Xenbase: key features and resources of the Xenopus model organism knowledgebase

Author:

Fisher Malcolm1ORCID,James-Zorn Christina1ORCID,Ponferrada Virgilio1ORCID,Bell Andrew J1ORCID,Sundararaj Nivitha1ORCID,Segerdell Erik1ORCID,Chaturvedi Praneet1ORCID,Bayyari Nadia1,Chu Stanley2,Pells Troy2ORCID,Lotay Vaneet2,Agalakov Sergei2,Wang Dong Zhuo2,Arshinoff Bradley I2,Foley Saoirse3ORCID,Karimi Kamran2ORCID,Vize Peter D2ORCID,Zorn Aaron M1ORCID

Affiliation:

1. Xenbase, Division of Developmental Biology, Cincinnati Children’s Hospital Medical Center , Cincinnati, OH 45229 , USA

2. Xenbase, Department of Biological Sciences, University of Calgary , Calgary, AB T2N 1N4 , Canada

3. Department of Biological Sciences, Carnegie Mellon University , Pittsburgh, PA 15213 , USA

Abstract

Abstract Xenbase (https://www.xenbase.org/), the Xenopus model organism knowledgebase, is a web-accessible resource that integrates the diverse genomic and biological data from research on the laboratory frogs Xenopus laevis and Xenopus tropicalis. The goal of Xenbase is to accelerate discovery and empower Xenopus research, to enhance the impact of Xenopus research data, and to facilitate the dissemination of these data. Xenbase also enhances the value of Xenopus data through high-quality curation, data integration, providing bioinformatics tools optimized for Xenopus experiments, and linking Xenopus data to human data, and other model organisms. Xenbase also plays an indispensable role in making Xenopus data 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 Xenopus high-throughput sequencing data from the NCBI Gene Expression Omnibus; curation of anatomical, physiological, and expression phenotypes with the newly created Xenopus Phenotype Ontology; Xenopus Gene Ontology annotations; new anatomical drawings of the Normal Table of Xenopus development; and integration of the latest Xenopus laevis v10.1 genome annotations. Finally, we highlight areas for future development at Xenbase as we continue to support the Xenopus research community.

Funder

Xenbase

Eunice Kennedy Shriver National Institute of Child Health and Human Development

Publisher

Oxford University Press (OUP)

Subject

Genetics

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