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 AI clients work with Pubmed MCP Advanced?

Pubmed MCP Advanced is compatible with Claude Desktop, Cursor, Claude Code, and most MCP clients that support stdio transport. It uses stdio transport.

Is Pubmed MCP Advanced actively maintained?

Pubmed MCP Advanced is less actively maintained — last commit was 107 days ago. It has 8 GitHub stars.

Pubmed MCP Advanced

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

StaleNot tested

AI / ML

★ 8GitHub

20DNo CVEsstale

Quick Install

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

Setup guide

No install config available. Check the server's README for setup instructions.

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

Should you use this server?

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

✓

Is it safe?

No package registry to scan.

No authentication — any process on your machine can connect.

License not specified.

Is it maintained?

Last commit 107 days ago. 8 stars.

Will it work with my client?

Transport: stdio. Works with Claude Desktop, Cursor, Claude Code, and most MCP clients.

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

Test This Server

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

Help improve this page

This server is missing a description. Tools and install config are also missing.If you've used it, help the community.

Add information

Score Breakdown

MCPpedia Score

Click each category to see evidence

20D

Last scored 8h ago

How we score →

Security

3/30

No known vulnerabilities.

○

Known CVEs — No package registry to scan

○

Tool safety — No tools to analyze

○

Tool poisoning — No tools to analyze

○

Injection vectors — No tools to analyze

✓

Tool stability — Tool definitions stable

○

Dependency health — No package to analyze

✗

License — No license specified

○

Authentication — No authentication required

○

Repository — active repo

CVEs checked daily via OSV.dev. Score algorithm is open source.

Reviews

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 AI clients work with Pubmed MCP Advanced?: Pubmed MCP Advanced is compatible with Claude Desktop, Cursor, Claude Code, and most MCP clients that support stdio transport. It uses stdio transport.
Is Pubmed MCP Advanced actively maintained?: Pubmed MCP Advanced is less actively maintained — last commit was 107 days ago. It has 8 GitHub stars.

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Discussion

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Has anyone used this with Cursor?How do you handle auth?Any alternatives?

🧬 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