Bioresearch Literature Analysis

Run a reproducible biomedical literature review via the BioResearch Agent literature workflow (PubMed retrieval, entity co-occurrence knowledge graph, structured review outline). Use when the user asks for a literature review, research-gap analysis, or a synthesized reading of PubMed papers on a biomedical topic.

Alim430 Updated

File contents

BioResearch Agent — Literature Analysis Skill

Capability

Performs a structured literature review over PubMed: retrieval → abstract parsing → biomedical entity extraction → co-occurrence knowledge graph → research-gap identification → structured outline. Produces data-derived artifacts instead of free-text summary only.

Run

bioresearch run literature --query "microglia Alzheimer's disease"

Outputs (in outputs/literature/)

  • lit_review_summary_table.csv — extracted entities per paper
  • lit_review_knowledge_graph.png — entity co-occurrence network
  • lit_review_knowledge_gaps.txt — identified gaps
  • lit_review_outline.md — structured review outline

Note

This skill dispatches to the framework's literature workflow. It adds no reasoning of its own; all computation runs in the workflow modules. Requires no LLM key — runs on public PubMed APIs with synthetic fallback.

Alim430/bioresearch-agent/tree/main/skills/biomedical/literature-analysis commit b0725e23e4

Frequently asked questions

npx skillmds@latest add alim430/bioresearch-literature-analysis