Which integrations are available for this server?

Retrieves Digital Object Identifier (DOI) metadata for biomedical publications, facilitating persistent linking and citation of research articles. Identifies and provides direct links to free full-text versions of scientific literature, including publisher open access content and PubMed Central records. Provides comprehensive access to the PubMed database, allowing users to search biomedical literature using full syntax, retrieve detailed metadata, track citations, and browse MeSH vocabulary.

How do I use mcp-pubmed?

1. Click on "Install Server". 2. Wait a few minutes for the server to deploy. Once ready, it will show a "Started" state. 3. In the chat, type @ followed by the MCP server name and your instructions, e.g., "@mcp-pubmed Find recent research on CRISPR treatments for sickle cell disease" That's it! The server will respond to your query, and you can continue using it as needed. Here is a step-by-step guide with screenshots.

mcp-pubmed

An MCP (Model Context Protocol) server that provides access to PubMed and NCBI's biomedical literature database. Search articles, retrieve metadata, track citations, explore related research, browse MeSH vocabulary, and find free full-text links — all through a standardized MCP interface.

Tools

Tool	Description
`search_articles`	Search PubMed by query with full PubMed syntax support (field tags, booleans, date ranges)
`get_article`	Get complete metadata for a PMID (title, abstract, authors, journal, date, DOI, MeSH terms)
`get_citations`	Find articles that cite a given PMID (forward citation tracking)
`get_related`	Get related articles ranked by NCBI's relevance algorithm
`search_mesh`	Search Medical Subject Headings (MeSH) vocabulary
`get_full_text_links`	Find free full-text links (PubMed Central, publisher open access)

Installation

npm install -g mcp-pubmed

Or clone and build:

git clone https://github.com/PetrefiedThunder/mcp-pubmed.git cd mcp-pubmed npm install npm run build

NCBI API Key (Optional)

Without an API key, requests are limited to 3 per second. With a key, the limit increases to 10 per second.

Register at NCBI
Go to Settings → API Key Management → Create
Set the environment variable:

export NCBI_API_KEY=your_key_here

Optionally set your email for NCBI's usage tracking:

export NCBI_EMAIL=you@example.com

MCP Client Configuration

Claude Desktop

Add to ~/Library/Application Support/Claude/claude_desktop_config.json:

{ "mcpServers": { "pubmed": { "command": "npx", "args": ["-y", "mcp-pubmed"], "env": { "NCBI_API_KEY": "your_key_here" } } } }

OpenClaw / Generic MCP Client

{ "mcpServers": { "pubmed": { "command": "node", "args": ["/path/to/mcp-pubmed/dist/index.js"], "env": { "NCBI_API_KEY": "your_key_here" } } } }

Example Queries

search_articles({ query: "CRISPR sickle cell", max_results: 5, sort: "pub_date" }) get_article({ pmid: "33526711" }) get_citations({ pmid: "33526711" }) get_related({ pmid: "33526711", max_results: 5 }) search_mesh({ query: "immunotherapy" }) get_full_text_links({ pmid: "33526711" })

PubMed Search Syntax

The search_articles tool supports full PubMed query syntax:

Field tags: cancer[Title], Smith J[Author], Nature[Journal]
Boolean operators: CRISPR AND sickle cell, diabetes OR obesity
MeSH terms: "Neoplasms"[MeSH]
Date ranges: use min_date/max_date params (2023, 2023/01, 2023/01/15)
Proximity: "asthma treatment"[Title:~3]

Development

npm install npm run dev # Run with tsx (hot reload) npm run build # Compile TypeScript npm test # Run unit tests RUN_INTEGRATION=1 npm test # Run integration tests (hits NCBI API)