MCP Simple Pubmed MCP Server

An MCP server that provides access to PubMed articles through the Entrez API.

Local serverstdioPython

What is the MCP Simple Pubmed MCP server?

An MCP server that provides access to PubMed articles through the Entrez API. That is what the mcp simple pubmed mcp server brings to an AI assistant: the same capability, reachable through the Model Context Protocol rather than a separate app or dashboard.

The tools it exposes

The server publishes 2 tools. What each one is for:

  • Tools — The Tools tool exposed by this server
  • Notes — Please note that the tool returns XML-ized version of full text. It is however more useful for AIs than a "human readable" text would have been as it

What it needs from you

Configuration is passed through the environment: PUBMED_EMAIL, PUBMED_API_KEY. Treat anything key-shaped as a real credential — scope it to the minimum the server needs, and rotate it if it ever lands in a shared config.

Getting it running

@smithery/cli on npm is all you need. Most clients run it directly, so configuration is a few lines and a restart.

How it compares

This sits in the planning and project tracking group, where several servers overlap in what they claim to do but differ sharply once you actually set them up. MCP Simple Pubmed's toolset — Tools, Notes — is a fair guide to whether it matches your workflow. It is maintained by andybrandt; worth a glance at recent repository activity before you build anything load-bearing on it.

We check each listing at SyncDev against the project's documentation before it goes live — if something here drifts out of date, it is a bug worth reporting.

Things to watch

  • It runs with your machine's permissions. That is convenient and also the reason to think about what you point it at before you approve a tool call.
  • Missing credentials fail quietly in some clients — if no tools show up, check the environment block first.
  • Keep per-call confirmation enabled while you learn its behaviour; it is the cheapest safeguard you have.

Available tools

ToolWhat it does
ToolsThe Tools tool exposed by this server.
NotesPlease note that the tool returns XML-ized version of full text. It is however more useful for AIs than a "human readable" text would have been as it gives them additional information about document's structure. At least

How to install the MCP Simple Pubmed MCP server

{
  "mcpServers": {
    "simple-pubmed": {
      "command": "python",
      "args": ["-m", "mcp_simple_pubmed"],
      "env": {
        "PUBMED_EMAIL": "your-email@example.com",
        "PUBMED_API_KEY": "your-api-key" 
      }
    }
  }
}

Configuration as documented by the project. Restart the client after saving.

Configuration

VariableDescriptionRequired
PUBMED_EMAILConfiguration value read at startup.Optional
PUBMED_API_KEYCredential the server authenticates with.Yes

Example prompts to try

  • Use MCP Simple Pubmed to Tools.
  • Use MCP Simple Pubmed to Notes.

Frequently asked questions

It connects MCP Simple Pubmed to MCP-compatible AI assistants such as Claude and Cursor, exposing 2 tools (Tools, Notes) that the assistant can call on your behalf. Instead of copying data back and forth by hand, the assistant works with MCP Simple Pubmed directly.