Datasetpublic

SkyWhal3/stxbp1-pubmed-central-fulltext

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)… See the full description on the dataset page: https://huggingface.co/datasets/SkyWhal3/stxbp1-pubmed-central-fulltext.

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Dataset Card

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
ClinVar Dataset	STXBP1 genetic variants	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.