Access Biomedical Research Data via NCBI APIs
Entrez MCP Server gives AI assistants zero-config access to NCBI's E-utilities, PubChem, and PMC APIs for biomedical research data.
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
Entrez MCP Server exposes NCBI's E-utilities, PubChem, and PMC APIs to AI assistants, giving them zero-configuration access to biomedical literature, chemical, and research databases. Use it when an AI assistant needs to search or retrieve data from NCBI's biomedical databases as part of a research workflow.
What it does
Entrez MCP Server is an MCP server that exposes NCBI's biomedical research APIs - E-utilities, PubChem PUG, and PMC - to AI assistants, giving them programmatic access to literature, chemical, and biomedical databases without needing to handle NCBI's request formats or rate limits directly.
When to use - and when NOT to
Use it when an AI assistant needs to search or pull data from NCBI's biomedical databases: PubMed-style literature via E-utilities, chemical data via PubChem, or full-text articles via PMC, as part of a research workflow. It works out of the box with no configuration required, though adding a free NCBI API key raises the request-rate ceiling. It is not the right tool if your work doesn't touch NCBI data - it wraps NCBI's APIs specifically, not general web or literature search.
Capabilities
- Complete NCBI API coverage: E-utilities, PubChem PUG, and PMC API
- Zero-configuration - works immediately with no setup
- Optional NCBI API key for a threefold improvement in request limits (3 requests/second without a key, 10 with one)
- Built-in rate limiting to stay compliant with NCBI's limits
- Deployable on Cloudflare Workers, connecting to both the Cloudflare AI Playground and Claude Desktop
- A performance test script (node test-rate-limits.js) to check throughput
How to install
Install from source:
git clone <this-repo>
cd entrez-mcp-server
npm install
npm start
Configuration is optional - the server works with no setup. To raise the request-rate ceiling, set the environment variable NCBI_API_KEY to a free NCBI API key, which raises the limit from 3 to 10 requests per second. When deploying to Cloudflare Code Mode, use underscores instead of hyphens in tool identifiers to avoid JavaScript syntax issues.
Who it's for
Researchers and developers building AI assistants or agents that need to query PubMed-style literature, PubChem chemical data, or PMC full-text articles as part of a biomedical research pipeline.
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.
FAQ
Common questions
Discussion
Questions & comments · 0
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