ryogena-pubmed-mcp

A small, focused Model Context Protocol server that exposes NCBI PubMed as MCP tools, so any MCP-compatible client (Claude Desktop, Claude Code, custom agents) can search the literature, fetch abstracts, walk the citation graph, and look up an author's publications without leaving the chat.

No API key required. An optional NCBI_API_KEY raises the rate limit from 3 → 10 requests/sec.

Tools

Tool	What it does
search_pubmed(query, max_results, sort)	Free-text or full-syntax PubMed query. Returns title, authors, journal, pubdate, DOI, PubMed URL.
fetch_article(pmid)	Full abstract for one PMID, with section labels preserved (Background / Methods / Results / Conclusions).
find_related(pmid, max_results)	NCBI's "related articles" neighbors — walk the citation graph from any paper.
search_by_author(author, max_results, sort)	Author publication list using the [au] field qualifier.

All tools are read-only; PubMed itself is read-only.

Install

pip install ryogena-pubmed-mcp

Or from source:

git clone https://github.com/KyleVick4/pubmed-mcp
cd pubmed-mcp
pip install -e .

Configure in Claude Desktop

Edit your claude_desktop_config.json:

{
  "mcpServers": {
    "pubmed": {
      "command": "python",
      "args": ["-m", "pubmed_mcp"],
      "env": {
        "NCBI_API_KEY": "<optional>",
        "NCBI_EMAIL":   "<optional, recommended by NCBI>"
      }
    }
  }
}

Restart Claude Desktop. The pubmed server should show up in the MCP panel with four tools.

Configure in Claude Code

claude mcp add pubmed -- python -m pubmed_mcp

Try it

Once wired up:

Find me the three most-cited papers on JAK2 V617F selectivity from 2023, then pull the abstract of the top hit.

Claude will plan a search_pubmed → fetch_article chain and cite each paper with its DOI and PubMed URL.

Verify the server before debugging your client

Use the MCP Inspector — it's the fastest way to see if the server starts cleanly and the tools register:

npx @modelcontextprotocol/inspector python -m pubmed_mcp

Run the tests

The test suite is hermetic — no NCBI requests, no network. Every HTTP call is intercepted by httpx.MockTransport.

pip install -e ".[dev]"
pytest -v

Why this exists

I built Pico, a closed-source AI-native drug discovery platform, with its own MCP server that exposes molecule and assay tools to Claude Desktop. Building ryogena-pubmed-mcp in the open lets me share the integration patterns I use — slim LLM-friendly projections, hermetic test design, error-envelope contracts — without exposing the domain code.

If you're building an MCP server and want a tiny reference, the server.py and tests/test_tools.py files together are about 500 lines and demonstrate the full pattern.

License

MIT — see LICENSE.