https://github.com/pride-archive/mcp_pride_archive_search
Model Context Protocol (MCP) PRIDE API Server implementation.
https://github.com/pride-archive/mcp_pride_archive_search
Last synced: 3 months ago
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Model Context Protocol (MCP) PRIDE API Server implementation.
- Host: GitHub
- URL: https://github.com/pride-archive/mcp_pride_archive_search
- Owner: PRIDE-Archive
- Created: 2025-04-08T20:18:07.000Z (6 months ago)
- Default Branch: main
- Last Pushed: 2025-04-08T20:34:37.000Z (6 months ago)
- Last Synced: 2025-06-17T13:16:14.698Z (4 months ago)
- Language: Python
- Size: 9.77 KB
- Stars: 2
- Watchers: 5
- Forks: 1
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
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README
# 🧬 MCP PRIDE Archive Search Server
This project implements a **Model Context Protocol (MCP)**-compliant API server that exposes tools to search the [PRIDE Archive](https://www.ebi.ac.uk/pride/), 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:
```bash
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):
```bash
python -m mcp_pride_archive_search --connection_type http --port 9999
```
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
```sql
+---------------------+ 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.