pubmed-database

Access PubMed REST API for biomedical literature searches with Boolean and MeSH queries.

1|Updated Jan 14, 2026

Search Tags:#research #api #literature search #ncbi #pubmed #biomedical

Ready to run

npx skills add https://github.com/Sologa/codex-pipeline --skill pubmed-database-sologa

💬 Prompt for ChatGPT / Claude Chat▼

Please help me install this Agent Skill.
Skill: pubmed-database
Source: https://github.com/Sologa/codex-pipeline/tree/main/.codex/skills/pubmed-database
Command: npx skills add https://github.com/Sologa/codex-pipeline --skill pubmed-database-sologa

SYSTEM DOCUMENTATION & REQUIREMENTS

💡 This Skill includes references (resource) components.

What problem does it solve?

This Skill provides direct programmatic access to the vast PubMed database, enabling users to search for biomedical and life sciences literature with advanced query capabilities.

Core Features & Use Cases

Advanced Search: Construct complex queries using Boolean operators, MeSH terms, and field tags.
E-utilities API: Programmatically retrieve article data, PMIDs, and summaries.
Use Case: Researchers can automate literature reviews by searching for specific topics, filtering by publication type and date, and retrieving abstracts for analysis.

Quick Start

Search PubMed for recent systematic reviews on diabetes treatment.

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 using MeSH terms and Boolean operators?▼

To search PubMed for biomedical literature, you can construct complex queries using MeSH terms, Boolean operators, and specific field tags. This enables precise, advanced literature searches directly via the REST API.

Can I automate a systematic literature review by batch processing PubMed articles?▼

Yes, you can automate systematic literature reviews by batch processing PubMed articles. The Skill supports programmatic data retrieval and batch processing to collect abstracts and article data efficiently.

What is the best way to programmatically retrieve PMIDs and article summaries from NCBI?▼

The best way to programmatically retrieve PMIDs and summaries from NCBI is by using E-utilities. This Skill provides direct REST API access to fetch article data, PMIDs, and summaries from the PubMed database.

Does PubMed API access support filtering search results by publication type and date?▼

Yes, PubMed API access supports filtering search results by publication type and date. You can automate literature reviews by searching specific topics, applying date and publication type filters, and retrieving targeted abstracts for analysis.

Are there limitations when using E-utilities for custom API implementations on PubMed?▼

While E-utilities enable custom API implementations and complex MeSH queries on PubMed, users must handle batch processing logic and adhere to NCBI's rate limits to ensure successful programmatic data retrieval without interruption.