Naïve Bayes Classifiers and accompanying dataset for Pseudomonas syringae isolate characterization.
Chad FauttEstelle CouradeauKevin L HockettPublished in: Scientific data (2024)
The Pseudomonas syringae species complex (PSSC) is a diverse group of plant pathogens with a collective host range encompassing almost every food crop grown today. As a threat to global food security, rapid detection and characterization of epidemic and emerging pathogenic lineages is essential. However, phylogenetic identification is often complicated by an unclarified and ever-changing taxonomy, making practical use of available databases and the proper training of classifiers difficult. As such, while amplicon sequencing is a common method for routine identification of PSSC isolates, there is no efficient method for accurate classification based on this data. Here we present a suite of five Naïve bayes classifiers for PCR primer sets widely used for PSSC identification, trained on in-silico amplicon data from 2,161 published PSSC genomes using the life identification number (LIN) hierarchical clustering algorithm in place of traditional Linnaean taxonomy. Additionally, we include a dataset for translating classification results back into traditional taxonomic nomenclature (i.e. species, phylogroup, pathovar), and for predicting virulence factor repertoires.
Keyphrases
- machine learning
- deep learning
- bioinformatics analysis
- big data
- biofilm formation
- escherichia coli
- electronic health record
- single cell
- randomized controlled trial
- climate change
- antimicrobial resistance
- systematic review
- public health
- multidrug resistant
- molecular docking
- body composition
- human health
- candida albicans
- risk assessment
- gram negative
- global health
- high intensity
- data analysis