ncbi-mcp 0.1.0

NCBI E-utilities MCP server for accessing NCBI databases

NCBI E-utilities MCP Server

A Machine Capability Protocol (MCP) server for accessing NCBI E-utilities API. This package provides programmatic access to NCBI databases including PubMed, Protein, Nucleotide, and more.

Features

• EInfo: Get list of Entrez databases or statistics for a specific database
• ESearch: Text-based search to retrieve UID lists from NCBI databases
• ESummary: Retrieve document summaries (DocSum) for UIDs
• EFetch: Fetch full formatted records for UIDs (core functionality)

Installation

pip install ncbi-mcp

Configuration

Create a .env file in your project root with the following variables:

API_KEY=your_ncbi_api_key  # Optional but recommended for higher rate limits
BASE_URL=https://eutils.ncbi.nlm.nih.gov/entrez/eutils/

Note: Without an API key, your requests are limited to 3 requests per second. With an API key, you can make up to 10 requests per second.

Getting an NCBI API Key

To get an NCBI API key, you need to:

1. Register for an NCBI account at https://www.ncbi.nlm.nih.gov/account/
2. Go to your account "Settings" page
3. Find the "API Key Management" area and click "Create an API Key"
4. Copy the generated key and use it in your .env file

For more information about NCBI API keys, visit: https://ncbiinsights.ncbi.nlm.nih.gov/2017/11/02/new-api-keys-for-the-e-utilities/

Usage

The server implements the MCP protocol and can be integrated with MCP-compatible clients.

Tools Available

EInfo

• Description: Query NCBI databases, get database statistics
• Parameters: db_name (optional), retmode (default: xml)

ESearch

• Description: Search for content by term in specified database
• Parameters: db_name (default: pubmed), term (search query)

ESummary

• Description: Get summary information for specified IDs
• Parameters: db_name (default: pubmed), ids (list of IDs)

EFetch

• Description: Get complete records for specified IDs
• Parameters: db_name (default: pubmed), ids (list of IDs), retmode (default: xml), rettype (default: abstract)

Requirements

• Python >= 3.8
• NCBI API key (recommended for higher rate limits)

License

MIT