skills.rest
biomaps-infra
biomaps-infraOFFICIAL
Explore all skills by this author →
GitHub

db-pubmed

Search and retrieve PubMed biomedical literature via REST API.

Updated Mar 13, 2026
Search Tags:#research#api#literature search#pubmed#biomedical#mesh#eutilities
One-click install
npx skills add https://github.com/biomaps-infra/blender-opencode --skill db-pubmed
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: db-pubmed
Source: https://github.com/biomaps-infra/blender-opencode/tree/main/.opencode/skills/db-pubmed
Command: npx skills add https://github.com/biomaps-infra/blender-opencode --skill db-pubmed

SYSTEM DOCUMENTATION & REQUIREMENTS

💡 This Skill includes references (resource) components.

What problem does it solve?

This Skill provides direct REST API access to PubMed, enabling users to search and retrieve comprehensive biomedical and life sciences literature for research, systematic reviews, and data analysis.

Core Features & Use Cases

  • Advanced Search: Construct complex queries using Boolean operators, MeSH terms, and field tags.
  • Programmatic Access: Utilize the E-utilities API for automated data retrieval and batch processing.
  • Use Case: A researcher needs to find all systematic reviews published in 2023 on the topic of Type 2 Diabetes treatment. This Skill can construct the precise query, fetch the relevant article IDs, and retrieve their abstracts.

Quick Start

Search PubMed for recent articles on 'CRISPR gene editing'.

Frequently Asked Questions about db-pubmed

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?▼

You can search PubMed using advanced Boolean operators, MeSH terms, and field tags to construct complex queries. This enables precise retrieval of biomedical literature for research and systematic reviews via direct REST API access.

What is the E-utilities API and how does it work for PubMed literature search?▼

The E-utilities API provides programmatic access to the PubMed database, enabling automated data retrieval and batch processing. It allows you to fetch article IDs and retrieve abstracts directly through REST API endpoints for biomedical literature search.

Can I use batch processing to retrieve abstracts for a systematic review?▼

Yes, batch processing is supported for retrieving abstracts and managing citations during systematic reviews. You can fetch relevant article IDs in batches and extract the data programmatically using the E-utilities API integration.

Does this method support citation management for biomedical research papers?▼

Yes, citation management is fully supported for biomedical research papers. The system retrieves article metadata and abstracts from PubMed, facilitating the organization of references needed for systematic reviews and data analysis.

What's the best way to automate data extraction from PubMed for biomedical literature?▼

The best way to automate data extraction from PubMed is by utilizing the E-utilities API for programmatic access. This allows you to construct precise queries, fetch article IDs, and retrieve abstracts in batches for automated data processing.

Related Skills

Explore More Education & Research Skills→
jaechang-hitsjaechang-hits
298

pubmed-database

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

Community
Advanced
nahisahonahisaho
3

scientific-literature-search

Aggregate scholarly literature metadata and citation networks from five databases.

Community
Advanced
erafaterafat
16

cite-them-all

Identify citation-worthy claims in Markdown manuscripts and search PubMed for supporting literature.

Community
Intermediate
Yezez9Yezez9

pubmed-database

Search and retrieve biomedical literature via the PubMed REST API.

Community
Advanced