pubmed-database

Search PubMed and retrieve article metadata via the NCBI E-utilities REST API.

298|27|Updated Feb 18, 2026
One-click install
npx skills add https://github.com/jaechang-hits/SciAgent-Skills --skill pubmed-database-jaechang-hits
Or copy as Structured Prompt for Agent
Please help me install this Agent Skill.
Skill: pubmed-database
Source: https://github.com/jaechang-hits/SciAgent-Skills/tree/main/skills/genomics-bioinformatics/pubmed-database
Command: npx skills add https://github.com/jaechang-hits/SciAgent-Skills --skill pubmed-database-jaechang-hits

SYSTEM DOCUMENTATION & REQUIREMENTS

💡 This Skill requires requests, and includes scripts (resource) and references (resource) components.

What problem does it solve?

This Skill provides programmatic access to the vast PubMed biomedical literature database, enabling efficient searching, retrieval, and analysis of scientific publications.

Core Features & Use Cases

  • Advanced Search: Construct complex queries using Boolean operators, MeSH terms, and field tags for precise literature retrieval.
  • Data Retrieval: Fetch article abstracts, metadata, and full records via E-utilities REST API.
  • Systematic Reviews: Facilitate the building of automated literature pipelines and systematic review search strategies.
  • Use Case: Automatically search for all randomized controlled trials on Type 2 Diabetes published in 2024, and retrieve their abstracts for further analysis.

Quick Start

Use the pubmed-database skill to search for articles on 'CRISPR AND 2024[dp]' and print the first 5 PMIDs.

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 biomedical literature using MeSH terms and Boolean operators?

You can search PubMed biomedical literature by constructing advanced queries with Boolean operators, MeSH terms, and field tags. This enables precise literature retrieval of specific article metadata and abstracts via the E-utilities REST API.

Can I fetch PubMed abstracts and full records via the NCBI E-utilities API?

Yes, you can fetch PubMed abstracts and full records programmatically via the NCBI E-utilities REST API. This allows automated retrieval of article metadata for building literature pipelines and systematic reviews.

How do I build an automated literature pipeline for a systematic review?

Build an automated literature pipeline for a systematic review by combining advanced search queries with automated data retrieval. This fetches relevant article metadata and abstracts from PubMed to streamline the review process.

Does this PubMed search approach work for retrieving specific study designs like randomized controlled trials?

Yes, this PubMed search approach works for retrieving specific study designs. You can construct complex queries using field tags and Boolean operators to isolate randomized controlled trials and fetch their abstracts for analysis.

Do I need the requests library to access the PubMed database?

Yes, you need the requests library to access the PubMed database. It handles the HTTP requests required to interface with the NCBI E-utilities REST API for executing literature searches and retrieving records.

What is the best way to retrieve recent biomedical publications using E-utilities?

The best way to retrieve recent biomedical publications using E-utilities is constructing targeted queries with publication date field tags. This filters the PubMed database precisely before fetching the article metadata and abstracts.