Datasets:

davidcechak
/

Zebrafish_DNA_v0

annotations_creators:
  - no-annotation
language_creators:
  - no-annotation
task_categories:
  - text-classification
tags:
  - genomics
  - dna
  - bioinformatics
  - zebrafish-dna
source_datasets:
  - zebrafish-reference-genome (unconfirmed)
language:
  - en
license: other
license_name: unspecified

`Zebrafish_DNA_v0`

Dataset Description

The davidcechak/Zebrafish_DNA_v0 is a dataset containing raw DNA sequences from the zebrafish reference genome (Danio rerio). It is intended as a foundational dataset for various machine learning and bioinformatics tasks, such as training models to recognize patterns in zebrafish DNA.

As a foundational dataset, it can be used directly for research or further processed into different formats, such as the 6-mer tokenized version, davidcechak/Zebrafish_DNA_v0_DNABert6tokenized. This allows for flexibility in using different model architectures, including those based on transformers like DNABert.

Dataset Structure

The dataset is available in the parquet format and is likely split into training and testing subsets, though this needs to be confirmed.

Data Fields

The dataset likely includes the following fields:

text: A raw DNA sequence string, consisting of the nucleotides A, T, C, and G.

Dataset Creation

Data Source

The raw DNA sequences are likely derived from the reference genome of Danio rerio.

Preprocessing and Format

The raw genomic sequences were extracted and formatted into parquet files, which are efficient for large-scale data processing in machine learning workflows.

Intended Uses

The dataset can be used for:

Bioinformatics Research: Exploring the applications of machine learning to analyze raw zebrafish genomic data.
Genomic Classification: Building models to identify specific features within zebrafish DNA.
Comparative Genomics: Comparing genomic features between different species (e.g., zebrafish, human, worm) by using this dataset alongside similar ones.

Limitations and Ethical Considerations

Unspecified Origin: Without an official dataset card from the author, the precise origin and collection methodology of the sequences are unknown. This may impact reproducibility and potential biases.
Licensing: The license is currently unspecified. For any public or commercial use, it is necessary to verify the terms with the author, David Cechak, on Hugging Face.

How to Get the Dataset

You can easily load this dataset from the Hugging Face Hub using the datasets library:

from datasets import load_dataset

# Load the dataset
dataset = load_dataset("davidcechak/Zebrafish_DNA_v0")

# Access the training split
train_dataset = dataset["train"]