1. Xenbase: key features and resources of the Xenopusmodel organism knowledgebase
- Author
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Fisher, Malcolm, James-Zorn, Christina, Ponferrada, Virgilio, Bell, Andrew J, Sundararaj, Nivitha, Segerdell, Erik, Chaturvedi, Praneet, Bayyari, Nadia, Chu, Stanley, Pells, Troy, Lotay, Vaneet, Agalakov, Sergei, Wang, Dong Zhuo, Arshinoff, Bradley I, Foley, Saoirse, Karimi, Kamran, Vize, Peter D, and Zorn, Aaron M
- Abstract
Xenbase (https://www.xenbase.org/), the Xenopusmodel organism knowledgebase, is a web-accessible resource that integrates the diverse genomic and biological data from research on the laboratory frogs Xenopus laevisand Xenopus tropicalis. The goal of Xenbase is to accelerate discovery and empower Xenopusresearch, to enhance the impact of Xenopusresearch data, and to facilitate the dissemination of these data. Xenbase also enhances the value of Xenopusdata through high-quality curation, data integration, providing bioinformatics tools optimized for Xenopusexperiments, and linking Xenopusdata to human data, and other model organisms. Xenbase also plays an indispensable role in making Xenopusdata interoperable and accessible to the broader biomedical community in accordance with FAIR principles. Xenbase provides annotated data updates to organizations such as NCBI, UniProtKB, Ensembl, the Gene Ontology consortium, and most recently, the Alliance of Genomic Resources, a common clearing house for data from humans and model organisms. This article provides a brief overview of key and recently added features of Xenbase. New features include processing of Xenopushigh-throughput sequencing data from the NCBI Gene Expression Omnibus; curation of anatomical, physiological, and expression phenotypes with the newly created XenopusPhenotype Ontology; XenopusGene Ontology annotations; new anatomical drawings of the Normal Table of Xenopusdevelopment; and integration of the latest Xenopus laevisv10.1 genome annotations. Finally, we highlight areas for future development at Xenbase as we continue to support the Xenopusresearch community.
- Published
- 2023
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