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

B Kirtley Amos(University of Liverpool), Cristina Aurrecoechea(University of Georgia), Matthieu Barba(European Bioinformatics Institute), Ana Barreto(University of Pennsylvania), Evelina Y. Basenko(University of Liverpool), Wojciech Bażant(Wellcome Centre for Molecular Parasitology), Robert Belnap(University of Georgia), Ann S. Blevins(University of Pennsylvania), Ulrike Böhme(University of Liverpool), John Brestelli(University of Pennsylvania), Brian P. Brunk(University of Pennsylvania), Mark X. Caddick(University of Liverpool), Danielle Callan(University of Pennsylvania), Lahcen Campbell(European Bioinformatics Institute), Mikkel Christensen(European Bioinformatics Institute), George K. Christophides(Imperial College London), Kathryn Crouch(Wellcome Centre for Molecular Parasitology), Kristina A. Davis(University of Notre Dame), Jeremy D. DeBarry(University of Georgia), Ryan Doherty(University of Pennsylvania), Yikun Duan(University of Pennsylvania), Michael E. Dunn(University of Notre Dame), Dave Falke(University of Georgia), Steve Fisher(University of Pennsylvania), Paul Flicek(European Bioinformatics Institute), Brett Fox(University of Notre Dame), Bindu Gajria(University of Pennsylvania), Gloria I. Giraldo-Calderón(University of Notre Dame), Omar S. Harb(University of Pennsylvania), Elizabeth I. Harper(University of Pennsylvania), Christiane Hertz‐Fowler(University of Liverpool), Mark J. Hickman(University of Pennsylvania), Connor Howington(University of Notre Dame), Sufen Hu(University of Pennsylvania), Jay C. Humphrey(University of Georgia), John Iodice(University of Pennsylvania), Andrew R. Jones(University of Liverpool), J. Judkins(University of Pennsylvania), Sarah Kelly(Imperial College London), Jessica C. Kissinger(University of Georgia), Dae Kun Kwon(University of Notre Dame), Kristopher Lamoureux(University of Georgia), Daniel J. Lawson(Imperial College London), Wei Li(University of Pennsylvania), Kallie Lies(University of Notre Dame), Disha Lodha(European Bioinformatics Institute), Jamie Long(University of Pennsylvania), Robert M. MacCallum(Imperial College London), G. Maslen(European Bioinformatics Institute), Mary Ann McDowell(University of Notre Dame), Jarosław Nabrzyski(University of Notre Dame), David S. Roos(University of Pennsylvania), Samuel S. C. Rund(University of Notre Dame), Stephanie Schulman(University of Pennsylvania), Achchuthan Shanmugasundram(University of Liverpool), Vasily Sitnik(European Bioinformatics Institute), Drew Spruill(University of Georgia), David Starns(University of Liverpool), Christian J. Stoeckert(University of Pennsylvania), Sheena Shah Tomko(University of Pennsylvania), Haiming Wang(University of Georgia), Susanne Warrenfeltz(University of Georgia), Robert Wieck(University of Notre Dame), Paul A. Wilkinson(University of Liverpool), Lin Xu(University of Pennsylvania), Jie Zheng(University of Pennsylvania)
Nucleic Acids Research
October 6, 2021
10.1093/nar/gkab929
Cited by 524Open Access
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Abstract

The Eukaryotic Pathogen, Vector and Host Informatics Resource (VEuPathDB, https://veupathdb.org) represents the 2019 merger of VectorBase with the EuPathDB projects. As a Bioinformatics Resource Center funded by the National Institutes of Health, with additional support from the Welllcome Trust, VEuPathDB supports >500 organisms comprising invertebrate vectors, eukaryotic pathogens (protists and fungi) and relevant free-living or non-pathogenic species or hosts. Designed to empower researchers with access to Omics data and bioinformatic analyses, VEuPathDB projects integrate >1700 pre-analysed datasets (and associated metadata) with advanced search capabilities, visualizations, and analysis tools in a graphic interface. Diverse data types are analysed with standardized workflows including an in-house OrthoMCL algorithm for predicting orthology. Comparisons are easily made across datasets, data types and organisms in this unique data mining platform. A new site-wide search facilitates access for both experienced and novice users. Upgraded infrastructure and workflows support numerous updates to the web interface, tools, searches and strategies, and Galaxy workspace where users can privately analyse their own data. Forthcoming upgrades include cloud-ready application architecture, expanded support for the Galaxy workspace, tools for interrogating host-pathogen interactions, and improved interactions with affiliated databases (ClinEpiDB, MicrobiomeDB) and other scientific resources, and increased interoperability with the Bacterial & Viral BRC.

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