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Bioresearch Literature Analysis

skill-alim430-bioresearch-agent-literature-analysis · by Alim430

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.

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Install

$ agentstack add skill-alim430-bioresearch-agent-literature-analysis

✓ scanned · ✓ verified — works with Claude Code, Cursor, and more.

Security review

✓ Passed

No issues found. Passed automated security review. · v0.1.0 How review works →

  • ✓ Prompt-injection patterns
  • ✓ Secret / credential exfiltration
  • ✓ Dangerous shell & filesystem operations
  • ✓ Untrusted network calls
  • ✓ Known-malicious package signatures

What it can access

  • ✓ Network access No
  • ✓ Filesystem access No
  • ✓ Shell / process execution No
  • ✓ Environment & secrets No
  • ✓ Dynamic code execution No

From automated source analysis of v0.1.0. “Used” means the capability is present in the source — more access means more to trust, not that it’s unsafe.

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About

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.

Source & license

This open-source skill is cataloged on AgentStack and links to its original source — we do not rehost the code.

Install and usage instructions live in the source repository linked above.

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Versions

  • v0.1.0 Imported from the upstream source.

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