SkyWhal3/STXBP1-RAG-Database

🧬 STXBP1-ARIA RAG Database v9 - BGE Embeddings

A pre-built ChromaDB vector database containing ~570,000 indexed text chunks from ~17,000 curated PubMed Central (PMC) biomedical papers related to STXBP1, Munc18-1, synaptic transmission, epileptic encephalopathy, and therapeutic research.

💡 This is the lightweight version — BGE-base runs efficiently on CPU/system RAM without requiring a GPU, making it ideal for free-tier deployments and local development. For maximum retrieval quality with NVIDIA's state-of-the-art 2048-dimensional embeddings (requires GPU with 2-4GB VRAM), see our premium database: STXBP1-RAG-Nemotron

🆕 What's New in v9

Feature	v8 (Previous)	v9 (Current)
Embedding Model	all-MiniLM-L6-v2	BGE-base-en-v1.5
Dimensions	384	768
Model Params	22M	110M
MTEB Score	~56	~63
Corpus	31,786 papers (unfiltered)	~17,000 papers (curated)
Chunks	1.19M (58% noise)	~570K (high relevance)
Quality Focus	Quantity	Precision

Why BGE?

• 2x embedding dimensions = finer semantic distinctions
• 5x larger model = better understanding of biomedical terminology
• Curated corpus = removed irrelevant papers, kept STXBP1-focused content
• MTEB benchmark leader = proven retrieval performance

📊 Dataset Statistics

Metric	Value
Total Chunks	~570,000
Source Papers	~17,000 PMC articles
Database Size	~8-10 GB
Embedding Model	BAAI/bge-base-en-v1.5 (768 dimensions)
Chunk Size	~1500 chars with 200 char overlap
Index Type	ChromaDB with HNSW
Build Date	January 2026

🎯 Purpose

This database powers the STXBP1-ARIA therapeutic discovery system, enabling:

• Literature-grounded responses with PMC citations
• Semantic search across decades of research
• Real-time retrieval for AI-assisted variant analysis
• Evidence-based therapeutic recommendations

📁 Contents

STXBP1-RAG-Database/
├── chroma.sqlite3                    # Main database
├── metadata.json                     # Build info
└── [uuid]/                           # HNSW index files
    ├── data_level0.bin               # Vector index
    ├── header.bin                    
    ├── index_metadata.pickle         
    ├── length.bin                    
    └── link_lists.bin                

🔧 Usage

Quick Start

from huggingface_hub import snapshot_download
import chromadb
from chromadb.config import Settings
from sentence_transformers import SentenceTransformer

# Download database
db_path = snapshot_download(
    repo_id="SkyWhal3/STXBP1-RAG-Database",
    repo_type="dataset"
)

# Load embedding model (MUST match indexing model!)
embedder = SentenceTransformer("BAAI/bge-base-en-v1.5")

# Connect to ChromaDB
client = chromadb.PersistentClient(
    path=db_path,
    settings=Settings(anonymized_telemetry=False)
)

# Get collection
collection = client.get_collection("stxbp1_papers")
print(f"Loaded {collection.count():,} chunks")

# Search (BGE recommends query prefix for retrieval)
query = "STXBP1 dominant negative mechanism therapeutic approaches"
query_embedding = embedder.encode(query, normalize_embeddings=True).tolist()

results = collection.query(
    query_embeddings=[query_embedding],
    n_results=10,
    include=["documents", "metadatas", "distances"]
)

for doc, meta, dist in zip(
    results['documents'][0],
    results['metadatas'][0],
    results['distances'][0]
):
    pmcid = meta.get('pmcid', meta.get('pmc_id', 'Unknown'))
    print(f"[{pmcid}] (distance: {dist:.3f})")
    print(f"{doc[:200]}...\n")

With ARIA Integration

See the full retriever implementation at: STXBP1-Variant-Lookup Space

📚 Curated Corpus

Unlike v8's broad collection, v9 uses a curated corpus filtered for STXBP1 relevance:

Primary Keywords (Auto-include)

• STXBP1, Munc18-1, Munc18, syntaxin binding protein
• UNC-18, N-Sec1

Related Keywords (Relevance filtered)

• Epilepsy: epileptic encephalopathy, Ohtahara, West syndrome, Dravet, infantile spasms
• Synaptic: SNARE complex, syntaxin-1, synaptic vesicle, exocytosis, neurotransmitter release
• Genetics: haploinsufficiency, dominant negative, nonsense/missense/frameshift mutations
• Therapeutics: gene therapy, AAV, ASO, CRISPR, base editing, prime editing
• Chaperones: 4-PBA, phenylbutyrate, protein folding, proteostasis
• Neurodevelopment: intellectual disability, developmental delay, autism

Curated Entries

Includes 24 hand-curated entries covering:

• Key primary research (Guiberson 2018, Kovacevic 2018, etc.)
• Therapeutic mechanism summaries
• Variant-specific knowledge
• Clinical trial information

🏗️ How It Was Built

1. Corpus Curation

• Filtered 27,000 multimodal PMC papers by relevance keywords
• Kept ~17,000 papers with direct STXBP1 relevance
• Added 41 targeted high-value papers
• Included 24 curated expert entries

2. Text Processing

• Chunked documents into ~1500 character segments
• 200 character overlap between chunks
• Preserved document metadata (PMC ID, title)

3. Embedding Generation

• Used BAAI/bge-base-en-v1.5 (768 dimensions)
• Normalized embeddings for cosine similarity
• GPU-accelerated batch processing

4. Index Building

• ChromaDB with persistent storage
• HNSW index optimized for semantic search
• Built on RTX 3080 in ~55 minutes

📋 Metadata Schema

Each chunk includes:

{
  "pmcid": "PMC1234567",
  "title": "Paper title",
  "chunk_idx": 0,
  "source": "multimodal_corpus"
}

Source types:

• multimodal_corpus - Papers from curated PMC collection
• targeted_paper - High-priority STXBP1 papers
• curated - Hand-written expert entries

🔬 Use Cases

1. Therapeutic Research - Find evidence for treatment approaches
2. Variant Analysis - Locate papers discussing specific mutations
3. Mechanism Understanding - Search for molecular pathway details
4. Clinical Context - Find case reports and trial results
5. Literature Review - Rapid survey of research landscape

⚡ Performance Notes

• Free Tier Compatible: BGE-base runs on CPU or minimal GPU
• Query Time: <100ms typical retrieval
• Memory: ~1-2GB RAM for embedding model

🔗 Related Resources

• STXBP1-ARIA MAX (Nemotron embeddings): Coming soon
• STXBP1-Variant-Lookup: HuggingFace Space
• STXBP1 Foundation: stxbp1disorders.org
• ClinVar STXBP1: NCBI ClinVar

📄 Citation

@dataset{stxbp1_rag_database_2026,
  author = {Freygang, Adam},
  title = {STXBP1-ARIA RAG Database v9: BGE-Embedded Biomedical Literature for Therapeutic Discovery},
  year = {2026},
  publisher = {HuggingFace},
  url = {https://huggingface.co/datasets/SkyWhal3/STXBP1-RAG-Database}
}

📧 Contact

Adam Freygang
AI/ML Engineer & STXBP1 Parent Researcher
SkyWhal3 on HuggingFace

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Built with ❤️ for the STXBP1 community

Part of the NeuroSenpai + STXBP1-ARIA therapeutic discovery system