Takumiy235 Uniprot MCP Server

🚀 UniProt MCP Server

A Model Context Protocol (MCP) server that provides access to UniProt protein information. This server allows AI assistants to directly obtain protein function and sequence information from UniProt.

✨ Features

• Retrieve protein information via UniProt accession numbers.
• Perform batch retrieval of information for multiple proteins.
• Utilize a cache with a 24-hour expiration time (24-hour TTL) to enhance performance.
• Implement error handling and logging.
• Provide the following information:
  • Protein name
  • Function description
  • Complete sequence
  • Sequence length
  • Biological species

🚀 Quick Start

1. Ensure that Python 3.10 or a higher version is installed.
2. Clone this repository:

   git clone https://github.com/TakumiY235/uniprot-mcp-server.git
   cd uniprot-mcp-server
   

3. Install the dependencies:

   # Use uv (recommended)
   uv pip install -r requirements.txt
   
   # Or use pip
   pip install -r requirements.txt
   

📚 Configuration

Add the following to your Claude Desktop configuration file:

• Windows: %APPDATA%\Claude\claude_desktop_config.json
• macOS: ~/Library/Application Support/Claude/claude_desktop_config.json
• Linux: ~/.config/Claude/claude_desktop_config.json

{
  "mcpServers": {
    "uniprot": {
      "command": "uv",
      "args": ["--directory", "path/to/uniprot-mcp-server", "run", "uniprot-mcp-server"]
    }
  }
}

💻 Usage Examples

After configuring the server in Claude Desktop, you can ask the following questions:

Can you get the protein information for UniProt accession number P98160?

For batch queries:

Can you get and compare the information of proteins P04637 and P02747?

📚 API Reference

Tools

1. get_protein_info

   • Retrieve information for a single protein.
   • Required parameter: accession (UniProt accession number).
   • Example response:

     {
       "accession": "P12345",
       "protein_name": "Example Protein Name",
       "function": ["Function description"],
       "sequence": "MLTVX...",
       "length": 123,
       "organism": "Homo sapiens"
     }
     

2. get_batch_protein_info

   • Retrieve information for multiple proteins.
   • Required parameter: accessions (an array of UniProt accession numbers).
   • Returns an array of protein information objects.

🛠️ Development

Set up the development environment

1. Clone the repository.
2. Create a virtual environment:

   python -m venv .venv
   ./.venv/bin/activate  # Use `.venv\Scripts\activate` on Windows
   

3. Install the dependencies:

   pip install -r requirements.txt
   

Run the server

python server.py

🔧 Technical Details

• Build the web interface using the Flask framework.
• Adopt simple file storage for data caching.
• Support RESTful API interfaces.

🐞 Issues and Feedback

If you encounter any issues or have suggestions for improvement, please contact the project maintainers.

Through the above steps, you can easily deploy and use the UniProt MCP server to obtain protein information.