Pubmed Rag Synthesizer
Vectorizes PubMed abstracts using PubMedBERT, builds FAISS indices, and instructs agents to synthesize clinical evidence with exact PMID citations.
Install
$ agentstack add skill-yulianuzhnenko-bioinformatics-agent-skills-pubmed-rag-synthesizer ✓ scanned · ✓ verified, works with Claude Code, Cursor, and more.
Security review
✓ PassedNo 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.
Verified badge
Passed review? Show it. Paste this badge into your README, it links to the public security report.
Links to your public security report.[](https://agentstack.voostack.com/security/report/skill-yulianuzhnenko-bioinformatics-agent-skills-pubmed-rag-synthesizer) Reliability & compatibility
Declared compatibility
Compatibility is declared by the source manifest. End-to-end runtime verification is coming, see below.
We're building live execution health for every listing: tool-call success rate, median latency, uptime, and last-checked timestamps, measured, not self-reported. It isn't live yet, so we don't show numbers we can't stand behind.
How agent discovery & health will work →About
Agent Skill: PubMed Literature RAG & Citation Agent Skill
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📌 Description
Vectorizes PubMed abstracts using PubMedBERT, builds FAISS indices, and instructs agents to synthesize clinical evidence with exact PMID citations.
🤖 Agent Execution Protocol
When an AI Agent is tasked with pubmed-rag-synthesizer:
- Input Validation: Verify that the required input files or coordinates are supplied.
- Environment Check: Ensure dependencies (
LangChain, PubMedBERT, FAISS, EUtils API) are installed. - Execution: Run the protocol pipeline snippet below.
- Output Generation: Produce actionable Markdown/JSON summaries with publication figures.
💻 Protocol Code Snippet
def build_pubmed_rag(pmid_list):
# Vector Search Pipeline
print(f"Indexing {len(pmid_list)} PubMed abstracts for RAG synthesis.")
📥 Input & Output Specifications
Input Contract
- Target Files: Valid input data matching domain formats.
- Parameters: Quality thresholds and cutoffs.
Output Contract
- Results Table: Structured summary dataframe or matrix.
- Visualization: Rendered SVG/PNG figures.
📄 License
Distributed under the MIT License. See LICENSE for details.
Source & license
This open-source skill is cataloged on AgentStack and links to its original source — we do not rehost the code.
- Author: YuliaNuzhnenko
- Source: YuliaNuzhnenko/bioinformatics-agent-skills
- License: MIT
Install and usage instructions live in the source repository linked above.
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Versions
- v0.1.0 Imported from the upstream source.