nexonco-mcp
nexonco-mcp is an advanced MCP server designed for accessing and analyzing clinical evidence data. It provides fast and flexible search capabilities across the CIViC (Clinical Interpretation of Variants in Cancer) database, supporting precision medicine and oncology research. Implemented in Python, it allows users to filter search results based on various parameters such as diseases, therapies, and genetic variants. This tool is particularly useful for researchers in the field of cancer, enabling them to analyze relevant data efficiently.
GitHub Stars
55
User Rating
Not Rated
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0
Views
124
Forks
8
Issues
1
Installation
Difficulty
IntermediateEstimated Time
10-20 minutes
Requirements
Python 3.xuvまたはDocker+1 more
Installation
Installation
Prerequisites
Please specify required software and versions:uv or Docker
Claude Desktop (for MCP integration)
Installation Steps
1. Clone Repository
bash
git clone https://github.com/Nexgene-Research/nexonco-mcp.git
cd nexonco-mcp
2. Install Dependencies
bash
pip install -r requirements.txt
3. Configure Claude Desktop
Editclaude_desktop_config.json to add the MCP server:
json
{
"mcpServers": {
"nexonco-mcp": {
"command": "python",
"args": ["server.py"]
}
}
}
4. Start Server
bash
python server.py
Troubleshooting
Common Issues
Issue: Server won't start Solution: Check Python version and reinstall dependencies. Issue: Not recognized by Claude Desktop Solution: Verify configuration file path and syntax.Configuration
Configuration
Basic Configuration
Claude Desktop Setup
Edit~/.config/claude-desktop/claude_desktop_config.json (macOS/Linux) or
%APPDATA%\Claude\claude_desktop_config.json (Windows):
json
{
"mcpServers": {
"nexonco-mcp": {
"command": "python",
"args": ["server.py"],
"env": {
"API_KEY": "your-api-key"
}
}
}
}
Environment Variables
Set the following environment variables as needed:bash
export API_KEY="your-api-key"
export DEBUG="true"
Advanced Configuration
Security Settings
Store API keys in environment variables or secure configuration files
Set appropriate file access permissions
Adjust logging levels
Performance Tuning
Configure timeout values
Limit concurrent executions
Set up caching
Configuration Examples
Basic Configuration
json
{
"mcpServers": {
"nexonco-mcp": {
"command": "python",
"args": ["server.py"],
"env": {
"PORT": "3000",
"LOG_LEVEL": "info"
}
}
}
}
Advanced Configuration
json
{
"mcpServers": {
"advanced-mcp": {
"command": "python",
"args": ["-m", "server"],
"cwd": "/path/to/server",
"env": {
"PYTHONPATH": "/path/to/modules",
"CONFIG_FILE": "/path/to/config.json"
}
}
}
}
Examples
Examples
Basic Usage
Here are basic usage examples for the MCP server:Using with Claude Desktop
1Verify MCP Server Startup
Open Claude Desktop and confirm that the configuration has been loaded correctly.
2Execute Basic Commands
Available tools from this MCP server:
- search_clinical_evidence: A MCP tool for querying clinical evidence data that returns formatted reports.
Programmatic Usage
python
Python example
import requests
def call_mcp_tool(tool_name, params):
response = requests.post(
'http://localhost:3000/mcp/call',
json={
'tool': tool_name,
'parameters': params
}
)
return response.json()
Usage example
result = call_mcp_tool('search_clinical_evidence', {
'disease_name': 'Lung Non-small Cell Carcinoma',
'therapy_name': 'Cetuximab'
})
print(result)
Advanced Examples
Automation Script
bash
#!/bin/bash
Batch processing example
for file in *.txt; do
mcp-tool process "$file"
done
API Integration
python
Python example
import requests
import json
def call_mcp_tool(tool_name, params):
response = requests.post(
'http://localhost:3000/mcp/call',
json={
'tool': tool_name,
'parameters': params
}
)
return response.json()
Usage example
result = call_mcp_tool('search_clinical_evidence', {
'input': 'sample data',
'options': {'format': 'json'}
})
Use Cases
Searching for information on genetic variants associated with specific cancers.
Collecting clinical evidence regarding the efficacy of new therapies.
Recommending appropriate treatments based on patient symptoms.
Analyzing research data to assist in writing scientific papers.