Literature analysis

Skill Alim430/bioresearch-agent/skills/biomedical/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.From its SKILL.md

Install

npx -y skills add Alim430/bioresearch-agent --skill literature-analysis

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SKILL.md

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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.

What ships with it

Read from the repository

Just SKILL.md. No reference files, no scripts.