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

Collapse authors list.
Amos, Beatrice, Aurrecoechea, Cristina, Barba, Matthieu, Barreto, Ana, Basenko, Evelina Y ORCID: 0000-0001-8611-5447, Bazant, Wojciech, Belnap, Robert, Blevins, Ann S, Bohme, Ulrike, Brestelli, John et al (show 56 more authors) , Brunk, Brian P, Caddick, Mark, Callan, Danielle, Campbell, Lahcen, Christensen, Mikkel B, Christophides, George K, Crouch, Kathryn, Davis, Kristina, DeBarry, Jeremy, Doherty, Ryan, Duan, Yikun, Dunn, Michael, Falke, Dave, Fisher, Steve, Flicek, Paul, Fox, Brett, Gajria, Bindu, Giraldo-Calderon, Gloria I, Harb, Omar S, Harper, Elizabeth, Hertz-Fowler, Christiane ORCID: 0000-0002-0729-6479, Hickman, Mark J, Howington, Connor, Hu, Sufen, Humphrey, Jay, Iodice, John, Jones, Andrew ORCID: 0000-0001-6118-9327, Judkins, John, Kelly, Sarah A, Kissinger, Jessica C, Kwon, Dae Kun, Lamoureux, Kristopher, Lawson, Daniel, Li, Wei, Lies, Kallie, Lodha, Disha, Long, Jamie, MacCallum, Robert M, Maslen, Gareth, McDowell, Mary Ann, Nabrzyski, Jaroslaw, Roos, David S, Rund, Samuel SC, Schulman, Stephanie Wever, Shanmugasundram, Achchuthan ORCID: 0000-0003-2349-6929, Sitnik, Vasily, Spruill, Drew, Starns, David ORCID: 0000-0001-6583-9067, Stoeckert, Christian J, Tomko, Sheena Shah, Wang, Haiming, Warrenfeltz, Susanne, Wieck, Robert, Wilkinson, Paul A ORCID: 0000-0002-8836-5439, Xu, Lin and Zheng, Jie (2022) VEuPathDB: the eukaryotic pathogen, vector and host bioinformatics resource center. NUCLEIC ACIDS RESEARCH, 50 (D1). D898-D911. ISSN 0305-1048, 1362-4962

Text gkab929.pdf - Published version Download (4MB) | Preview

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.

Item Type:	Article
Additional Information:	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.
Uncontrolled Keywords:	Animals, Humans, Nematoda, Apicomplexa, Diplomonadida, Bacteria, Fungi, Communicable Diseases, Computational Biology, Disease Vectors, Phylogeny, Virulence, Phenotype, Internet, User-Computer Interface, Databases, Factual, Host-Pathogen Interactions, Workflow, Data Mining, Insecta
Divisions:	Faculty of Health and Life Sciences Faculty of Health and Life Sciences > Institute of Systems, Molecular and Integrative Biology
Depositing User:	Symplectic Admin
Date Deposited:	09 Nov 2021 08:32
Last Modified:	06 Dec 2024 19:05
DOI:	10.1093/nar/gkab929
Related URLs:	Author Publisher
URI:	https://livrepository.liverpool.ac.uk/id/eprint/3142948