PathoFact 2.0 Datasets

The PathoFact2_datasets.tar.gz archive contains datasets used for training, validation, and benchmarking of PathoFact 2.0. The dataset is organised into the following folders:

1. BenchMarking/

Contains test datasets used to benchmark the performance of PathoFact 2.0 against other prediction tools.

• Toxin_module/
• 1000_TEST_non-toxin_ToxinPred2BenchMarking.faa

Non-toxin test dataset used when benchmarking PathoFact 2.0 against ToxinPred2.

• 1000_TEST_toxin_ToxinPred2BenchMarking.faa

Toxin test dataset used when benchmarking PathoFact 2.0 against ToxinPred2.

• VF_module/
• VF_Test_dataset_VirulentHunterBenchmarking.faa

Virulence factor test dataset used when benchmarking PathoFact 2.0 against VirulentHunter.

• non-VF_Test_dataset_VirulentHunterBenchmarking.faa

Non-virulence-factor test dataset used for benchmarking PathoFact 2.0 against VirulentHunter.

2. Toxin_module/

Contains datasets used for training and validating the PathoFact 2.0 Toxin prediction module.

• Toxin-related.faa
• non-toxin.faa
• splits/ — datasets divided into 80% training and 20% test sets:
• TRAIN_Positive_TOX.faa
• TRAIN_Negative_TOX.faa
• Test_Positive_TOX.faa
• Test_Negative_TOX.faa

3. VF_module/

Contains datasets used for training and validating the PathoFact 2.0 Virulence Factor prediction module.

• VF_dataset.faa
• non-VF.faa
• splits/ — datasets divided into 80% training and 20% test sets:
• TRAIN_Positive_VF.faa
• TRAIN_Negative_VF.faa
• Test_Positive_VF.faa
• Test_Negative_VF.faa

The DOME-ML_PathoFact2.json is the DOME, the community standard for transparent machine learning json file created for PathoFact 2.0.