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PubMed MCP Server

Pubmed Claude Remote MCP

Installation

Add the following to your MCP client configuration file.

Configuration

{
  "mcpServers": {
    "aglitch120-pubmed-remote": {
      "url": "https://pubmed-mcp-server.onrender.com/sse",
      "headers": {
        "HOST": "0.0.0.0",
        "PORT": "8000",
        "NODE_ENV": "production",
        "LOG_LEVEL": "info",
        "NCBI_EMAIL": "[email protected]",
        "MAX_RESULTS": "100",
        "MCP_TRANSPORT": "sse",
        "REQUEST_TIMEOUT": "30000"
      }
    }
  }
}

You run a PubMed MCP Server to access biomedical literature data through structured Model Context Protocol transports. It enables you to search PubMed, retrieve abstracts and full text where available, export citations, analyze metrics, and perform batch processing with reliable remote or local transports suitable for cloud deployments and desktop workflows.

How to use

Connect your MCP client to the PubMed MCP Server using either the remote SSE/HTTP transport or the local stdio transport. The remote mode exposes HTTP/SSE endpoints for cloud deployments, while the local mode runs as a standard process on your machine and communicates via stdin and stdout. Once connected, you can perform targeted searches, fetch abstracts or full texts, export citations, and run batch operations across multiple PMIDs.

How to install

Prerequisites: you need Node.js v18.x or higher and a package manager such as npm or yarn.

Option 1. Deploy to a remote host (recommended for remote access)

Step 1: Start a remote MCP server on a cloud platform that supports the transport mode you choose (SSE/HTTP). The remote endpoint URL is used to connect your MCP client.

Step 2: Configure environment variables in the hosting environment. Required variables include at minimum: NCBI_EMAIL and MCP_TRANSPORT set to sse, along with host and port settings as needed.

Step 3: Your remote service will be reachable at a URL similar to the one provided after deployment.

Option 2. Run locally in stdio mode

Step 1: Install dependencies and build the project locally.

Step 2: Run the local stdio server with the appropriate command so your client can connect via stdin/stdout.

Configuration and usage notes

Configure your Claude Desktop or preferred MCP client with one or both of the following connection methods if you need to support multiple environments.

/* Remote, HTTP/SSE endpoint configuration example */
{
  "mcpServers": {
    "pubmed-remote": {
      "url": "https://pubmed-mcp-server.onrender.com/sse"
    }
  }
}

Or, for local development and testing in stdio mode, use a local process invocation that points to the built server runtime.

{
  "mcpServers": {
    "pubmed": {
      "command": "node",
      "args": ["/path/to/pubmed-mcp-remote/dist/index.js"],
      "env": {
        "NCBI_EMAIL": "[email protected]"
      }
    }
  }
}

Available tools

search_pubmed

Search PubMed with comprehensive summaries and metadata

get_full_abstract

Retrieve complete abstracts by PMID

get_full_text

Extract full text from PMC open access articles

export_ris

Export citations in RIS format for reference managers

get_citation_counts

Analyze citation metrics using NCBI elink API

optimize_search_query

Transform natural language to optimized PubMed queries with MeSH terms

find_similar_articles

Find similar articles using NCBI's similarity algorithm

batch_process

Process multiple PMIDs with multiple operations efficiently