# PubMed Search

An MCP server that connects your agent to PubMed, Europe PMC, OpenAlex and CORE: article search, citations, full texts and figure captions.

- MCP server · `type=mcp` · Claude Code, Codex, Cursor, GitHub Copilot, Windsurf (Devin Desktop), Cline, Zed, Gemini CLI · ★ 28
- Author: u9401066
- License: not stated · policy=link-only · description only; the file stays with the author
- Source: https://github.com/u9401066/pubmed-search-mcp
- Updated: 2026-10-20
- HTML: https://affpapa.org/en/nevibecode/mcp/pubmed-search

## What it does

You run it from PyPI with `uvx` over stdio. The package exposes 41 tools: plain search, pipeline mode, citation snowballing and a research chronicle whose rebuilds get compared between revisions. Open-access PMC articles also yield figure captions, image links and PDFs.

NCBI calls are keyed, so `NCBI_API_KEY` and `NCBI_EMAIL` go into the environment at install time. There is a multi-tenant mode with per-tenant sessions, caches and bearer-token auth, meant for serving several agents from one deployment.

Bundled extras include 26 workflow skills aimed at Claude and a Copilot setup guide for VS Code. If the same article keeps coming back in a session, `options="exclude_seen"` drops PMID and DOI identities already returned — outside pipeline mode, which rejects the flag with `pipeline=`.

## Requirements
- Needs: Python and uv (commands run via uvx)
- Environment variables: `NCBI_EMAIL`, `NCBI_API_KEY` — keys and tokens: ask the human for the values, never commit them or put them in shared files.

## Install

### Claude Code (native platform)

**Platform CLI**
```bash
claude mcp add --env NCBI_EMAIL=<NCBI_EMAIL> --env NCBI_API_KEY=<NCBI_API_KEY> --transport stdio pubmed-search -- uvx pubmed-search-mcp
```
Replace <…> with your own values. uvx runs the command named after the package; if the README names another one, use uvx --from pubmed-search-mcp <command>

### Codex

**Platform CLI**
```bash
codex mcp add pubmed-search --env NCBI_EMAIL=<NCBI_EMAIL> --env NCBI_API_KEY=<NCBI_API_KEY> -- uvx pubmed-search-mcp
```
Replace <…> with your own values. uvx runs the command named after the package; if the README names another one, use uvx --from pubmed-search-mcp <command>

### Cursor

**Config file**
File `.cursor/mcp.json`:
```json
{
    "mcpServers": {
        "pubmed-search": {
            "command": "uvx",
            "args": [
                "pubmed-search-mcp"
            ],
            "env": {
                "NCBI_EMAIL": "<NCBI_EMAIL>",
                "NCBI_API_KEY": "<NCBI_API_KEY>"
            }
        }
    }
}
```
Replace <…> with your own values. uvx runs the command named after the package; if the README names another one, use uvx --from pubmed-search-mcp <command>

### GitHub Copilot

**Config file**
File `.vscode/mcp.json`:
```json
{
    "servers": {
        "pubmed-search": {
            "type": "stdio",
            "command": "uvx",
            "args": [
                "pubmed-search-mcp"
            ],
            "env": {
                "NCBI_EMAIL": "<NCBI_EMAIL>",
                "NCBI_API_KEY": "<NCBI_API_KEY>"
            }
        }
    }
}
```
Replace <…> with your own values. uvx runs the command named after the package; if the README names another one, use uvx --from pubmed-search-mcp <command>

### Gemini CLI

**Platform CLI**
```bash
gemini mcp add -e NCBI_EMAIL=<NCBI_EMAIL> -e NCBI_API_KEY=<NCBI_API_KEY> pubmed-search uvx pubmed-search-mcp
```
Replace <…> with your own values. uvx runs the command named after the package; if the README names another one, use uvx --from pubmed-search-mcp <command>

## When to use it
- search PubMed and Europe PMC for a topic in one call
- follow which papers cite a key study
- pull figure captions and PDF links from open-access PMC articles
- diff two runs of a search pipeline
- serve several agents from one server with separate sessions

## Example prompts
- Search PubMed for CRISPR reviews from the last two years, most cited first
- Snowball the citations of the paper with PMID 31234567 across PubMed and Europe PMC
- Run an OpenAlex search and skip anything already returned in this session

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