VEuPathDB: the eukaryotic pathogen, vector and host bioinformatics resource center in 2023
Author:
Alvarez-Jarreta Jorge1, Amos Beatrice2, Aurrecoechea Cristina3, Bah Saikou4, Barba Matthieu1, Barreto Ana5, Basenko Evelina Y2, Belnap Robert3, Blevins Ann6, Böhme Ulrike3, Brestelli John5, Brown Stuart5, Callan Danielle5, Campbell Lahcen I1, Christophides George K7, Crouch Kathryn4ORCID, Davison Helen R2, DeBarry Jeremy D3, Demko Richard5, Doherty Ryan5, Duan Yikun5, Dundore Walter3, Dyer Sarah1, Falke Dave3, Fischer Steve5, Gajria Bindu5, Galdi Daniel5, Giraldo-Calderón Gloria I8ORCID, Harb Omar S5ORCID, Harper Elizabeth5, Helb Danica5, Howington Connor8, Hu Sufen5, Humphrey Jay3, Iodice John5, Jones Andrew2ORCID, Judkins John5, Kelly Sarah A7, Kissinger Jessica C3, Kittur Nupur3ORCID, Kwon Dae Kun8, Lamoureux Kristopher3, Li Wei5, Lodha Disha1, MacCallum Robert M7, Maslen Gareth7, McDowell Mary Ann8, Myers Jeremy5, Nural Mustafa Veysi3, Roos David S5, Rund Samuel S C8ORCID, Shanmugasundram Achchuthan29, Sitnik Vasily1, Spruill Drew3, Starns David2, Tomko Sheena Shah5, Wang Haiming3, Warrenfeltz Susanne3ORCID, Wieck Robert8, Wilkinson Paul A2, Zheng Jie5
Affiliation:
1. European Bioinformatics Institute , Hinxton CB10 1SD , UK 2. Institute of Systems, Molecular and Integrative Biology, University of Liverpool , Liverpool L69 7ZB, UK 3. University of Georgia , Athens , GA 30602 , USA 4. School of Infection and Immunity, University of Glasgow , Glasgow, UK 5. University of Pennsylvania , Philadelphia , PA 19104 , USA 6. University of Pennsylvania School of Veterinary Medicine , Philadelphia , PA 19104 , USA 7. Imperial College London, South Kensington , London SW7 2BU , UK 8. University of Notre Dame , Notre Dame , IN 46556 , USA 9. Genomics England Limited , London E14 5AB, UK
Abstract
Abstract
The Eukaryotic Pathogen, Vector and Host Informatics Resource (VEuPathDB, https://veupathdb.org) is a Bioinformatics Resource Center funded by the National Institutes of Health with additional funding from the Wellcome Trust. VEuPathDB supports >600 organisms that comprise invertebrate vectors, eukaryotic pathogens (protists and fungi) and relevant free-living or non-pathogenic species or hosts. Since 2004, VEuPathDB has analyzed omics data from the public domain using contemporary bioinformatic workflows, including orthology predictions via OrthoMCL, and integrated the analysis results with analysis tools, visualizations, and advanced search capabilities. The unique data mining platform coupled with >3000 pre-analyzed data sets facilitates the exploration of pertinent omics data in support of hypothesis driven research. Comparisons are easily made across data sets, data types and organisms. A Galaxy workspace offers the opportunity for the analysis of private large-scale datasets and for porting to VEuPathDB for comparisons with integrated data. The MapVEu tool provides a platform for exploration of spatially resolved data such as vector surveillance and insecticide resistance monitoring. To address the growing body of omics data and advances in laboratory techniques, VEuPathDB has added several new data types, searches and features, improved the Galaxy workspace environment, redesigned the MapVEu interface and updated the infrastructure to accommodate these changes.
Funder
National Institute of Allergy and Infectious Diseases National Institutes of Health Department of Health and Human Services Wellcome Trust University of Pennsylvania
Publisher
Oxford University Press (OUP)
Cited by
36 articles.
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