seq-to-pheno/filtered_orthologs

Zoonomia Filtered Orthologs Dataset

This dataset has been filtered to remove:

1. Proteins longer than 1000 amino acids
2. 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 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.