# puumed [Health: Active]

**Category:** 🧬 Biology & Bioinformatics  
**Repository:** https://github.com/pipeworx-io/mcp-pubmed  
**GitHub Stars:** 1  
**Views:** 2  
**Installs:** 0  
**Upvotes:** 0  
**Directory Page:** https://allmcps.com/mcp/puumed

## Description
PubMed MCP — wraps the NCBI E-utilities API (biomedical literature, free, no auth)

## Claude Desktop Quick Installation
Install path detected from listing signals. Uses `npx` (confidence: high):

```json
"mcpServers": {
  "puumed": {
    "command": "npx",
    "args": ["-y","@pipeworx/mcp-pubmed"]
  }
}
```

## Documentation

## What the puumed MCP server does

The puumed MCP server exposes PubMed data to MCP-compatible AI clients. PubMed contains biomedical and life-science citations indexed by the U.S. National Library of Medicine, with MeSH terms that support structured searching. The server is suited to finding literature, inspecting individual records, and summarizing patterns across a query’s results.

Its search workflow can handle ordinary keywords, MeSH fields, author queries, title or abstract fields, and publication-date limits. For a specific article, a PMID lookup can return the title, abstract, authors, MeSH tags, and related record information. Summary results also include author affiliations and email addresses when those details appear in the indexed record and can be detected in the affiliation text.

## How it works

The server calls the NCBI E-utilities API and presents the results as MCP tools. The gateway endpoint is available at `https://gateway.pipeworx.io/pubmed/mcp`; a full Pipeworx gateway connection can also reach the same PubMed tools. Gateway connections include shared Pipeworx meta-tools, while the local package exposes only the PubMed pack’s tools.

The puumed MCP server can also run locally through the `@pipeworx/mcp-pubmed` package. In that mode, it communicates over standard input and output and does not require a Pipeworx account or a gateway round trip. HTTP callers can invoke tools through the gateway’s REST-style endpoint instead of using an MCP client.

NCBI requests are free and do not require authentication. Unkeyed requests are limited to three per second; an optional NCBI API key raises the limit to ten per second. The key can be passed through the tool’s `_apiKey` parameter.

## Tools and capabilities

The documented PubMed tools include:

- `search_pubmed` for keyword, MeSH, author, fielded, and date-bounded searches.
- `get_summary` for retrieving detailed information for returned PMIDs, including author detail when indexed.
- `pubmed_evidence_landscape` for counting categories such as clinical trials, randomized trials, systematic reviews, meta-analyses, observational studies, and case reports.
- `pubmed_publication_trend` for annual publication counts over a bounded period.
- `pubmed_integrity_check` for finding NLM-indexed retractions, expressions of concern, errata, updates, and related notices.

Use quotation marks for an exact technical phrase, optionally with a field such as `[tiab]`. Date bounds use four-digit `from_year` and `to_year` values. MeSH searches can target exact headings, major topics, titles, or authors through PubMed field syntax.

## Limitations and notes

The puumed MCP server relies on PubMed’s indexing. Recent papers may not have MeSH terms yet, so keyword searches can be more appropriate for new literature. Author-name searches can be ambiguous, particularly for common names, and older records may not have enough information for reliable disambiguation.

PubMed generally focuses on formally published literature and does not serve as a comprehensive preprint index. Many records provide abstracts rather than full text, and a PubMed inclusion is not a guarantee of journal quality. Publication-type counts can overlap, the current year may be incomplete, and counts do not establish evidence quality or treatment efficacy. Integrity checks report relationships indexed by NLM; an unflagged citation has not been independently validated.

_Full upstream README: https://allmcps.com/mcp/puumed/readme_