dbSNP MCP Plugin

This MCP plugin allows you to retrieve genetic variant information from NCBI's dbSNP database directly in your development environment.

Features

• Retrieve detailed information about SNPs using rs IDs
• Search for SNPs by various terms (gene names, phenotypes, etc.)
• Get clinical significance information for variants

Installation

Prerequisites

• Python 3.7+
• MCP CLI tool

Setup

1. Install the required dependencies:

pip install mcp requests

2. Install the MCP server:

mcp install server.py

3. (Optional) To use higher rate limits, get an NCBI API key and add it to your configuration:

mcp install server.py -v NCBI_API_KEY=your_api_key_here

Usage

Get SNP by rs ID

Retrieves detailed information about a specific SNP by its rs ID.

# Example: Get details for rs6311
result = mcp.dbsnp.get_snp_by_rs("rs6311")

Search for SNPs

Search for SNPs using various terms like gene names or phenotypes.

# Example: Search for SNPs related to BRCA1
results = mcp.dbsnp.search_snps("BRCA1", limit=5)

Get Clinical Significance

Retrieve clinical significance data for a specific SNP.

# Example: Get clinical significance for rs397507444
clinical_data = mcp.dbsnp.get_snp_clinical_significance("rs397507444")

Rate Limits

Without an API key, NCBI limits requests to 3 per second. With an API key, you can make up to 10 requests per second.

To obtain an NCBI API key:

1. Register for an NCBI account at https://www.ncbi.nlm.nih.gov/
2. Go to your account settings to generate an API key

Troubleshooting

If you encounter issues:

• Check your internet connection
• Verify the rs ID format is correct
• Ensure your API key is valid (if using one)
• Check the error messages for specific API response issues

License

MIT