README.md

Nature Communications Articles Dataset - natcomm_2512_001

Dataset Description

This dataset contains scraped Nature Communications articles with comprehensive extraction of:

• Main figures with captions and citations
• Tables with full HTML and data
• Supplementary figures with citation contexts
• Supplementary tables with citation contexts
• Supplementary files (PDFs, Excel files)
• Article sections with hierarchical structure (h2=section, h3=subsection)
• Figure/table citation contexts linking to sections

Dataset Structure

Files

• images_tables_natcomm_2512_001.zip: Contains all article images and tables

  • files/[article_id]/images/: Main figure images
  • files/[article_id]/tables/: Table HTML files

• metadata_natcomm_2512_001.zip: Contains JSON metadata for each article

  • metadata/[article_id].json: Complete metadata including:
    • article_id: Article identifier
    • url: Original article URL
    • title: Article title
    • image_set: Dict of main figures with captions and citations
    • table_set: Dict of tables with captions and data
    • supplementary_image_set: Dict of supplementary figures with citations
    • supplementary_table_set: Dict of supplementary tables with citations
    • supplementary_files: List of supplementary file links
    • section_set: Dict of article sections with hierarchical structure

Statistics

• Total Articles: 277
• Scraping Date: 2025-12-11

Content Summary

• Main Figures: 1182 (4.3 per article)
• Tables: 105 (0.4 per article)
• Supplementary Figures: 1605 (5.8 per article)
• Supplementary Tables: 322 (1.2 per article)
• Supplementary Files: 2211 (8.0 per article)
• Sections: 4876 (17.6 per article)

Features

Section Hierarchy

Each section includes:

• level: 2 (h2 main section) or 3 (h3 subsection)
• type: "section" or "subsection"
• title: Section heading
• content: Full section text

Excluded Metadata Sections

Administrative sections are filtered out:

• Acknowledgements, Author information, Contributions
• Peer review, Ethics declarations, Rights and permissions
• Similar content recommendations

Citation Tracking

Each figure/table has contexts array with:

• section: Section title where cited
• text: ±100 character context around citation
• full_content: Complete section content

Usage

import json
import zipfile

# Load article metadata
with open('metadata_natcomm_2512_001/metadata/s41467-025-65722-y.json', 'r') as f:
    article = json.load(f)

# Access sections with hierarchy
for sec_id, sec_info in article['section_set'].items():
    if sec_info['level'] == 2:
        print(f"Section: {sec_info['title']}")
    else:
        print(f"  Subsection: {sec_info['title']}")

# Access figures with citations
for fig_id, fig_info in article['image_set'].items():
    print(f"{fig_id}: {fig_info['caption']}")
    print(f"  Cited in: {[c['section'] for c in fig_info['contexts']]}")

Version Notes

natcomm_2512_001 (December 2025):

• Fixed section extraction to exclude recommendation sections
• Added section hierarchy tracking (h2/h3 levels)
• Improved metadata section filtering
• Enhanced supplementary material citation tracking

License

This dataset is derived from Nature Communications articles. Please respect original article licenses and cite appropriately.

Created By

Batch Name: natcomm_2512_001 Scraping Tool: Nature Communications Comprehensive Scraper Date: 2025-12-11 Repository: https://huggingface.co/datasets/ZexiK/natcomSS