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LeonChaoX
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pubmed-database

Construct Boolean and MeSH queries and retrieve PubMed records via E-utilities.

783|65|Updated Feb 27, 2026
Search Tags:#systematic review#literature search#pubmed#api automation#mesh terms#e-utilities#pmid extraction
One-click install
npx skills add https://github.com/LeonChaoX/qinyan-academic-skills --skill pubmed-database-leonchaox
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: pubmed-database
Source: https://github.com/LeonChaoX/qinyan-academic-skills/tree/main/skills/01-%E8%AE%BA%E6%96%87%E6%A3%80%E7%B4%A2%E4%B8%8E%E6%96%87%E7%8C%AE%E7%AE%A1%E7%90%86/pubmed-database
Command: npx skills add https://github.com/LeonChaoX/qinyan-academic-skills --skill pubmed-database-leonchaox

SYSTEM DOCUMENTATION & REQUIREMENTS

💡 This Skill includes references (resource) components.

What problem does it solve?

It solves the problem of building accurate, reproducible PubMed literature searches and retrieving PubMed records programmatically for biomedical research and systematic reviews.

Core Features & Use Cases

  • Advanced Boolean & MeSH Query Building: Compose complex queries with field tags, MeSH terms, publication types, and date filters to narrow or broaden results reliably.
  • E-utilities API Automation: Use PubMed’s E-utilities (ESearch/EFetch/ESummary/ELink) to fetch PMIDs, abstracts, and structured records for downstream screening and analysis.
  • Batch Workflows for Large Result Sets: Apply rate-limit-aware batching (including history server patterns) to support large-scale evidence gathering.
  • Citation Discovery & Export: Match citations by identifiers (PMID/DOI/PMC) and export records for citation management workflows.

Quick Start

Ask your AI agent to search PubMed for “diabetes mellitus” articles from 2023 to 2024 that are systematic reviews and return the top PMIDs and titles using the E-utilities API.

Frequently Asked Questions about pubmed-database

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

FAQPage Schema
How do I retrieve PubMed records programmatically for a systematic review?▼

PubMed record retrieval for systematic reviews requires using E-utilities endpoints such as ESearch and EFetch to construct advanced Boolean and MeSH queries. This approach supports batch workflows via history-server patterns to gather large-scale evidence.

What is the best way to build advanced MeSH term queries for biomedical literature searches?▼

Building advanced MeSH term queries for biomedical literature searches involves composing complex statements with field tags, publication types, and date filters. This method narrows or broadens search results reliably for reproducible systematic reviews and data extraction.

Can I use E-utilities API automation to batch fetch PMIDs and abstracts at scale?▼

Yes, E-utilities API automation supports batch fetching of PMIDs and abstracts at scale. It applies rate-limit-aware batching and history server patterns to safely retrieve structured records for large-scale evidence gathering.

Do I need an API key to handle rate limits when extracting PMIDs from PubMed?▼

An optional API key is required to handle rate limits safely during PMID extraction from PubMed. Including it in your E-utilities requests allows higher query thresholds, preventing retrieval failures when automating large-scale systematic review searches.

How does citation discovery by PMID or DOI work with PubMed E-utilities?▼

Citation discovery by PMID or DOI works by using PubMed E-utilities like ELink and ECitMatch to match citations by identifiers including PMID, DOI, and PMC. This allows you to export structured records for citation management workflows.

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