pubmed-mcp-server
A Model Context Protocol (MCP) server enabling AI agents to intelligently search, retrieve, and analyze biomedical literature from PubMed via NCBI E-utilities. Includes a research agent scaffold. STDIO & HTTP
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Installation
Difficulty
AdvancedEstimated Time
20-45 minutes
Installation
[Node.js (>=20.0.0)](https://nodejs.org/)
[npm](https://www.npmjs.com/) (comes with Node.js)
NCBI API Key (recommended for higher rate limits) - [Get one here](https://ncbiinsights.ncbi.nlm.nih.gov/2017/11/02/new-api-keys-for-the-e-utilities/)
Add the following to your MCP client's configuration file (e.g., cline_mcp_settings.json).
This configuration uses npx to run the server, which will automatically install the package if not already present.
All environment variables are optional, but recommended for production use. NCBI API key is recommended to avoid rate limiting issues.
```json
{
"mcpServers": {
"pubmed-mcp-server": {
"command": "npx",
"args": ["@cyanheads/pubmed-mcp-server"],
"env": {
"MCP_LOG_LEVEL": "debug",
"MCP_TRANSPORT_TYPE": "http",
"MCP_HTTP_PORT": "3017",
"NCBI_API_KEY": "YOUR_NCBI_API_KEY_HERE"
}
}
}Additional Resources
Author Information
Software Engineer | Building AI Infrastructure with the Model Context Protocol (MCP)
Seattle, WA
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