Nexonco (CIViC Precision Oncology)

🚀 Nexonco Clinical Evidence Query Tool

Nexonco, provided by Nexgene Research, is a server based on the MCP protocol. It enables access to clinical evidence from the CIViC (Clinical Interpretation of Variants in Cancer) database, supporting rapid and flexible searches for mutation, disease, drug, and phenotype information to aid in precision oncology research.

🚀 Quick Start

Demo

https://github.com/user-attachments/assets/02129685-5ba5-4b90-89e7-9d4a39986210

Watch the full video: here

📦 Installation

Dependencies

Python >= 3.6
Jupyter Notebook
requests
pandas

Configuration Steps

1. Clone the repository:

   git clone https://github.com/Nexgene-Research/nexonco-mcp.git
   cd nexonco-mcp
   

2. Install dependencies:

   pip install -r requirements.txt
   

3. Start the server:

   python server.py
   

✨ Features

Core Features

• Real-time Data Query: Retrieve the latest clinical evidence from the CIViC database.
• Multi-condition Search: Support combined queries for mutations, diseases, drugs, and phenotypes.
• Result Visualization: Present query results in tables and charts for easy analysis.

💻 Usage Examples

Basic Usage

# Query the efficacy of a specific drug
results = query_therapies("Imatinib", "leukemia")
print(results)

📚 Documentation

Input Format

{
  "query": {
    "therapy": "Imatinib",
    "disease": "leukemia"
  },
  "options": {
    "include": ["evidence_level", "clinical_significance"]
  }
}

Output Format

[
  {
    "therapy": "Imatinib",
    "disease": "leukemia",
    "evidence_level": "Level 1",
    "clinical_significance": "Effective"
  },
  ...
]

Example Queries

• Question: Which therapies are associated with pancreatic cancer evidence?
• Query Code:

  results = query_therapies(disease="pancreatic cancer")
  print(results)
  

📄 License

This project is licensed under the MIT License. Please see the LICENSE file for specific terms.

⚠️ Important Note

This tool is for research purposes only. It cannot replace professional medical advice, diagnosis, or treatment.

Contributors

• Obada Qasem (@obadaqasem), Nexgene AI
• Kutsal Ozkurt (@Goodsea), Nexgene AI