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Datasets:
SkyWhal3
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stxbp1-pubmed-central-fulltext

Tasks:
Text Generation
Question Answering
Summarization
Modalities:
Tabular
Text
Formats:
parquet
Languages:
English
Size:
10K - 100K
Tags:
medical
biomedical
neuroscience
epilepsy
rare-disease
STXBP1
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pandas
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metadata
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 

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 

import pandas as pd

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

Example Queries 

# 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 

@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.