PubMedSAFE
🔍 Enable AI assistants to search, access, and analyze PubMed articles through a simple MCP interface.
Overview
From the repository's own README, as read at the audited commit. Badges and raw HTML are left out.
[](https://mseep.ai/app/jackkuo666-pubmed-mcp-server)
[](https://smithery.ai/server/@JackKuo666/pubmed-mcp-server)
🔍 Enable AI assistants to search, access, and analyze PubMed articles through a simple MCP interface.
The PubMed MCP Server provides a bridge between AI assistants and PubMed's vast repository of biomedical literature through the Model Context Protocol (MCP). It allows AI models to search for scientific articles, access their metadata, and perform deep analysis in a programmatic way.
🤝 Contribute • 📝 Report Bug
✨ Core Features
- 🔎 Paper Search: Query PubMed articles with keywords or advanced search ✅
- 🚀 Efficient Retrieval: Fast access to paper metadata ✅
- 📊 Metadata Access: Retrieve detailed metadata for specific papers ✅
- 📊 Research Support: Facilitate biomedical sciences research and analysis ✅
- 📄 Paper Access: Attempt to download full-text PDF content ✅
- 🧠 Deep Analysis: Perform comprehensive analysis of papers ✅
- 📝 Research Prompts: A set of specialized prompts for paper analysis ✅
🚀 Quick Start
Prerequisites
- Python 3.10+
- FastMCP library
Installation
Installing via Smithery
To install pubmed-mcp-server for Claude Desktop automatically via Smithery:
claude
npx -y @smithery/cli install @JackKuo666/pubmed-mcp-server --client claude
Cursor
Paste the following into Settings → Cursor Settings → MCP → Add new server:
- Mac/Linux
npx -y @smithery/cli@latest run @JackKuo666/pubmed-mcp-server --client cursor --config "{}" Windsurf
npx -y @smithery/cli@latest install @JackKuo666/pubmed-mcp-server --client windsurf --config "{}"CLine
npx -y @smithery/cli@latest install @JackKuo666/pubmed-mcp-server --client cli
2ca3242028a2OBSERVED · 2026-10-07Connect
Built from this server's own package name, version and transport as found in its source — not copied from anyone's documentation, so it cannot drift against a page we do not control.
claude mcp add mcp-server-pubmed -- uvx mcp-server-pubmed
{
"mcpServers": {
"mcp-server-pubmed": {
"command": "uvx",
"args": [
"mcp-server-pubmed"
]
}
}
}Exposed tools (4)
4 read · 0 write · 0 destructive.
| Tool | Risk | Description |
|---|---|---|
download_pubmed_pdf | read | logging.info(f |
get_pubmed_article_metadata | read | logging.info(f |
search_pubmed_advanced | read | logging.info(f |
search_pubmed_key_words | read | logging.info(f |
Trust audit
SAFEgrade B · trust 89/100 Nothing in the source contradicts what it says it does. Grade A is reserved for packages that have also passed the behavioural sandbox.
| Layer | What it checks | Result |
|---|---|---|
| L0 | Provenance & inventory | PASS |
| L1 | Static analysis of the code | PASS |
| L2 | Instruction surface (what it tells the agent) | PASS |
| L3 | Class-specific surface | PASS |
| L4 | Behavioural (sandbox) | SKIPPED |
What the source does
- Filesystem
- none-observed
- Network
- declared (5 observation(s))
- Shell
- none-observed
- Dependencies
- not all pinned
- Secrets in source
- none-found
Findings (1)
requests, bs4, mcp
Gates applied: no_behavioural_pass.
2ca3242028a2full audit observations/trust-audit/mcp-server/jackkuo666__pubmed.json · Report an issue / request a re-scanAudit history
Every audit this server has had. A grade with a past is a grade somebody is still checking.
| Date | Source | Verdict | Grade | Score | Change |
|---|---|---|---|---|---|
| 2026-10-07 | 2ca3242028a2 | SAFE | B | 89 | first audit |
Questions
What is the PubMed MCP server?
🔍 Enable AI assistants to search, access, and analyze PubMed articles through a simple MCP interface.
What tools does PubMed expose?
4 in total: 4 read-only, 0 that write, and 0 that can delete or overwrite. Every one is listed on this page with its risk.
Is PubMed safe to connect to an agent?
The audit found nothing in the source that contradicts what it says it does, and graded it B (89/100). Grade A is held back for packages that have also passed a sandboxed behavioural run, which is why a clean server reads B.
What credentials does PubMed need?
No credential environment variables were found in its source, so it appears to need none.
How does PubMed run?
It speaks stdio, so it runs as a local process your client starts. It is published on PyPI as mcp-server-pubmed.
How current is this page?
The grade is for one exact copy of the source (2ca3242028a2), read on 2026-10-07. The repository is watched and re-audited when it changes.