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license: mit
tags:
- biology
---
# SwissIPG
> SwissProt-based Protein Function (InterPro and Gene Ontology) Benchmark Datasets
This repository provides benchmark datasets for protein function evaluation, constructed from **UniProt/SwissProt**, **InterPro (IPR)**, and **Gene Ontology (GO)**.
It includes both test sets and training sets, supporting **keyword-guided** and **description-guided** protein design/evaluation tasks.
## 📖 Dataset Overview
**Keyword-guided protein tasks** previously lacked a **publicly available, high-quality evaluation dataset**. To address this gap, we curated a novel dataset from SwissProt, together with their **IPR entries** and **GO terms**. Note that the GO terms are restricted to **Molecular Function (MF)**.
| Subset | Num of Proteins | Num of IPR entries | Num of GO terms |
| ------------ | --------------- | ------------------ | --------------- |
| Test Set | 1,057 | 1,297 | 380 |
| Train Set | 555543 | 39431 | 8110 |
## 🔧 Dataset Construction
1. Protein selection
Extracted proteins from UniProt/SwissProt released between `2025-01-01` and `2025-08-25` for testing. The remaining proteins are used for training.
2. Keyword collection
Retrieved corresponding protein sequences, InterPro IDs, and GO terms.
3. Instruction construction for description-guided task
Following [Mol-Instructions](https://github.com/zjunlp/Mol-Instructions), we concatenated text descriptions of InterPro entries and GO terms to form natural-language prompts.
| Keyword | Description |
|---------------------------------------|-------------------------------------------------------------------------------------------------|
| InterPro (Domain) | The protein should contain one or more *{}* that are essential for its biological function |
| InterPro (Family) | The protein should belong to *{}* that shares evolutionary origin and functional similarity |
| InterPro (Homologous_Superfamily) | The protein should be classified within *{}* sharing conserved structural features |
| InterPro (Repeat) | The protein should include one or more *{}* that provide structural or functional support |
| InterPro (Conserved_Site) | The protein should contain *{}* that is preserved across related proteins |
| InterPro (Active_Site) | The protein must have *{}* that is conserved among related catalytic enzymes |
| InterPro (Binding_Site) | The protein should include a *{}* that enables ligand binding under diverse conditions |
| InterPro (PTM) | The protein should contain *{}* that allow regulation through chemical modifications |
| Gene Ontology (molecular function) | The protein must be able to perform the *{}* required for its activity. |
4. Final curation
Curated into **test** and **train** sets with consistent formats.
## 📂 Dataset Structure
| File | Func-Seq Pairs | Description |
| ------------------- | -------------- | -------------------------- |
| `go_test.json` | 693 | Test set for GO task. |
| `go_train.json` | 492124 | Train set for GO task. |
| `ipr_test.json` | 870 | Test set for IPR task. |
| `ipr_train.json` | 555543 | Train set for IPR task. |
| `ipr_go_test.json` | 674 | Test set for IPR&GO task. |
| `ipr_go_train.json` | 487848 | Train set for IPR&GO task. |
| `SwissIPG.py` | - | Building Class |
## 🎯 Intended Use
- **Benchmarking protein design models** under keyword-guided and description-guided settings
- **Training and fine-tuning** models using consistent annotation standards
- Facilitating **fair comparison** across models through a unified dataset
## 🔍 Evaluation Metrics
Our work, [PDFBench](https://github.com/PDFBench/PDFBench), provides a comprehensive evaluation for both tasks. For further details, please refer to the repository.
## 📑 Citation
If you use this dataset, please cite:
```bibtex
@misc{kuang2025pdfbenchbenchmarknovoprotein,
title={PDFBench: A Benchmark for De novo Protein Design from Function},
author={Jiahao Kuang and Nuowei Liu and Changzhi Sun and Tao Ji and Yuanbin Wu},
year={2025},
eprint={2505.20346},
archivePrefix={arXiv},
primaryClass={cs.LG},
url={https://arxiv.org/abs/2505.20346},
}
``` |