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pubmed-database

Search PubMed and retrieve biomedical literature and citation metadata via NCBI E-utilities.

66|8|Updated Mar 13, 2026
Search Tags:#ncbi#pubmed#literature-search#esummary#efetch#pmid#citation-lookup
One-click install
npx skills add https://github.com/mikkelkrogsholm/skills --skill pubmed-database-mikkelkrogsholm
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: pubmed-database
Source: https://github.com/mikkelkrogsholm/skills/tree/main/skills/pubmed-database
Command: npx skills add https://github.com/mikkelkrogsholm/skills --skill pubmed-database-mikkelkrogsholm

SYSTEM DOCUMENTATION & REQUIREMENTS

💡 This Skill includes references (resource) components.

What problem does it solve?

Provides accurate, up-to-date access to biomedical and life sciences literature so users can find, read, and cite primary research without guessing or relying on stale knowledge.

Core Features & Use Cases

  • Search PubMed using full query syntax (MeSH, field tags, Boolean operators) and retrieve ranked PMIDs.
  • Fetch abstracts or MEDLINE records for one or more PMIDs and retrieve full bibliographic metadata for a single PMID.
  • Match partial citations to PMIDs using ECitMatch for citation lookup and discovery.
  • Output results in JSON for programmatic use, table for quick human review, or plain text for reading.
  • Use Case: A researcher assembling evidence for a systematic review can run precise queries, page through results, extract abstracts, and collect citation metadata for screening.

Quick Start

Search PubMed for randomized controlled trials on GLP-1 receptor agonists for obesity and return the five most recent PMIDs and abstracts.

Frequently Asked Questions about pubmed-database

High-intent search queries and answers about installing and using this skill.

FAQPage Schema
How do I search PubMed for biomedical literature and retrieve abstracts?▼

Search PubMed by executing full query syntax with MeSH terms and Boolean operators to retrieve ranked PMIDs, then fetch abstracts or MEDLINE records containing bibliographic metadata for literature review.

Can I look up a PubMed citation using a PMID or DOI?▼

Yes, you can look up PubMed citations by fetching full bibliographic metadata for a single PMID or DOI, or by using ECitMatch to match partial citations to PMIDs for citation discovery.

How do I find randomized controlled trials and clinical trials on PubMed?▼

Find clinical trials on PubMed by applying clinical trial and publication-type filters to your search query, returning ranked PMIDs that match specific study designs for evidence retrieval.

Does PubMed E-utilities support pagination and rate-limit handling for systematic reviews?▼

Yes, NCBI E-utilities support pagination and rate-limit handling with retry and backoff logic, enabling researchers to page through large result sets for systematic review evidence screening.

What output formats can I get when fetching MEDLINE records from PubMed?▼

Fetch MEDLINE records from PubMed and output results in JSON for programmatic use, table format for quick human review, or plain text for reading abstracts and bibliographic metadata.

What is ECitMatch used for in PubMed citation lookup?▼

ECitMatch is used for citation lookup and discovery by matching partial citation information to PMIDs, allowing users to retrieve accurate PubMed identifiers from incomplete bibliographic references.

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