MCP Pride Archive Search

🚀 PRIDE Archive MCP Search Server

This project implements an API server compliant with the Model Context Protocol (MCP), offering a tool to search the PRIDE Archive, a major proteomics data repository. It enables AI models (such as Claude or other MCP-compatible large language models) to programmatically interact with proteomics datasets through structured function calls.

🚀 Quick Start

This server allows AI models to interact with proteomics datasets in PRIDE Archive. It supports multiple connection modes and can be easily extended with more tools.

✨ Features

• ✅ An MCP server powered by FastMCP.
• 🔍 A PRIDE Archive search tool that can query datasets by keywords, submission dates, popularity, etc.
• 🤖 AI tools friendly to biomedical and proteomics research.
• ⚡ Supports both http (SSE) and stdio connection modes.
• 🛠️ Can be easily extended by adding more tools.

📦 Installation

Clone the repository and install the dependencies:

git clone https://github.com/PRIDE-Archive/mcp_pride_archive_search.git
cd mcp_pride_archive_search
poetry install  # or pip install -r requirements.txt

💻 Usage Examples

Basic Usage

Start the MCP server with your preferred connection type (http or stdio):

python -m mcp_pride_archive_search --connection_type http --port 9999

Command-line Arguments

📚 Documentation

search_archive_tool(...)

Retrieve proteomics datasets from the PRIDE Archive database.

Use cases:

• Search for proteomics research data.
• Query mass spectrometry datasets.
• Explore biomedical datasets (e.g., cancer-related).
• Find popular or specific proteomics projects.

🔧 Technical Details

Integration with LLMs

This server is suitable for any LLM that supports the Model Context Protocol, including:

• Anthropic Claude
• Google Gemini
• Open-source MCP clients
• Custom RAG pipelines

Architecture Overview

+---------------------+       Tool Call        +-----------------------------+
|  Claude / Gemini AI |  <--------------------> | MCP PRIDE API Server        |
+---------------------+                         | - search_archive_tool()     |
                                                | - server_status()           |
                                                +-----------------------------+
                                                           |
                                                           v
                                              +---------------------------+
                                              | PRIDE Archive REST API    |
                                              | (https://www.ebi.ac.uk    |
                                              |   /pride/ws/archive/      |
                                              |  v3/search/projects)      |
                                              +---------------------------+