virulence factors, BGCs, etc.)

• Access statistics, project information, and citation details

• Provide guidance on data download and usage policies

Features

• 13 MCP Tools: Comprehensive coverage of gcType database functionality

• MCP Protocol Compliant: Built on the official MCP SDK with stdio transport

• Bilingual: All documentation available in both English and Chinese

• TypeScript: Full type safety and modern ES module implementation

• Lightweight: Minimal dependencies, fast startup

• Extensible: Clean architecture for easy addition of new tools

Quick Start

Prerequisites

• Node.js >= 18.0.0

• An MCP-compatible AI client (e.g., Claude Desktop)

Install & Configure

1. Clone the repository:

git clone https://github.com/ZengZichao/gcType-MCP.git
cd gcType-MCP

2. Install dependencies and build:

npm install
npm run build

3. Configure your MCP client:

Add the following to your MCP client configuration (e.g., Claude Desktop's claude_desktop_config.json):

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

Replace /path/to/gcType-MCP/dist/index.js with the actual absolute path to the built server.

4. Restart your AI client and start asking questions about microbial type strains!

Installation

From Source

git clone https://github.com/ZengZichao/gcType-MCP.git
cd gcType-MCP
npm install
npm run build

Using npx (coming soon)

npx gctype-mcp

Configuration

MCP Client Configuration

The gcType-MCP server uses stdio transport and requires no additional configuration files. Simply point your MCP client to the built server entry point.

Claude Desktop

Edit claude_desktop_config.json:

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

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

{
  "mcpServers": {
    "gctype": {
      "command": "node",
      "args": ["C:\\path\\to\\gcType-MCP\\dist\\index.js"]
    }
  }
}

Cursor / VS Code

Add to your MCP settings:

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

Environment Variables

The server works without any environment variables. The following options are available for customization (via code constants in src/config.ts):

Available Tools

The gcType-MCP server provides 13 tools:

Search & Browse

Functional Annotations

Discovery & Metadata

Policy & Citation

For detailed tool schemas and parameters, see the Tools Documentation.

Usage Examples

Example 1: Search for a Type Strain

Ask your AI assistant:

"Search the gcType database for Streptomyces rubiginosus"

The AI will use the search_type_strains tool:

{
  "query": "Streptomyces rubiginosus",
  "searchType": "species_name"
}

Example 2: Browse Type Strain Genomes

"Show me the type strain genomes available in gcType"

The AI will use the browse_data_category tool:

{
  "category": "type_strain_genomes"
}

Example 3: Query Antibiotic Resistance Data

"What antibiotic resistance genes are available in gcType?"

The AI will use the query_function_annotation tool:

{
  "category": "antibiotics_resistance"
}

Example 4: Search 16S rDNA Sequences

"Find 16S rDNA sequences for Escherichia coli"

The AI will use the search_16s_rdna tool:

{
  "speciesName": "Escherichia coli"
}

Example 5: Get Database Statistics

"How many species and genomes are in the gcType database?"

The AI will use the get_statistics tool.

Project Structure

gcType-MCP/
├── src/
│   ├── index.ts          # MCP server entry point
│   ├── config.ts         # Configuration constants and URL mappings
│   ├── api.ts            # gcType API client
│   ├── tools.ts          # MCP tool definitions
│   └── types.ts          # TypeScript type definitions
├── docs/
│   ├── installation.md       # Installation guide (English)
│   ├── installation.zh.md    # Installation guide (Chinese)
│   ├── tools.md              # Tools reference (English)
│   ├── tools.zh.md           # Tools reference (Chinese)
│   ├── architecture.md       # Architecture documentation (English)
│   └── architecture.zh.md    # Architecture documentation (Chinese)
├── package.json
├── tsconfig.json
├── .gitignore
├── .npmignore
├── LICENSE
├── README.md             # English README
├── README.zh.md          # Chinese README
├── CHANGELOG.md          # English changelog
├── CHANGELOG.zh.md       # Chinese changelog
└── eslint.config.js

Development

Building

npm run build

This compiles TypeScript to JavaScript in the dist/ directory.

Development Mode

npm run dev

Runs the server using tsx for hot-reload during development.

Type Checking

npm run typecheck

Linting

npm run lint
npm run lint:fix

Testing the Server

After building, you can test the server by running:

npm start

The server communicates via stdio. You can send MCP protocol messages to stdin and receive responses on stdout.

Contributing

Contributions are welcome! Here's how you can contribute:

1. Fork the repository

2. Create a feature branch: git checkout -b feature/my-feature

3. Commit your changes: git commit -am 'Add my feature'

4. Push to the branch: git push origin feature/my-feature

5. Open a Pull Request

Guidelines

• Follow the existing code style (TypeScript, ES modules)

• Add bilingual documentation (English and Chinese) for any new features

• Update the CHANGELOG files

• Ensure npm run typecheck and npm run lint pass

• Test your changes with an MCP-compatible AI client

License

This project is licensed under the MIT License - see the LICENSE file for details.

Acknowledgments

• gcType Database: Operated by the World Data Centre for Microorganisms (WDCM) and National Microbiology Data Center (NMDC)

• MCP SDK: Built with the Model Context Protocol SDK

• Project Contact: Dr. Linhuan Wu (wulh@im.ac.cn) / gcm_admin@wdcm.org

• Citation: Please cite the gcType database appropriately when using data. See the Citation page for details.