Skip to main content
Glama
Sign In

PubMed MCP Server

by cyanheads
npmGitHub
TypeScript
Apache 2.0
155
3
OverviewInspectNewSchemaRelated ServersReviewsScore
Need Help?View Source CodeReport Issue

PubMed MCP Server Pubmed

Unlock the power of biomedical literature for your AI agents with the PubMed MCP Server!

This server acts as a bridge, connecting your AI to NCBI's PubMed and E-utilities through the Model Context Protocol (MCP). It empowers language models to seamlessly search, retrieve, and analyze biomedical articles and data. Built with TypeScript and adhering to the MCP 2025-03-26 specification, it's designed for robustness and includes production-grade utilities.

🚀 Core Capabilities: PubMed Tools 🛠️

This server equips your AI with specialized tools to interact with PubMed:

Tool NameDescriptionKey Features
search_pubmed_articlesSearches PubMed for articles based on your query. (See Example)- Filter by max results, sort order, date range, publication types.- Uses NCBI ESearch for PMIDs.- Optionally fetches brief summaries (title, authors, source, dates) via ESummary.
fetch_pubmed_contentRetrieves detailed information for PubMed articles. Can use a list of PMIDs or ESearch history (queryKey/webEnv) with pagination. (See Example)- Flexible detailLevel: abstract_plus (parsed details, optional MeSH/grant), full_xml (JSON representation of the PubMedArticle XML structure), medline_text (MEDLINE format), citation_data (minimal for citations).- Supports direct PMID list or queryKey/webEnv from ESearch history.- Supports retstart/retmax for pagination with history.- Uses NCBI EFetch.
get_pubmed_article_connectionsFinds related articles (cited by, similar, references) or formats citations for a PMID. (See Ex.1, Ex.2)- Uses NCBI ELink for relationships.- Uses NCBI EFetch for citation data (RIS, BibTeX, APA, MLA).- Filter by max related results.
pubmed_research_agentGenerates a standardized JSON research plan outline from component details. (See Example)- Accepts granular inputs for all research phases.- Optionally embeds instructive prompts for agent execution.- Structures rough ideas into a formal, machine-readable plan for further processing.
generate_pubmed_chartGenerates a chart image (SVG) from given input data. (See Bar, Line, Scatter)- Supports 'bar', 'line', and 'scatter' chart types.- Takes data values and field specifications for axes and encoding.- Constructs a Vega-Lite specification internally and renders it as an SVG.

✨ Key Features Beyond Tools

Feature CategoryDescription
🔌 MCP CompliantFully functional server supporting stdio and http (SSE) transports.
🚀 Production-Ready UtilsIncludes robust logging, error handling, ID generation, rate limiting, request context tracking, and input sanitization.
🔒 Secure & Type-SafeBuilt with TypeScript & Zod for strong type checking and input validation. Manages NCBI API keys, implements rate limiting, and features JWT-based auth middleware for HTTP.
⚙️ Advanced Error HandlingConsistent error categorization, detailed logging, and centralized handling, including specific error types for NCBI interactions.
📚 Well-DocumentedComprehensive JSDoc comments, API references, and project specifications.
🤖 Agent-FriendlyIncludes a .clinerules developer cheatsheet tailored for LLM coding agents using this server.
🛠️ Developer UtilitiesScripts for cleaning builds, setting executable permissions, generating directory trees, and fetching OpenAPI specifications.

🚀 Quick Start

Get the PubMed MCP server running in minutes:

  1. Clone the repository:
    git clone https://github.com/cyanheads/pubmed-mcp-server.git cd pubmed-mcp-server
  2. Install dependencies:
    npm install
  3. Configure Environment Variables (.env file): Create a .env file in the project root. Key variables:
    # REQUIRED FOR HTTP TRANSPORT MCP_AUTH_SECRET_KEY=generate_a_strong_random_32_plus_char_secret_key # RECOMMENDED FOR NCBI E-UTILITIES (for higher rate limits) # NCBI_API_KEY=your_ncbi_api_key_here # NCBI_ADMIN_EMAIL=your_email@example.com # Recommended if using an API key # NCBI_TOOL_IDENTIFIER=@cyanheads/pubmed-mcp-server/1.0.13 # Optional: Tool identifier for NCBI (defaults to current version)
    For all options, see the Configuration section below or the Developer Cheatsheet (.clinerules).New example files for each tool are available in the examples/ directory (e.g., examples/search_pubmed_articles_example.md, examples/generate_pubmed_chart_example_bar.svg).
  4. Build the project:
    npm run build # Or use 'npm run rebuild' for a clean install (deletes node_modules, logs, dist)
  5. Format the code (Optional but Recommended):
    npm run format
  6. Run the Server:
    • Via Stdio (Default): Many MCP host applications will run this automatically using stdio. To run manually for testing:
      npm start # or 'npm run start:stdio'
    • Via HTTP (SSE): (Ensure MCP_TRANSPORT_TYPE=http and MCP_AUTH_SECRET_KEY are set in your .env)
      npm run start:http
      This starts an HTTP server (default: http://127.0.0.1:3010) using Server-Sent Events.

⚙️ Configuration

Server Configuration (Environment Variables)

Configure the PubMed MCP server's behavior using environment variables (typically in a .env file).

VariableDescriptionDefault
MCP_TRANSPORT_TYPEServer transport: stdio or http.stdio
MCP_HTTP_PORTPort for the HTTP server (if MCP_TRANSPORT_TYPE=http).3010
MCP_HTTP_HOSTHost address for the HTTP server (if MCP_TRANSPORT_TYPE=http).127.0.0.1
MCP_ALLOWED_ORIGINSComma-separated allowed origins for CORS (if MCP_TRANSPORT_TYPE=http).(none)
MCP_LOG_LEVELServer logging level (debug, info, warning, error, etc.).debug
LOGS_DIRDirectory for log files.logs/ (in project root)
NODE_ENVRuntime environment (development, production).development
MCP_AUTH_SECRET_KEYRequired for HTTP transport. Secret key (min 32 chars) for signing/verifying auth tokens (JWT).(none - MUST be set in production)
NCBI_API_KEYOptional, but highly recommended. Your NCBI API Key for higher rate limits (10/sec vs 3/sec).(none)
NCBI_ADMIN_EMAILOptional, but recommended if using an API key. Your email for NCBI contact.(none)
NCBI_TOOL_IDENTIFIEROptional. Tool identifier sent to NCBI.@cyanheads/pubmed-mcp-server/<version>
NCBI_REQUEST_DELAY_MSMilliseconds to wait between NCBI requests. Dynamically set (e.g., 100ms with API key, 334ms without).(see src/config/index.ts)
NCBI_MAX_RETRIESMaximum number of retries for failed NCBI requests.3

Note on HTTP Port Retries: If the MCP_HTTP_PORT is busy, the server automatically tries the next port (up to 15 times).

Security Note for HTTP Transport: When using MCP_TRANSPORT_TYPE=http, authentication is mandatory as per the MCP specification. This server includes JWT-based authentication middleware. You MUST set a strong, unique MCP_AUTH_SECRET_KEY in your production environment.

For a comprehensive list of all available environment variables, their descriptions, and default values, please review the configuration loader at src/config/index.ts.

🏗️ Project Structure Overview

The src/ directory contains the core logic:

  • config/: Environment variable loading and package information.
  • mcp-server/: The heart of the PubMed MCP server.
    • server.ts: Initializes the server instance and registers all tools and resources.
    • resources/: Implementations for MCP resources (e.g., server status, PubMed statistics).
    • tools/: Implementations for MCP tools (like searchPubMedArticles, fetchPubMedContent, getPubMedArticleConnections).
    • transports/: Handles stdio and http (SSE) communication, including authentication for HTTP.
  • services/: Integrations with external services.
    • NCBI/ncbiService.ts: Manages all interactions with NCBI E-utilities, including API calls, rate limiting, and response parsing.
    • llm-providers/: (Optional) For integrating LLM capabilities directly within the server.
  • types-global/: Shared TypeScript definitions, especially for errors and MCP types.
  • utils/: A comprehensive suite of reusable utilities for logging, error handling, security, parsing, metrics, and more.

For a detailed file tree, run: npm run tree or see Directory Tree.

🧩 Extending with More PubMed Capabilities

Adding new tools or resources is straightforward:

  1. Directory Setup: Create a new directory under src/mcp-server/tools/yourNewTool/ or src/mcp-server/resources/yourNewResource/.
  2. Implement Core Logic (logic.ts):
    • Define Zod schemas for input validation.
    • Write the function that interacts with src/services/NCBI/ncbiService.ts (e.g., ncbiService.eLink(...)).
    • Parse the NCBI response and format it according to MCP specifications (CallToolResult or ReadResourceResult).
  3. Register the Capability (registration.ts):
    • For tools: server.tool(name, description, zodSchemaShape, handlerFunction)
    • For resources: server.resource(registrationName, template, metadata, handlerFunction)
    • Always wrap your logic in ErrorHandler.tryCatch for robust error management.
  4. Export and Integrate: Export the registration function from your new directory's index.ts and call it within src/mcp-server/server.ts.

🌍 Learn More

📜 License

This project is licensed under the Apache License 2.0. See the LICENSE file for details.

This server cannot be installed

-
security - not tested
A
license - permissive license
-
quality - not tested

A bridge connecting AI agents to NCBI's PubMed database through the Model Context Protocol, enabling seamless searching, retrieval, and analysis of biomedical literature and data.

  1. 🚀 Core Capabilities: PubMed Tools 🛠️
    1. ✨ Key Features Beyond Tools
      1. 🚀 Quick Start
        1. ⚙️ Configuration
          1. Server Configuration (Environment Variables)
        2. 🏗️ Project Structure Overview
          1. 🧩 Extending with More PubMed Capabilities
            1. 🌍 Learn More
              1. 📜 License

                Related MCP Servers

                • PubMed MCP Server

                  rikachu225
                  -
                  security
                  F
                  license
                  -
                  quality
                  An MCP server implementation that enables searching and retrieving research articles from PubMed with specific focus on open access content filtering and full-text link retrieval.
                  Last updated -
                  4
                  3
                  JavaScript

                • medRxiv-MCP-Server

                  JackKuo666
                  -
                  security
                  F
                  license
                  -
                  quality
                  🔍 Enable AI assistants to search and access medRxiv papers through a simple MCP interface. The medRxiv MCP Server provides a bridge between AI assistants and medRxiv's preprint repository through the Model Context Protocol (MCP). It allows AI models to search for health sciences preprints and acce
                  Last updated -
                  1
                  Python
                  • Linux
                  • Apple

                • mcp-cortellis

                  uh-joan
                  -
                  security
                  A
                  license
                  -
                  quality
                  An MCP server enabling AI assistants to search and analyze pharmaceutical data through Cortellis. Features comprehensive drug search, ontology exploration, and real-time clinical trial data access.
                  Last updated -
                  Python
                  MIT License
                  • Linux
                  • Apple

                • MedAdapt Content Server

                  ryoureddy
                  -
                  security
                  A
                  license
                  -
                  quality
                  A specialized Model Context Protocol server that enhances AI-assisted medical learning by connecting Claude Desktop to PubMed, NCBI Bookshelf, and user documents for searching, retrieving, and analyzing medical education content.
                  Last updated -
                  Python
                  MIT License
                  • Apple

                View all related MCP servers

                New MCP Servers

                MCP directory API

                We provide all the information about MCP servers via our MCP API.

                curl -X GET 'https://glama.ai/api/mcp/v1/servers/cyanheads/pubmed-mcp-server'

                If you have feedback or need assistance with the MCP directory API, please join our Discord server