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---
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
<!-- Provide a longer summary of what this dataset is. -->
### 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
<!-- Address questions around how the dataset is intended to be used. -->
### Example usage
```
from datasets import load_dataset
```
### Out-of-Scope Use
<!-- This section addresses misuse, malicious use, and uses that the dataset will not work well for. -->
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
<!-- This section provides a description of the dataset fields, and additional information about the dataset structure such as criteria used to create the splits, relationships between data points, etc. -->
[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
<!-- This section describes the data collection and processing process such as data selection criteria, filtering and normalization methods, tools and libraries used, etc. -->
[More Information Needed]
#### Who are the source data producers?
<!-- This section describes the people or systems who originally created the data. It should also include self-reported demographic or identity information for the source data creators if this information is available. -->
[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]` |