Pubmed RAG Synthesizer

Agent Skill: PubMed Literature RAG & Citation Agent Skill

📌 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:

1. Input Validation: Verify that the required input files or coordinates are supplied.
2. Environment Check: Ensure dependencies (LangChain, PubMedBERT, FAISS, EUtils API) are installed.
3. Execution: Run the protocol pipeline snippet below.
4. 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.