MCPmed/PLSDBmcp

PLSDB MCP Server

Model Context Protocol server for interacting with the PLSDB (Plasmid Database) API. This server provides tools to search, filter, and retrieve plasmid data from PLSDB.

Installation

From PyPI (Recommended)

pip install plsdb-mcp

From Source

git clone <repository-url>
cd PLSDBmcp
pip install -e .

Usage

Command Line

After installation, you can run the MCP server using:

plsdb-mcp

MCP Configuration

Add this to your MCP configuration file:

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

Available Tools

The PLSDB MCP server provides the following tools:

Plasmid Information

• get_plasmid_summary: Get plasmid summary information for a given NUCCORE_ACC

FASTA Downloads

• start_fasta_download: Start preparing FASTA download for multiple plasmid accessions
• get_fasta_download: Get results from FASTA download job

Sequence Search

• start_sequence_search: Start sequence search in PLSDB using various search methods
• get_sequence_search_results: Get results from sequence search job

Filtering

• filter_plasmids_by_nuccore: Filter PLSDB plasmids based on nuccore attributes
• filter_plasmids_by_biosample: Filter PLSDB plasmids based on biosample attributes
• filter_plasmids_by_taxonomy: Filter PLSDB plasmids based on taxonomy attributes

API Endpoints

The server connects to the PLSDB API at: https://ccb-microbe.cs.uni-saarland.de/plsdb2025/api

Requirements

• Python 3.8 or higher
• mcp >= 1.0.0
• aiohttp >= 3.8.0

Development

Setup Development Environment

git clone <repository-url>
cd PLSDBmcp
pip install -e ".[dev]"

Running Tests

python -m pytest

Building Package

python -m build

Claude integration

inlcude following in your Claude app:

{
  "mcpServers": {
    "plsdb": {
      "command": "plsdb-mcp",
      "env": {}
    }
  }
}

Contributing

1. Fork the repository
2. Create a feature branch
3. Make your changes
4. Add tests
5. Submit a pull request

Support

For issues and questions, please open an issue on the GitHub repository.