metadata

license: mit
task_categories:
  - token-classification
dataset_info:
  features:
    - name: transcript
      dtype: string
    - name: protein
      dtype: string
    - name: mapped_to
      dtype: string
    - name: species
      dtype: string
  splits:
    - name: train
      num_bytes: 169280946
      num_examples: 1763994
configs:
  - config_name: default
    data_files:
      - split: train
        path: filtered_mapped_orthologs.csv
tags:
  - biology
  - chemistry
  - zoonomia
  - sequence
  - DNA
  - protein
  - transcript
pretty_name: Zoonomica Mapped Orthologs
size_categories:
  - 10M<n<100M

Zoonomia Filtered Orthologs Dataset

This dataset has been filtered to remove:

Proteins longer than 1000 amino acids
Proteins with more than {MAX_NUMBER_ORTHOLOGS} orthologs in any species

Original number of mapped orthologs: {len(all_mapped_ortholog_df)} Filtered number of mapped orthologs: {num_examples}

Dataset Description

Point of Contact: [Your Name or Organization]
Dataset Summary: This dataset provides information about orthologous proteins across various species from the Zoonomia Project, mapped to human proteins.
Supported Tasks: Comparative genomics, evolutionary studies, protein function prediction
Languages: Not applicable (genomic data)
Source Data: Zoonomia Project

Dataset Structure

The dataset consists of a single CSV file with the following columns:

transcript: Human transcript ID
protein: Human protein name
mapped_to: Non-human (query) organism transcript ID
species: Name of the query species

Data Splits

This dataset contains only a train split, which includes all the data.

Dataset Creation

Curation Rationale

This dataset was created to facilitate comparative genomics studies and to provide easy access to ortholog mappings across various species from the Zoonomia Project.

Source Data

The source data was obtained from the Zoonomia Project, specifically from protein alignment files available at http://genome.senckenberg.de/download/TOGA/human_hg38_reference/.

Annotations

The dataset does not contain additional annotations beyond the ortholog mappings provided in the original data.

Considerations for Using the Data

Social Impact of Dataset

This dataset can contribute to advancements in comparative genomics and evolutionary studies, potentially leading to better understanding of genetic diseases and evolutionary processes.

Discussion of Biases

The dataset may have biases inherent in the original data collection and alignment processes used by the Zoonomia Project. Users should be aware of potential biases in species representation and alignment quality.

Other Known Limitations

The dataset only includes species available in the Zoonomia Project.
Alignment quality may vary across different species and proteins.

Additional Information

Dataset Curators

[Your Name or Organization]

Licensing Information

{license}

Citation Information

If you use this dataset, please cite both this dataset and the original Zoonomia Project:

[Include citation for this dataset and the Zoonomia Project]

Contributions

Thanks to the Zoonomia Project for making the original data available.