---
license: cc-by-4.0
language:
- en
tags:
- medical
- biomedical
- neuroscience
- epilepsy
- rare-disease
- STXBP1
- STXBP2
- Munc18
- Munc18-1
- syntaxin-binding-protein
- CRISPR
- CRISPR-Cas9
- gene-therapy
- gene-editing
- base-editing
- prime-editing
- AAV
- PubMed
- PMC
- full-text
- research
- encephalopathy
task_categories:
- text-generation
- question-answering
- summarization
- feature-extraction
pretty_name: STXBP1 PubMed Central Full-Text Dataset
size_categories:
- 10K<n<100K
---

source_datasets:
  - PubMed Central
---

# STXBP1 PubMed Central Full-Text Dataset v2

A comprehensive collection of **31,786 full-text scientific articles** from PubMed Central related to STXBP1, synaptic function, and neurological research.

## 🆕 Version 2 Updates (December 2025)

- Complete re-extraction with improved HTML parsing
- Full main text with proper section headers
- Enhanced metadata extraction
- 99.7% figure-image matching (see companion multimodal dataset)

---

## Dataset Overview

| Metric | Value |
|--------|-------|
| Total Articles | **31,786** |
| Articles with STXBP1 mentions | 1,335 |
| Articles with Munc18 mentions | 1,200+ |
| Articles with abstract: 30,856 |
| Total Abstract Characters | ~45 million |
| Articles with main_text: 31,684 |
| Total Main Text Characters | **~1.44 billion** |
| Average Abstract Length | 1,421 chars |
| Average Main Text Length | 45,391 chars |

---

## Schema

| Column | Type | Description |
|--------|------|-------------|
| `pmc_id` | string | PubMed Central ID (e.g., "PMC10196665") |
| `title` | string | Article title |
| `abstract` | string | Article abstract |
| `main_text` | string | Full article text with section headers |
| `authors` | string | Author list |
| `journal` | string | Journal name |
| `doi` | string | Digital Object Identifier |
| `pmid` | string | PubMed ID |
| `publish_date` | string | Publication date |
| `stxbp1_mentions` | int | Count of STXBP1 mentions in text |
| `munc18_mentions` | int | Count of Munc18 mentions in text |
| `num_figures` | int | Number of figures in article |
| `num_images` | int | Number of matched figure images |
| `abstract_length` | int | Character count of abstract |
| `main_text_length` | int | Character count of main text |

---

## Usage

### Load with Hugging Face Datasets

```python
from datasets import load_dataset

dataset = load_dataset("SkyWhal3/stxbp1-pubmed-central-fulltext")

# Access the data
df = dataset['train'].to_pandas()

# Filter STXBP1-specific articles
stxbp1_articles = df[df['stxbp1_mentions'] > 0]
print(f"Found {len(stxbp1_articles)} STXBP1-related articles")
```

### Load with Pandas

```python
import pandas as pd

df = pd.read_parquet("hf://datasets/SkyWhal3/stxbp1-pubmed-central-fulltext/stxbp1_pubmed_articles.parquet")
```

### Example Queries

```python
# Find articles about specific topics
seizure_articles = df[df['main_text'].str.contains('seizure', case=False, na=False)]

# Get articles with most STXBP1 mentions
top_stxbp1 = df.nlargest(10, 'stxbp1_mentions')[['pmc_id', 'title', 'stxbp1_mentions']]

# Find articles by keyword in title
crispr_articles = df[df['title'].str.contains('CRISPR|gene therapy', case=False, na=False)]
```

---

## Related Resources

| Resource | Description | Link |
|----------|-------------|------|
| Multimodal Dataset | Same articles + 170K figure images | [SkyWhal3/STXBP1_PubMed_Central_Multimodal_Dataset](https://huggingface.co/datasets/SkyWhal3/STXBP1_PubMed_Central_Multimodal_Dataset) |
| ClinVar Dataset | STXBP1 genetic variants | [SkyWhal3/stxbp1-clinvar](https://huggingface.co/datasets/SkyWhal3/stxbp1-clinvar) |
| Trained Model | Fine-tuned Qwen3-VL-8B | Coming soon! |

---

## About STXBP1

**STXBP1** (Syntaxin-Binding Protein 1), also known as **Munc18-1**, is essential for synaptic vesicle fusion and neurotransmitter release. Mutations cause **STXBP1 Encephalopathy**, a rare neurological disorder characterized by:

- Early-onset epilepsy
- Developmental delays
- Movement disorders
- Intellectual disability

This dataset supports AI-powered research into understanding and treating STXBP1-related conditions.

---

## Citation

```bibtex
@dataset{stxbp1_fulltext_2025,
  author = {SkyWhal3},
  title = {STXBP1 PubMed Central Full-Text Dataset},
  year = {2025},
  publisher = {Hugging Face},
  url = {https://huggingface.co/datasets/SkyWhal3/stxbp1-pubmed-central-fulltext}
}
```

---

## License

CC-BY-4.0. Source articles are from PubMed Central's Open Access subset.

---

## Changelog

### v2.0 (December 2025)
- Complete re-extraction with improved parsing
- Added section headers to main_text
- Enhanced metadata fields
- Added figure/image counts
- Added text length statistics

### v1.0 (December 2025)
- Initial release


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