|
--- |
|
license: apache-2.0 |
|
task_categories: |
|
- fill-mask |
|
- text-classification |
|
tags: |
|
- biology |
|
--- |
|
|
|
Dataset Summary |
|
This repository contains datasets derived from UniProt and SwissProt databases for analyzing biological sequences. |
|
The data includes raw sequences, processed files, and benchmark datasets split using hierarchical strategies to ensure diversity and |
|
discourage model bias. The datasets are organized into different folders for balanced and unbalanced splits, with additional variations |
|
where full-length sequences are chunked into smaller sequences. |
|
|
|
Dataset Structure |
|
The file directory is structured as follows: |
|
|
|
UniprotAndSwissprotDatasets: |
|
SwissprotDatasets: |
|
BalancedSwissprot: train.csv, validation.csv |
|
UnbalancedSwissprot: train.csv, validation.csv |
|
**test.csv, test1.csv, test2.csv` |
|
SwissprotDatasetsChunked: |
|
Contains the same data as SwissprotDatasets, but each full-length sequence is split into smaller sequences of 20 read length. |
|
BalancedSwissprot: train.csv, validation.csv |
|
UnbalancedSwissprot: train.csv, validation.csv |
|
**test.csv, test1.csv, test2.csv` |
|
UniprotDatasets: |
|
BalancedUniprot: train.csv, validation.csv |
|
UnbalancedUniprot: train.csv, validation.csv |
|
**test.csv, test1.csv, test2.csv` |
|
UniprotDatasetsChunked: |
|
Contains the same data as UniprotDatasets, but each full-length sequence is split into smaller sequences of 20 read length. |
|
BalancedUniprot: train.csv, validation.csv |
|
UnbalancedUniprot: train.csv, validation.csv |
|
**test.csv, test1.csv, test2.csv` |
|
Data Description |
|
The datasets are derived from: |
|
|
|
UniProt: Contains two main sections: |
|
TrEMBL: Automatically annotated; contains homology-based annotations with more errors. |
|
SwissProt: Manually curated with experimental evidence of functional annotations. |
|
Preprocessing Steps: |
|
Organism Filtering: Only prokaryotic organisms (bacteria and archaea) were included. |
|
Data Mapping: UniProt IDs were mapped to UniRef clusters (UniRef50, UniRef90, UniRef100) and EMBL CDS IDs. |
|
Data Cleaning: |
|
Removed records with missing or partial EC numbers. |
|
Split records with multiple EC numbers into individual entries. |
|
Dataset Splitting |
|
A hierarchical splitting strategy ensured sequences from the same cluster do not appear in more than one set: |
|
|
|
Train, Validation, and Test Sets are derived based on UniRef50, UniRef90, or UniRef100 clusters. |
|
Special test sets include: |
|
In-Distribution (Test Set-I): Contains sequences with EC numbers present in the training sets. |
|
Out-of-Distribution (Test Set-II): Contains sequences with EC numbers absent from the training sets. |
|
Benchmarks |
|
Four benchmark datasets were created: |
|
|
|
Benchmark-I: SwissProt+TrEMBL (unbalanced). |
|
Benchmark-II: SwissProt+TrEMBL (balanced). |
|
Benchmark-III: SwissProt only (unbalanced). |
|
Benchmark-IV: SwissProt only (balanced). |
|
Chunked Sequences |
|
ChunkedSwissProt and ChunkedUniProt folders contain the same data as their respective non-chunked counterparts but with each full-length sequence divided into smaller 20 read-length sequences. |
|
These chunked datasets are especially useful for sequence alignment and similarity-based tasks. |
|
Dataset Generation |
|
To generate the dataset, follow the instructions in the notebooks: |
|
|
|
DatasetGeneration.ipynb: Processes raw data to create final datasets. |
|
DatasetSplitting.ipynb: Splits the dataset into training, validation, and test sets. |
|
Citation |
|
If using this dataset, please cite the original UniProt and SwissProt resources: |
|
|
|
UniProt: https://www.uniprot.org/ |
|
SwissProt: https://www.uniprot.org/uniprotkb?query=reviewed:true |
|
License |
|
This dataset is licensed under the Apache 2.0 License. |
