task_categories:
- text-generation
language:
- en
tags:
- proteins
- biology
- uniprot
size_categories:
- 100K<n<1M
Dataset Card for PAIR
This dataset contains all the text annotations we collected and parsed from UniProt Swiss-Prot February 2023 and used to train PAIR -- a simple framework to finetune protein language models using text annotations. You can read more details about PAIR here: https://www.biorxiv.org/content/10.1101/2024.07.22.604688v2.abstract
Dataset Details
Dataset Description
Dataset Sources
- Repository: (coming soon!)
- Paper: https://www.biorxiv.org/content/10.1101/2024.07.22.604688v2.abstract
- Model checkpoints: https://huggingface.co/h4duan
Uses
Example usage
from datasets import load_dataset
Out-of-Scope Use
This dataset contains text annotations from Swiss-Prot February 2023; our models were trained on all of them. Please be mindful about potential data leakage from time splits/identical protein sequences on any downstream tasks in your setup.
Dataset Structure
[More Information Needed]
Dataset Creation
Source Data
This data was collected from the Swiss-Prot checkpoint from February 2023, found here: XXX
Data Collection and Processing
[More Information Needed]
Who are the source data producers?
[More Information Needed]
Annotations
I don't think we did any annotations for parsing only for loading (double check)
Personal and Sensitive Information
To our knowledge, this dataset does not contain any private information.
Bias, Risks, and Limitations
In general, the dataset is highly imbalanced in terms of how many and what protein sequences in Swiss-Prot have an annotation for a given annotation type. This dataset is sparse
Citation
BibTeX:
@article{duan2024boosting,
title={Boosting the Predictive Power of Protein Representations with a Corpus of Text Annotations},
author={Duan, Haonan and Skreta, Marta and Cotta, Leonardo and Rajaonson, Ella Miray and Dhawan, Nikita and Aspuru-Guzik, Alán and Maddison, Chris J},
journal={bioRxiv},
pages={2024--07},
year={2024},
publisher={Cold Spring Harbor Laboratory}
}
Dataset Card Authors
[More Information Needed]
Dataset Card Contact
For any issues with this dataset, please contact [email protected] or [email protected]