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pubmed-literature-search

pubmed-literature-search

github.com/open-medicaProductivity2782 installsUpdated 30w ago
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About pubmed-literature-search

pubmed-literature-search is a skill for AI agents to search biomedical citations through the NCBI E-utilities API. It supports field-specific Boolean queries, MeSH terms, filters, citation metadata, and available full-text links.

Key features

  1. 01Boolean and field-specific search
  2. 02MeSH term expansion
  3. 03Citation metadata retrieval
  4. 04Date, language, and species filters
  5. 05PMC and DOI access links

Use cases

  1. 01Find studies for systematic reviews
  2. 02Look up evidence on adverse reactions
  3. 03Collect trials for guideline development
  4. 04Identify gaps in biomedical research

Install

Copy the command and run it in a terminal.

$npx skills add https://github.com/open-medica/open-medical-skills --skill pubmed-literature-search

After installing, type/pubmed-literature-searchin Claude Code to confirm it loaded.

Details

From the project README

PubMed Medical Literature Search

Search over 36 million biomedical citations from PubMed and PubMed Central using the NCBI E-utilities API. This skill enables AI agents to perform advanced literature searches with boolean operators, MeSH term expansion, author and journal filtering, date range restrictions, and direct full-text access links -- bringing the power of systematic literature review directly into clinical and research AI workflows.

Quick Install

npx skills add Open-Medica/open-medical-skills --skill pubmed-literature-search

What It Does

  • Advanced boolean search across PubMed's entire 36M+ citation database using AND, OR, NOT operators with field-specific qualifiers (title, abstract, author, journal, MeSH)
  • MeSH term integration for standardized medical vocabulary searches, including automatic term explosion to capture narrower descriptors in the MeSH hierarchy
  • Citation metadata retrieval including authors, journal, publication date, DOI, PubMed ID, abstract text, MeSH headings, and publication type
  • Full-text access links via PubMed Central (PMC) when articles are available open-access, with fallback to DOI resolver links
  • Date-range and filter support to restrict results by publication year, article type (RCT, meta-analysis, review, case report), language, and species (human/animal)

Clinical Use Cases

  • Systematic literature review: A researcher preparing a systematic review on SGLT2 inhibitors in heart failure can construct complex boolean queries with MeSH terms, retrieve all matching citations with abstracts, and export structured results for screening -- replacing hours of manual PubMed navigation.
  • Point-of-care evidence lookup: A hospitalist encountering an unusual drug reaction can quickly search for case reports and pharmacovigilance studies linking the specific drug and adverse event, receiving summarized abstracts within seconds.
  • Guideline development support: A clinical guideline committee can programmatically search for all RCTs and meta-analyses on a specific intervention, filter by date range and quality indicators, and generate a structured evidence table for committee review.
  • Research gap identification: An academic physician planning a grant proposal can query existing literature on a topic, identify the most recent publications, and determine where evidence gaps remain to justify new research.

Safety & Evidence

  • Safety Classification: Safe -- This skill queries a public, read-only database (NCBI PubMed). It does not make clinical decisions, alter patient data, or prescribe treatments. All returned data consists of published, peer-reviewed citations.
  • Evidence Level: High -- PubMed is the gold-standard biomedical literature database maintained by the U.S. National Library of Medicine (NLM). The E-utilities API is the official programmatic interface used by thousands of research institutions worldwide.

Example Usage

Search for recent meta-analyses on metformin and cardiovascular outcomes:

Search PubMed for meta-analyses published in the last 5 years
examining metformin's effect on cardiovascular mortality in
type 2 diabetes. Use MeSH terms and restrict to English-language
articles.

Find case reports of a rare adverse drug reaction:

Search PubMed for case reports of pembrolizumab-induced
myocarditis. Include the abstract text and PMC full-text links
where available. Sort by most recent first.

Technical Details

  • Category: Research
  • Author: OMS Contributors (original: Augmented-Nature)
  • License: MIT
  • API: NCBI E-utilities (ESearch, EFetch, ESummary, ELink)
  • Rate Limits: NCBI allows 3 requests/second without API key, 10 requests/second with a free NCBI API key
  • Dependencies: HTTP client (curl/fetch), XML/JSON parser

References

This skill is part of Open Medical Skills, a curated marketplace of medical AI skills maintained by physicians for physicians and the healthcare industry.

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