what is dbSNP MCP Plugin?
The dbSNP MCP Plugin is a tool that allows developers to retrieve genetic variant information from NCBI's dbSNP database directly within their development environment.
how to use dbSNP MCP Plugin?
To use the dbSNP MCP Plugin, install the required dependencies, set up the MCP server, and use the provided functions to retrieve SNP information by rs ID or search for SNPs using various terms.
key features of dbSNP MCP Plugin?
- Retrieve detailed information about SNPs using rs IDs.
- Search for SNPs by gene names, phenotypes, and other terms.
- Access clinical significance information for genetic variants.
use cases of dbSNP MCP Plugin?
- Researchers can quickly access SNP data for genetic studies.
- Developers can integrate SNP retrieval into bioinformatics applications.
- Clinicians can obtain clinical significance data for variants in patient reports.
FAQ from dbSNP MCP Plugin?
- What are the prerequisites for using the dbSNP MCP Plugin?
You need Python 3.7+ and the MCP CLI tool installed.
- How can I increase my request rate limit?
Obtain an NCBI API key and configure it in your setup to increase the limit from 3 to 10 requests per second.
- What should I do if I encounter issues?
Check your internet connection, verify the rs ID format, ensure your API key is valid, and review error messages for specific issues.
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
- Install the required dependencies:
pip install mcp requests
- Install the MCP server:
mcp install server.py
- (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:
- Register for an NCBI account at https://www.ncbi.nlm.nih.gov/
- 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