| --- |
| 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. |
