Moretto Marco, Sonego Paolo, Pilati Stefania, Matus José Tomás, Costantini Laura, Malacarne Giulia, Engelen Kristof
Unit of Computational Biology, Research and Innovation Centre, Fondazione Edmund Mach, San Michele all'Adige, Italy.
Unit of Plant Biology and Physiology, Research and Innovation Centre, Fondazione Edmund Mach, San Michele all'Adige, Italy.
Front Plant Sci. 2022 Feb 24;13:815443. doi: 10.3389/fpls.2022.815443. eCollection 2022.
Successfully integrating transcriptomic experiments is a challenging task with the ultimate goal of analyzing gene expression data in the broader context of all available measurements, all from a single point of access. In its second major release VESPUCCI, the integrated database of gene expression data for grapevine, has been updated to be FAIR-compliant, employing standards and created with open-source technologies. It includes all public grapevine gene expression experiments from both microarray and RNA-seq platforms. Transcriptomic data can be accessed in multiple ways through the newly developed COMPASS GraphQL interface, while the expression values are normalized using different methodologies to flexibly satisfy different analysis requirements. Sample annotations are manually curated and use standard formats and ontologies. The updated version of VESPUCCI provides easy querying and analyzing of integrated grapevine gene expression (meta)data and can be seamlessly embedded in any analysis workflow or tools. VESPUCCI is freely accessible and offers several ways of interaction, depending on the specific goals and purposes and/or user expertise; an overview can be found at https://vespucci.readthedocs.io/.
成功整合转录组实验是一项具有挑战性的任务，其最终目标是在所有可用测量的更广泛背景下分析基因表达数据，所有这些都来自单一访问点。在其第二个主要版本VESPUCCI中，葡萄基因表达数据的集成数据库已更新为符合FAIR原则，采用了标准并使用开源技术创建。它包括来自微阵列和RNA测序平台的所有公共葡萄基因表达实验。转录组数据可以通过新开发的COMPASS GraphQL接口以多种方式访问，而表达值则使用不同方法进行归一化，以灵活满足不同的分析要求。样本注释经过人工整理，并使用标准格式和本体。VESPUCCI的更新版本提供了对集成葡萄基因表达（元）数据的轻松查询和分析，并且可以无缝嵌入任何分析工作流程或工具中。VESPUCCI可免费访问，并根据特定目标和用途及/或用户专业知识提供多种交互方式；概述可在https://vespucci.readthedocs.io/上找到。
