Dataset for the article "A descriptor-free machine learning framework to improve antigen discovery for bacterial pathogens"

Dataset for the article "A descriptor-free machine learning framework to improve antigen discovery for bacterial pathogens" The data used in the study are provided as a .zip file Once unzipped, the raw data in FASTA format will be located in the following folders: data/fasta├── benchmark│ ├── test│ │ └── test.fasta # test sequences for benchmark│ └── training│ ├── negative.fasta # non-PA sequences for benchmark│ └── positive.fasta # PA-sequences for benchmark└── lobo ├── negative.fasta # non-PA sequences for LOBO evaluation └── positive.fasta # PA sequences for LOBO evaluation The annotated sequences used in the experiments (and the corresponding PSE/descriptors) are stored in .parquet format. They can be loaded with python as follows (please note that parquet files need the pandas and pyarrow libraries installed to be loaded): import pandas as pd example_path = "data/descriptors/lobo/test/UP000000425.parquet"df = pd.read_parquet(example_path) Here is the annotated sequences folder structure: data├── descriptors│ └── lobo│ ├── test # Descriptors for candidate antigen selection│ │ ├── UP000000425.parquet # N. meningitidis│ │ ├── UP000000586.parquet # S. pneumoniae│ │ ├── UP000000625.parquet # E. coli│ │ ├── UP000000750.parquet # S. pyogenes│ │ ├── UP000000799.parquet # C. jejuni│ │ ├── UP000000800.parquet # C. muridarum│ │ ├── UP000001432.parquet # A. pleuropneumoniae│ │ ├── UP000001584.parquet # M. tuberculosis│ │ ├── UP000006386.parquet # S. aureus│ │ └── UP000326807.parquet # Y. pestis│ └── training│ ├── negative.parquet # non-PA descriptors for LOBO│ └── positive.parquet # PA descriptors for LOBO└── pses ├── benchmark │ ├── test │ │ └── test.parquet # test PSEs for benchmark │ └── training │ ├── negative.parquet # non-PA PSEs for benchmark │ └── positive.parquet # PA PSEs for benchmark └── lobo ├── test # PSEs for candidate antigen selection │ ├── UP000000425.parquet # N. meningitidis │ ├── UP000000586.parquet # S. pneumoniae │ ├── UP000000625.parquet # E. coli │ ├── UP000000750.parquet # S. pyogenes │ ├── UP000000799.parquet # C. jejuni │ ├── UP000000800.parquet # C. muridarum │ ├── UP000001432.parquet # A. pleuropneumoniae │ ├── UP000001584.parquet # M. tuberculosis │ ├── UP000006386.parquet # S. aureus │ └── UP000326807.parquet # Y. pestis └── training ├── negative.parquet # non-PA PSEs for LOBO └── positive.parquet # non-PA PSEs for LOBO