Datasets:

midjuly
/

InsectBase

license: cc-by-4.0
task_categories:
  - feature-extraction
  - table-to-text
tags:
  - biology
  - bioinformatics
  - genomics
  - protein-structure
  - alphafold3
  - insect-science
pretty_name: InsectBase 3.0 Genomics and Protein Structures
configs:
  - config_name: default
    data_files:
      - split: train
        path: InsectBase_Genome/*

InsectBase 3.0: A Comprehensive Multi-omics Resource for Insects

InsectBase is a specialized bioinformatics database providing extensive genomic and multi-omic resources for the insect research community. This repository hosts the high-throughput genomic sequences and predicted protein structures associated with the InsectBase 3.0 update.

Dataset Description

Homepage: https://www.insect-genome.com/
Paper: Nucleic Acids Research (2025)
Repository Contents:
- InsectBase_Genome/: Large-scale insect genomic sequences (FASTA format).
- InsectBase_Protein_Structure/: High-confidence protein structures predicted via AlphaFold 3.

1. InsectBase_Genome

This subset contains the comprehensive insect genome assembly files in FASTA format.

File Reconstruction

Due to the massive size of the genomic data (~400GB), the archive has been split into multiple chunks (7-10 parts) to ensure stable downloading. To reconstruct the original file, please use the following commands in your terminal:

# Navigate to the download folder
cd InsectBase_Genome

# Merge the split parts back into a single tar.gz file
cat InsectBase_genome.tar.gz.part* > InsectBase_genome.tar.gz

# Extract the FASTA files
tar -zxvf InsectBase_genome.tar.gz

# (Optional) Verify integrity if sha256.txt is provided
sha256sum -c sha256.txt

2. InsectBase_Protein_Structure

This subset provides structural data for 29 specific gene families. These structures were generated using AlphaFold 3, providing state-of-the-art accuracy for protein-insect physiological research and evolutionary analysis.

Format: .pdb or .mmCIF (compressed within family-specific archives).
Scope: Covers major gene families critical to insect development, immunity, and metabolic processes.

Citation

If you use this dataset or the resources from InsectBase in your research, please cite the following paper published in Nucleic Acids Research:

Zuoqi Wang, Hao Chen, Shuo Jin, Zonghuan Li, Yang Mei, Yiqi Xiao, Chenfan Zhao, Tianyu Zhou, Fei Li, Ying Liu, Kang He, InsectBase 3.0: a comprehensive multi-omics resource for insects, Nucleic Acids Research, 2025;, gkaf1248, https://doi.org/10.1093/nar/gkaf1248

Contact & Support

For more detailed information, interactive tools, and additional omics data (Transcriptomics, Metabolomics, etc.), please visit our official website: https://www.insect-genome.com/

For technical issues regarding the data hosted on Hugging Face, please open an issue in this repository.