Institute of Systems, Molecular & Integrative Biology, University of Liverpool, Liverpool L69 7ZB, UK.
Center for Tropical & Emerging Global Diseases, University of Georgia, Athens, GA 30602, USA.
Nucleic Acids Res. 2022 Jan 7;50(D1):D898-D911. doi: 10.1093/nar/gkab929.
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.
真核病原体、媒介和宿主信息资源（VEuPathDB，https://veupathdb.org）是 VectorBase 与 EuPathDB 项目在 2019 年合并的产物。作为一个由美国国立卫生研究院资助的生物信息学资源中心，并得到惠康信托基金会的额外支持，VEuPathDB 支持包括无脊椎动物媒介、真核病原体（原生动物和真菌）以及相关的自由生活或非致病性物种或宿主在内的 500 多种生物。该资源旨在为研究人员提供访问组学数据和生物信息学分析的能力，VEuPathDB 项目整合了超过 1700 个经过预处理的数据集（以及相关元数据），并具有高级搜索功能、可视化和图形界面中的分析工具。使用标准化工作流程分析各种数据类型，包括用于预测同源性的内部 OrthoMCL 算法。在这个独特的数据挖掘平台中，可以轻松地在数据集、数据类型和生物体之间进行比较。新的全站搜索为经验丰富和新手用户都提供了便利的访问途径。升级后的基础设施和工作流程支持对网络界面、工具、搜索和策略进行大量更新，并支持 Galaxy 工作区，用户可以在其中私下分析自己的数据。即将进行的升级包括云就绪的应用程序架构、对 Galaxy 工作区的扩展支持、用于探究宿主-病原体相互作用的工具以及与附属数据库（ClinEpiDB、MicrobiomeDB）和其他科学资源的改进交互，以及与细菌和病毒 BRC 的互操作性增强。
