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A Comparative Approach to Characterize the Landscape of Host-Pathogen Protein-Protein Interactions

A Comparative Approach to Characterize the Landscape of Host-Pathogen Protein-Protein Interactions

Published on: July 18, 2013

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

Beatrice Amos¹, Cristina Aurrecoechea², Matthieu Barba³

¹Institute of Systems, Molecular & Integrative Biology, University of Liverpool, Liverpool L69 7ZB, UK.

Nucleic Acids Research

|October 31, 2021

Summary

VEuPathDB integrates omics data for over 500 eukaryotic pathogens, vectors, and hosts. This bioinformatics resource empowers researchers with advanced tools for data mining and analysis across diverse organisms and datasets.

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Area of Science:

Bioinformatics
Computational Biology
Genomics

Background:

VEuPathDB (Eukaryotic Pathogen, Vector and Host Informatics Resource) is a merger of VectorBase and EuPathDB projects.
Funded by NIH and Wellcome Trust, it supports over 500 organisms, including invertebrate vectors, eukaryotic pathogens (protists, fungi), and hosts.
It serves as a Bioinformatics Resource Center.

Purpose of the Study:

To provide researchers with access to omics data and bioinformatic analyses for eukaryotic pathogens, vectors, and hosts.
To integrate diverse datasets and analysis tools within a user-friendly graphical interface.
To facilitate comparative analyses across different datasets, data types, and organisms.

Main Methods:

Integration of over 1700 pre-analyzed datasets with associated metadata.
Standardized analysis workflows, including the OrthoMCL algorithm for orthology prediction.
Development of advanced search capabilities, visualizations, and a graphical user interface.
Upgraded infrastructure supporting a Galaxy workspace for private data analysis.

Main Results:

A comprehensive data mining platform supporting over 500 organisms.
Integration of diverse omics data types with advanced search and analysis tools.
Enhanced user access through a new site-wide search and upgraded web interface.
Support for private data analysis via an expanded Galaxy workspace.

Conclusions:

VEuPathDB is a unique, powerful resource for researchers studying eukaryotic pathogens, vectors, and hosts.
The platform facilitates data exploration, comparative analysis, and private data analysis.
Ongoing upgrades aim to enhance cloud-readiness, host-pathogen interaction tools, and interoperability with other resources.