MCP PRIDE Archive Search Server

This project implements a Model Context Protocol (MCP)-compliant API server that exposes tools to search the PRIDE Archive, a major repository for proteomics data. It allows AI models (such as Claude or other MCP-compatible LLMs) to interact with proteomics datasets programmatically using structured function calling.

Features

• MCP Server powered by FastMCP
• PRIDE Archive Search Tool to query datasets by keyword, submission date, popularity, etc.
• AI-friendly tools for biomedical and proteomics-related research
• Supports both http (SSE) and stdio connection modes
• Easily extendable with additional tools

Installation

Clone the repo and install 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

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

Tool APIs

search_archive_tool(…)

Fetches proteomics datasets from the PRIDE Archive database.

Use this when:

• Searching for proteomics research data
• Mass spectrometry dataset queries
• Biomedical dataset exploration (e.g., cancer-related)
• Finding popular or specific proteomics projects

Integration with LLMs

This server works with any LLM that supports Model Context Protocol, including:

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

Architecture Overview

+---------------------+       Tool Calls        +-----------------------------+
|  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)      |
                                              +---------------------------+

License

MIT License. See LICENSE for details.