Update README.md

README.md

@@ -5,4 +5,74 @@ task_categories:
 - 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.