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

Jorge Alvarez-Jarreta1, Beatrice Amos2, Cristina Aurrecoechea3

  • 1European Bioinformatics Institute, Hinxton CB10 1SD, UK.

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|November 12, 2023
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Summary

The Eukaryotic Pathogen, Vector and Host Informatics Resource (VEuPathDB) provides access to omics data for over 600 organisms. It supports research on eukaryotic pathogens, vectors, and hosts with advanced data mining and analysis tools.

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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.