biomedical-literature-search

Search PubMed and bioRxiv for biomedical papers with structured metadata.

1.1k|132|Updated Apr 13, 2023
One-click install
npx skills add https://github.com/PharMolix/OpenBioMed --skill biomedical-literature-search
Or copy as Structured Prompt for Agent
Please help me install this Agent Skill.
Skill: biomedical-literature-search
Source: https://github.com/PharMolix/OpenBioMed/tree/main/skills/biomedical-literature-search
Command: npx skills add https://github.com/PharMolix/OpenBioMed --skill biomedical-literature-search

SYSTEM DOCUMENTATION & REQUIREMENTS

What problem does it solve?

Biomedical researchers often spend excessive time locating and summarizing relevant literature. This skill streamlines discovery by integrated PubMed and bioRxiv lookups, delivering concise, structured results.

Core Features & Use Cases

  • PubMed keyword search to find papers with titles and abstracts.
  • bioRxiv date-range retrieval to fetch recent preprints, with optional category filtering.
  • Structured outputs including title, abstract, authors, DOI, date, and link to source for quick literature reviews or drug discovery planning.
  • Use Case: build a literature brief on a disease topic and export key papers for an evidence map.

Quick Start

Ask me to search PubMed for "PD-1 inhibitor cancer" and fetch recent bioRxiv preprints on that topic.

Frequently Asked Questions about biomedical-literature-search

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

FAQPage Schema
How do I search biomedical literature across PubMed and bioRxiv?

Search biomedical literature by entering keyword queries for PubMed to find peer-reviewed papers or specifying date ranges and categories to fetch recent preprints from bioRxiv. Results include titles, abstracts, authors, DOIs, dates, and source links.

Can I retrieve bioRxiv preprints by date range and category?

Yes, you can retrieve bioRxiv preprints by specifying a date range and applying optional category filtering. This fetches recent preprints, returning structured metadata including titles, authors, DOIs, dates, and links to the source documents.

How does PubMed keyword search handle papers with missing abstracts?

PubMed keyword search handles missing abstracts robustly by returning the available metadata such as title, authors, DOI, and date without failing the query. This ensures you still receive structured, machine-friendly output for literature reviews.

What is the best way to build a literature brief on a disease topic?

Build a literature brief by running a keyword-based PubMed search for the disease topic and fetching related bioRxiv preprints. This delivers structured outputs with titles, abstracts, authors, and DOIs suitable for rapid literature review or drug discovery planning.

Does biomedical literature search return structured output for downstream analysis?

Yes, biomedical literature search returns machine-friendly structured output containing titles, abstracts, authors, DOIs, dates, and links. This structured format is designed specifically for downstream analysis, evidence mapping, and literature brief generation.