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 paperlit_review_knowledge_graph.png— entity co-occurrence networklit_review_knowledge_gaps.txt— identified gapslit_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.