VEuPathDB: the eukaryotic pathogen, vector and host bioinformatics resource center in 2023

Area of Science:

• Bioinformatics
• Computational Biology
• Pathogen Genomics

Background:

• VEuPathDB is a major bioinformatics resource center supporting research on eukaryotic pathogens, vectors, and hosts.
• It has been analyzing public omics data since 2004, integrating diverse datasets and analysis tools.

Purpose of the Study:

• To describe the VEuPathDB resource and its recent updates and enhancements.
• To highlight its capabilities in supporting hypothesis-driven research through data mining and comparative analysis.

Main Methods:

• Analysis of omics data using contemporary bioinformatic workflows, including orthology predictions (OrthoMCL).
• Integration of analysis results with data mining platforms, visualization tools, and advanced search functionalities.
• Provision of a Galaxy workspace for large-scale private dataset analysis and a MapVEu tool for spatial data exploration.

Main Results:

• VEuPathDB supports over 600 organisms, including invertebrate vectors, eukaryotic pathogens (protists, fungi), and hosts.
• The platform offers over 3000 pre-analyzed datasets, facilitating cross-dataset, cross-data type, and cross-organism comparisons.
• New data types, searches, features, an improved Galaxy workspace, and a redesigned MapVEu interface have been implemented.

Conclusions:

• VEuPathDB is a valuable, evolving resource for exploring omics data related to eukaryotic pathogens, vectors, and hosts.
• Recent updates enhance its capacity to handle growing omics data and support advanced research in the field.