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Puumed

Searches PubMed and retrieves biomedical literature records, evidence counts, publication trends, and NLM-indexed integrity notices.

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Install Puumed

Pick your client, then add it in one click or paste the config.

STDIONode.js
~/Library/Application Support/Claude/claude_desktop_config.json
claude_desktop_config.json
{
  "mcpServers": {
    "puumed": {
      "command": "npx",
      "args": [
        "-y",
        "@pipeworx/mcp-pubmed"
      ]
    }
  }
}

Settings → Developer → Edit Config, merge this into mcpServers, then fully quit and reopen Claude Desktop.

We couldn’t confirm it starts correctly

The install command started, but didn't respond the way we expected when we tried to talk to it.

npx -y @pipeworx/mcp-pubmed

initialize succeeded but no response to tools/list.

This is an experimental automated check and can have false negatives — missing environment variables, a slow cold install, etc. It doesn’t necessarily mean something’s wrong. Last checked 6d ago.

Overview

The puumed MCP server connects AI clients to PubMed through the NCBI E-utilities API. It supports literature searches, PMID summaries, MeSH-aware queries, evidence-landscape counts, publication trends, and integrity checks for indexed notices. Use it for biomedical research, clinical evidence reviews, drug-related questions, or citation investigation. It runs through the Pipeworx gateway or locally as a stdio MCP server, with no authentication required.

Use cases

  • Search recent biomedical literature with date and MeSH filters
  • Retrieve PMID records with author affiliations and contact details
  • Measure evidence types across a PubMed query
  • Track annual publication volume for a research topic
  • Check citations for NLM-indexed retractions and corrections

Key features

  • PubMed search through NCBI E-utilities
  • MeSH and fielded query support
  • PMID summaries with indexed author details
  • Evidence-landscape counts
  • Publication-trend analysis
  • Integrity and retraction checks

Security & health

What it can reach and how reliably it runs — from our own checks, not the maintainer’s claims.

ActiveLast checked 2d ago

Recent health check succeeded.

7/7 checks healthy over the last 46d

Supply-chain signal

No high-severity advisories surfaced by our automated scan.

Critical 0High 0Medium 0Low 0

Scanned 14d ago via OSV.dev · @pipeworx/mcp-pubmed (npm)

Adoption & maintenance

Factual signals from GitHub, npm, and our automated checks — not a rating.

GitHub stars1Stargazers on the source repository.
Last commit14d agoMost recent push to the default branch.
Install checkInconclusiveStarted but did not complete the MCP handshake in our test.
Directory activity2 viewsConfig copies, upvotes, and views on AllMCPs.

How Puumed works

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.

Read the full README View source on GitHub

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Frequently Asked Questions about Puumed

puumed is an MCP server that connects AI clients to PubMed through NCBI E-utilities. Its main tools search PubMed records, retrieve summaries with author affiliations and detected emails, measure evidence landscapes and publication trends, and check indexed integrity notices such as retractions, errata, and expressions of concern.

Install it locally with `npx -y @pipeworx/mcp-pubmed` and configure an MCP client to run that command. The package communicates over stdio and does not require a Pipeworx account. You can also connect to the hosted endpoint at `https://gateway.pipeworx.io/pubmed/mcp`.

Yes, puumed works with Cursor through the hosted MCP endpoint. Add `https://gateway.pipeworx.io/pubmed/mcp` as an MCP server URL. Cursor is also one of the clients named in the project documentation.

No, puumed does not require authentication for NCBI E-utilities access. Requests without a key are throttled to three per second, while a free NCBI API key can raise the limit to ten per second and may be passed through `_apiKey`.

Put the phrase in double quotes and optionally add a PubMed field tag such as `[tiab]`. For example, use `"cell-free RNA"[tiab]` with `from_year` and `to_year` to restrict the search and avoid unwanted automatic term expansion.

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