Provides access to the PRIDE Archive proteomics repository through MCP-compatible tools for exploring mass spectrometry datasets and biomedical research data.
🧬 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) andstdio
connection modes - 🛠️ Easily extendable with additional tools
📦 Installation
Clone the repo and install dependencies:
👨💻 Usage
Start the MCP server with your preferred connection type (http or stdio):
Command-line Arguments
| Argument | Description | Default | |--------------------| ------------------------------------- |-----| | --connection_type |Type of connection: http or stdio | http | | --port |Port to run the server (for HTTP mode) | 9999 |
🔧 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
📝 License
MIT License. See LICENSE for details.
This server cannot be installed
remote-capable server
The server can be hosted and run remotely because it primarily relies on remote services or has no dependency on the local environment.
A Model Context Protocol server that enables AI models to programmatically search and interact with proteomics datasets from the PRIDE Archive repository through structured function calling.
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