Is Pubmed MCP Advanced safe to use?

Pubmed MCP Advanced has no known CVEs as of the latest MCPpedia security scan. It does not require authentication, so any local process can connect — keep this in mind in shared environments.

How do I install Pubmed MCP Advanced?

Pubmed MCP Advanced can be installed by cloning its GitHub repository and following the setup instructions in the README.

What can Pubmed MCP Advanced do?

Pubmed MCP Advanced provides 16 tools: pubmed_search, pmc_search, mesh_term_search, advanced_search, global_search and 11 more. See the full tools list on the server page for descriptions and parameters.

What AI clients work with Pubmed MCP Advanced?

Pubmed MCP Advanced is compatible with claude-desktop, cursor, claude-code. It uses sse and http transport.

Is Pubmed MCP Advanced actively maintained?

Pubmed MCP Advanced is less actively maintained — last commit was 181 days ago. It has 8 GitHub stars.

Pubmed MCP Advanced

Name: Pubmed MCP Advanced
Author: SuyashEkhande

by SuyashEkhande

A comprehensive Model Context Protocol (MCP) server that exposes PubMed and PubMed Central research literature APIs as intelligent tools for LLM applications.

8 16 tools GitHub

No known CVEs

No license

Stale

Last commit 181d ago

Works with most clients

Transport: sse, http

16 tools · ~1.5k tok

Grade C · 0.8% of 200K ctx

Edit this pageView history

Health Education

Step 1

Install in your client

Config is the same across clients — only the file and path differ.

Supported in Claude Desktopsse, http · Node 18+

Paste into ~/Library/Application Support/Claude/claude_desktop_config.json

{
  "mcpServers": {
    "pubmed-mcp-advanced": {
      "command": "<see-readme>",
      "args": []
    }
  }
}

Are you the author?

Add this badge to your README to show your security score and help users find safe servers.

Embed in your READMEAbout badges →

[![MCPpedia Score](https://mcppedia.org/api/badge/pubmed-mcp-advanced)](https://mcppedia.org/s/pubmed-mcp-advanced)

Read me

What Pubmed MCP Advanced does

A comprehensive Model Context Protocol (MCP) server that exposes PubMed and PubMed Central research literature APIs as intelligent tools for LLM applications.

Test This Server

No automated test available for this server. Check the GitHub README for setup instructions.

Loading README…

Scored, not listed

Why this score

Five weighted categories — click any category to see the underlying evidence.

Score breakdown

53/100across 5 weighted dimensions

How we score →

0255075100

−47

Security

Maintenance

Efficiency

Documentation

Compatibility

Categoriesclick a row to see evidence

Security

OSV.dev

No known CVEs.

No package registry to scan.

Inventory

Tools (16)

Click any tool to inspect its schema.

~1.5k tokens total

Community

Reviews

Be the first to review

Have you used this server?

Share your experience — it helps other developers decide.

How easy was setup?Did it work reliably?How was the documentation?

Frequently Asked Questions

Is Pubmed MCP Advanced safe to use?: Pubmed MCP Advanced has no known CVEs as of the latest MCPpedia security scan. It does not require authentication, so any local process can connect — keep this in mind in shared environments.
How do I install Pubmed MCP Advanced?: Pubmed MCP Advanced can be installed by cloning its GitHub repository and following the setup instructions in the README.
What can Pubmed MCP Advanced do?: Pubmed MCP Advanced provides 16 tools: pubmed_search, pmc_search, mesh_term_search, advanced_search, global_search and 11 more. See the full tools list on the server page for descriptions and parameters.
What AI clients work with Pubmed MCP Advanced?: Pubmed MCP Advanced is compatible with claude-desktop, cursor, claude-code. It uses sse and http transport.
Is Pubmed MCP Advanced actively maintained?: Pubmed MCP Advanced is less actively maintained — last commit was 181 days ago. It has 8 GitHub stars.

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Get CVE alerts and security updates for Pubmed MCP Advanced and similar servers.

Community

Discussion

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Health Education

Step 1

Install in your client

Config is the same across clients — only the file and path differ.

Supported in Claude Desktopsse, http · Node 18+

Paste into ~/Library/Application Support/Claude/claude_desktop_config.json

{
  "mcpServers": {
    "pubmed-mcp-advanced": {
      "command": "<see-readme>",
      "args": []
    }
  }
}

Are you the author?

Add this badge to your README to show your security score and help users find safe servers.

Embed in your READMEAbout badges →

[![MCPpedia Score](https://mcppedia.org/api/badge/pubmed-mcp-advanced)](https://mcppedia.org/s/pubmed-mcp-advanced)

Read me

What Pubmed MCP Advanced does

A comprehensive Model Context Protocol (MCP) server that exposes PubMed and PubMed Central research literature APIs as intelligent tools for LLM applications.

Test This Server

No automated test available for this server. Check the GitHub README for setup instructions.

README

🧬 PubMed Advanced MCP Server

A comprehensive Model Context Protocol (MCP) server that exposes PubMed and PubMed Central research literature APIs as intelligent tools for LLM applications.

Built with ❤️ by Suyash Ekhande

Features • Quick Start • Tools • Examples • Architecture

https://github.com/user-attachments/assets/892978f7-88d8-4b26-992e-41ba87c1b1cf

🌟 Features

16 Intelligent Tools organized into 5 categories for comprehensive biomedical literature access
34M+ PubMed Articles - Search across the world's largest biomedical abstract database
7M+ PMC Full-Text Articles - Access complete article content from PubMed Central
Smart Rate Limiting - Automatic compliance with NCBI rate limits (3-10 req/sec)
Cross-Database Linking - Connect articles to genes, proteins, clinical variants, and more
ID Conversion - Seamlessly convert between PMID, PMCID, DOI, and Manuscript IDs
BioC Format Support - Pre-parsed text for NLP and text mining applications
Pipeline Operations - Build complex multi-step queries using Entrez History Server
Batch Processing - Efficiently handle 10K+ articles with chunked operations

📦 Installation

Prerequisites

Python 3.10 or higher
pip or uv package manager

Install from source

# Clone the repository
git clone https://github.com/yourusername/pubmed-advanced-mcp.git
cd pubmed-advanced-mcp

# Create virtual environment
python -m venv venv
source venv/bin/activate  # On Windows: venv\Scripts\activate

# Install dependencies
pip install -r requirements.txt

# Or install as package
pip install -e .

Configure API Key (Recommended)

# Copy example environment file
cp .env.example .env

# Edit .env and add your NCBI API key
# Get one at: https://www.ncbi.nlm.nih.gov/account/

Note: Without an API key, you're limited to 3 requests/second. With an API key, you get 10 requests/second.

🚀 Quick Start

Run the MCP Server

# Using Python directly (Streamable HTTP on port 8000)
python -m src.server

# With custom host/port
MCP_HOST=127.0.0.1 MCP_PORT=9000 python -m src.server

Transport: This server uses Streamable HTTP as the only transport protocol. It runs on http://0.0.0.0:8000/mcp by default.

Run with Docker

# Build the image
docker build -t pubmed-mcp .

# Run the container
docker run -d -p 8000:8000 --name pubmed-mcp pubmed-mcp

# Run with NCBI API key for higher rate limits
docker run -d -p 8000:8000 -e NCBI_API_KEY=your-api-key pubmed-mcp

🛠 Available Tools

Category 1: Search & Discovery (5 tools)

Tool	Description	Example Use Case
`pubmed_search`	Search 34M+ PubMed abstracts	Find reviews on CAR-T therapy
`pmc_search`	Full-text search in PMC	Search methods sections for protocols
`mesh_term_search`	MeSH controlled vocabulary search	Find all cancer therapy articles
`advanced_search`	Multi-field Boolean queries	Complex author + topic + date searches
`global_search`	Cross-database hit counts	Discover data across NCBI

Category 2: Document Retrieval (4 tools)

Tool	Description	Example Use Case
`fetch_article_summary`	Get article metadata	Retrieve author and abstract info
`fetch_full

... View full README on GitHub

Loading README…

Scored, not listed

Why this score

Five weighted categories — click any category to see the underlying evidence.

Score breakdown

53/100across 5 weighted dimensions

How we score →

0255075100

−47

Security

Maintenance

Efficiency

Documentation

Compatibility

Categoriesclick a row to see evidence

Security

OSV.dev

No known CVEs.

No package registry to scan.

Inventory

Tools (16)

Click any tool to inspect its schema.

~1.5k tokens total

Community

Reviews

Be the first to review

Have you used this server?

Share your experience — it helps other developers decide.

How easy was setup?Did it work reliably?How was the documentation?

Frequently Asked Questions

Is Pubmed MCP Advanced safe to use?: Pubmed MCP Advanced has no known CVEs as of the latest MCPpedia security scan. It does not require authentication, so any local process can connect — keep this in mind in shared environments.
How do I install Pubmed MCP Advanced?: Pubmed MCP Advanced can be installed by cloning its GitHub repository and following the setup instructions in the README.
What can Pubmed MCP Advanced do?: Pubmed MCP Advanced provides 16 tools: pubmed_search, pmc_search, mesh_term_search, advanced_search, global_search and 11 more. See the full tools list on the server page for descriptions and parameters.
What AI clients work with Pubmed MCP Advanced?: Pubmed MCP Advanced is compatible with claude-desktop, cursor, claude-code. It uses sse and http transport.
Is Pubmed MCP Advanced actively maintained?: Pubmed MCP Advanced is less actively maintained — last commit was 181 days ago. It has 8 GitHub stars.