MCP

Access Biomedical Research Data via NCBI APIs

Name: Access Biomedical Research Data via NCBI APIs
Availability: OnlineOnly
Author: QuentinCody

Entrez MCP Server provides access to NCBI APIs, including E-utilities, PubChem, and PMC services for biomedical research data.

Connect

Works with cloudflare

QuentinCody

Maintainer?

Spark score

out of 100

Updated 4 months ago

Version 1.0.0

Models

claude

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Why it matters

Connect to comprehensive NCBI APIs for biomedical research, including E-utilities, PubChem, and PMC services. Streamline data access and analysis for research purposes.

Outcomes

What it gets done

Access E-utilities, PubChem, and PMC APIs

Retrieve and process biomedical research data

Integrate with Cloudflare Workers and Claude Desktop

Optionally boost request limits with an NCBI API key

Install

Add it to your toolbox

Run in your project directory:

curl -fsSL https://spark.entire.vc/get/vb-entrez | bash

Overview

Entrez MCP Server

What it does

MCP server for NCBI biomedical research APIs

How it connects

When you need programmatic access to NCBI E-utilities, PubChem, and PMC services through a Model Context Protocol interface

Source README

A comprehensive MCP server providing access to NCBI APIs, including E-utilities, PubChem, and PMC services for biomedical research data.

Installation

From Source Code

git clone <this-repo>
cd entrez-mcp-server
npm install
npm start

Configuration

Claude Desktop

{
  "mcpServers": {
    "calculator": {
      "command": "npx",
      "args": [
        "mcp-remote",
        "http://localhost:8787/mcp"  // or remote-mcp-server-authless.your-account.workers.dev/mcp
      ]
    }
  }
}

Features

Complete NCBI API coverage: E-utilities, PubChem PUG, PMC API
Zero-configuration: Works immediately without any setup
Optional performance boost: Add your free NCBI API key for threefold improvement in request limits
Rate limiting: Built-in compliance with NCBI limits (3/sec → 10/sec with API key)
User-friendly: Designed for both technical and non-technical users

Environment Variables

Optional

NCBI_API_KEY - Optional NCBI API key for improved request limits (10 requests/second versus 3 requests/second)

Notes

The server supports deployment on Cloudflare Workers and can be connected to both Cloudflare AI Playground and Claude Desktop. Performance testing is available through 'node test-rate-limits.js'. For Cloudflare Code Mode, use tool identifiers with underscores instead of hyphens to avoid JavaScript syntax issues.

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