ragbio 2.0.2

A study-aware biomedical RAG framework for PubMed retrieval, citation-grounded summaries, and downstream omics integration

RAG-Powered Gene Discovery Assistant (ragbio)

ragbio is a study-aware, retrieval-augmented generation (RAG) toolkit for biomedical knowledge discovery built on PubMed literature, FAISS vector search, and Ollama-based large language models (DeepSeek, LLaMA-family).

It is designed as a reusable Python package that can operate standalone or as a backend service inside larger platforms such as OmniBioAI, powering chat, literature summarization, and downstream bioinformatics workflows.

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Key Capabilities

ragbio enables:

• Semantic search over PubMed abstracts using FAISS
• Study-scoped ingestion and indexing for reproducibility
• Multi-study search (single study or global across all studies)
• Instant PMID retrieval (FAISS-only, no LLM calls)
• LLM-based biomedical summarization grounded in retrieved literature
• Structured JSON outputs for literature summarizers and reporting
• Optional drug–target–disease extraction and KG population
• Progress reporting hooks for real-time UI dashboards
• Cache-aware retrieval for low-latency interactive use

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Example Questions

• Which genes are associated with oxidative stress in Alzheimer’s disease?
• What therapies target amyloid pathways according to recent literature?
• Summarize evidence linking TP53 variants to cancer therapies.
• Return PMIDs related to BRCA1 drug resistance (no summarization).

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High-Level Architecture

User Query
│
├─► FAISS Retrieval (study-specific or multi-study)
│
├─► Top-K PubMed Abstracts
│
├─► (Optional) LLM Summarization (RAG)
│
├─► (Optional) Structured Extraction (JSON)
│
└─► Outputs:
     • PMIDs (instant)
     • Grounded summaries
     • Structured JSON (literature summarizer / KG)

Important design choice (v1.1): FAISS retrieval is executed exactly once per request, and all downstream steps reuse the same retrieved documents. There is no duplicate search.

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Installation

Install from PyPI (recommended)

pip install ragbio

Development install (from source)

git clone https://github.com/man4ish/omnibioai-rag.git
cd omnibioai-rag
pip install -e .

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Data Organization (Study-Aware)

By default, all PubMed data is organized under:

data/PubMed/
├── Abstracts/<study>/
├── Metadata/<study>/
├── PDFs/<study>/
└── Index/<study>/

This enables:

• Clean separation of case studies
• Reproducible indexing
• Safe multi-study search

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Usage Guide

1️⃣ Ingest PubMed Literature (Study-Aware)

python -m ragbio.utils.rag_data_loader \
  --study Alzheimer_CaseStudy \
  --search "Alzheimer Disease AND therapy" \
  --retmax 500 \
  --retstart 0

This step:

• Fetches PubMed abstracts and metadata
• Stores results under Abstracts/<study>/
• Optionally downloads open-access PDFs

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2️⃣ Generate Embeddings & Build FAISS Index

python -m ragbio.embeddings.embedding_engine \
  --study Alzheimer_CaseStudy

• Reads abstracts from Abstracts/<study>/
• Generates embeddings via Ollama
• Writes FAISS index to Index/<study>/

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3️⃣ Run RAG Queries (CLI)

python -m ragbio.pipeline.rag_pipeline \
  --query "Which therapies target amyloid pathways in Alzheimer’s disease?" \
  --top_k 10 \
  --structured \
  --study Alzheimer_CaseStudy

Outputs include:

• Grounded summary
• Supporting PMIDs
• Optional structured JSON
• Optional Neo4j KG updates

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4️⃣ Instant PMID Retrieval (No LLM)

For low-latency applications (chat, TES, pipelines):

python -m ragbio.pipeline.rag_pipeline \
  --query "TP53 apoptosis cancer therapy" \
  --pmids-only \
  --top_k 20

✔ FAISS-only ✔ Cache-aware ✔ Suitable for real-time UI

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Python API (Recommended for Integration)

Public API (v1.1)

from ragbio.pipeline import (
    RAGAssistant,
    get_pmids,
    run_rag_json,
)

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Instant PMID Retrieval

pmids = get_pmids(
    query="BRCA1 drug resistance",
    top_k=20,
    study=None,   # search across ALL studies
)

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Structured RAG Output (Literature Summarizer)

result = run_rag_json(
    query="TP53 variants and chemotherapy response",
    top_k=10,
    study="Cancer_Study",
)

Returns structured JSON suitable for:

• Literature summarization
• ReportingService
• Downstream AI agents

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Advanced Usage (Long-Lived Assistant)

assistant = RAGAssistant(study="Alzheimer_CaseStudy")

pmids = assistant.get_pmids("amyloid beta clearance")

data = assistant.run_rag_json(
    "amyloid beta clearance therapies",
    structured=True,
)

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Multi-Study Search (v1.1)

• study="default" → search one study
• study=None or "*" → search all indexed studies
• Results are merged, ranked, and deduplicated

This allows:

• Cross-project reuse of indexed literature
• Global chat-style queries
• Meta-analysis across studies

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Caching & Performance

• PMID retrieval results are cached per:

  • query
  • study
  • index version
  • embedding model

• Cache invalidates automatically if index changes

• Designed for sub-second responses in chat workflows

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Progress Reporting (UI-Ready)

All major steps emit progress events that can be wired to:

• OmniBioAI progress bars
• WebSocket updates
• TES run monitors

Example stages:

• retrieval_start
• retrieval_complete
• llm_summarization
• structured_extraction_complete

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Technologies Used

Category	Tools
Language	Python 3.10+
Retrieval	FAISS
Embeddings	Ollama embedding models
LLMs	DeepSeek, LLaMA-family (via Ollama)
Data Source	PubMed (NCBI Entrez)
Graph (optional)	Neo4j
UI (optional)	Streamlit, Cytoscape

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Design Principles

• Study-first organization
• Explicit retrieval control
• No hidden FAISS calls
• Composable APIs
• Safe defaults, override when needed
• Platform-friendly (OmniBioAI, TES, agents)

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Roadmap

v1.1 (current)

• Multi-study search
• Instant PMID retrieval
• Structured JSON output
• Cache-aware retrieval
• Public Python API

v1.2+

• Streaming RAG responses
• Retrieval metrics & dashboards
• Neo4j-first knowledge graphs
• FastAPI / Django service mode
• Citation confidence scoring
• Multi-study comparative dashboards

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License

MIT License