SkyWhal3/stxbp1-pubmed-central-fulltext

source_datasets: - PubMed Central

STXBP1 PubMed Central Full-Text Dataset

Dataset Description

A comprehensive collection of 31,598 scientific articles from PubMed Central (PMC) related to STXBP1 (Syntaxin Binding Protein 1), Munc18-1, and associated neurological conditions. This dataset contains full-text articles where available, making it one of the most complete publicly available resources for STXBP1 research.

About STXBP1

STXBP1 (also known as Munc18-1) is a gene that encodes a protein essential for neurotransmitter release at synapses. Mutations in STXBP1 cause STXBP1 Encephalopathy, a rare neurological disorder characterized by:

• Early-onset epilepsy (often within the first months of life)
• Developmental delays and intellectual disability
• Movement disorders
• Autism spectrum features

STXBP1-related disorders affect approximately 1 in 30,000 live births, making research aggregation critically important for advancing understanding and developing treatments.

Dataset Details

Source

• Origin: PubMed Central (PMC) Open Access Subset
• Collection Date: June 2025
• Search Strategy: Articles matching STXBP1, Munc18, and related neurological/epilepsy terms

Content

Field	Type	Description
title	string	Article title
abstract	string	Article abstract
main_text	string	Full article text (where available)
authors	string	Comma-separated author names
pmid	string	PubMed ID
doi	string	Digital Object Identifier
publication_date	string	Publication date
journal	string	Journal name
keywords	string	Comma-separated keywords
stxbp1_count	int	Count of "STXBP1" mentions in text
munc18_count	int	Count of "Munc18" mentions in text
pmc_id	string	PubMed Central ID
url	string	URL to original article
download_date	string	ISO timestamp of download
source_file	string	Original source filename

STXBP Family Terms:

STXBP1, STXBP2, STXBP3, STXBP4, STXBP5, STXBP6, STXBP11 Munc18, Munc18-1, Munc-18, Munc 18 Munc18 syntaxin, syntaxin binding protein

CRISPR/Gene Therapy Terms:

CRISPR Cas9, CRISPR-Cas9, CRISPR/Cas9 CRISPR Cas12, CRISPR-Cas12, CRISPR/Cas12 CRISPR Cas13, CRISPR-Cas13 base editing, prime editing

Combination Searches:

STXBP1/Munc18/syntaxin binding protein combined with: CRISPR, gene therapy, gene editing, AAV, antisense

Statistics

• Total Articles: ~31,000
• Articles with Full Text: Majority (exact count varies)
• Date Range: Historical to June 2025
• Primary Language: English

Usage

Loading the Dataset

from datasets import load_dataset

# Load the full dataset
dataset = load_dataset("SkyWhal3/stxbp1-pubmed-fulltext")

# Access the data
for article in dataset['train']:
    print(article['title'])
    print(article['abstract'][:500])

Filtering for High-Relevance Articles

# Filter for articles that directly mention STXBP1
stxbp1_direct = dataset.filter(lambda x: x['stxbp1_count'] > 0)

# Filter for articles mentioning Munc18
munc18_articles = dataset.filter(lambda x: x['munc18_count'] > 0)

# High-relevance articles (multiple mentions)
high_relevance = dataset.filter(lambda x: x['stxbp1_count'] >= 5)

Example Use Cases

1. Literature Review: Comprehensive search across STXBP1 research
2. RAG Systems: Build retrieval-augmented generation for rare disease Q&A
3. Research Trends: Analyze publication patterns over time
4. Fine-tuning: Train domain-specific language models
5. Knowledge Graphs: Extract relationships between genes, symptoms, treatments

Limitations and Known Issues

What This Dataset Contains

• ✅ Full article text where available from PMC
• ✅ Structured metadata (authors, dates, journals, DOIs)
• ✅ Abstract for all articles
• ✅ Keyword counts for relevance filtering

What This Dataset Does NOT Contain

• ❌ Images/Figures: Figure captions are included but not the actual images
• ❌ Structured Tables: Tables are converted to linear text, not preserved as structured data
• ❌ Mathematical Equations: LaTeX/MathJax equations are flattened to text
• ❌ Supplementary Materials: Links to supplements may be present but files are not included
• ❌ Section Demarcation: Text is continuous; sections (Introduction, Methods, etc.) are not tagged

Relevance Notes

• This dataset was collected using broad search terms to capture related research
• Some articles may be tangentially related (e.g., general epilepsy research, synaptic biology)
• Use the stxbp1_count and munc18_count fields to filter for directly relevant articles
• Articles with stxbp1_count = 0 and munc18_count = 0 may still be relevant to the broader research context

Ethical Considerations

• All articles are from the PMC Open Access Subset and are available under various open licenses
• This dataset is intended for research and educational purposes
• Users should cite original articles when using specific findings
• This dataset should not be used as a substitute for professional medical advice

Citation

If you use this dataset, please cite:

@dataset{stxbp1_pubmed_fulltext_2025,
  title={STXBP1 PubMed Central Full-Text Dataset},
  author={[Adam Freygang]},
  year={2025},
  publisher={Hugging Face},
  url={https://huggingface.co/datasets/SkyWhal3/stxbp1-pubmed-fulltext}
}

Acknowledgments

This dataset was curated by a parent advocate in the STXBP1 community to accelerate research into treatments and potential cures for STXBP1-related disorders.

Special thanks to:

• The researchers whose work is represented in this dataset
• PubMed Central for providing open access to scientific literature
• The STXBP1 Foundation and patient advocacy community
• Anthropic Claude Code

Version History

Version	Date	Changes
1.0.0	12-07-2025	Initial release

Contact

For questions, corrections, or contributions, please open an issue on this repository.

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This dataset is dedicated to all children and families affected by STXBP1 Encephalopathy.