Xenbase, the Xenopus model organism database, is a web accessible resource that integrates all the diverse genomic and biological data from Xenopus research. The goal of Xenbase is to empower Xenopus research, enhance the impact of Xenopus research data and to facilitate the dissemination of this data. Xenopus frogs are one of the major vertebrate animal models used for biomedical research. Comparative functional genomics between humans and model organisms such as Xenopus have led to a wealth of discoveries and in this post genomic era and with thousands of scientific publications annually and the exponential growth of large-scale datasets, resources such as Xenbase are essential to translate this vast body of data into a meaningful biological synthesis. Xenbase is the only central repository for the enormous amount of data generated from Xenopus research. Our relational database and user-friendly interface make this data easy to query, and allows investigators to quickly interrogate and link different data types in ways that would otherwise be difficult, time consuming, or impossible. Xenbase also enhances the value of Xenopus data through high quality curation, data integration, providing bioinformatics tools optimized for Xenopus experiments, and by linking Xenopus data to humans and other model organisms. Xenbase plays an indispensable role in making Xenopus data accessible to the broader biomedical community by continually providing annotated data updates to organizations such as NCBI, UniProtKB and Ensemble. Xenbase accelerates discovery, enabling investigators to make novel connections between molecular pathway in Xenopus and human disease. Xenbase plays an essential role in maximizing the NIH's ~$130 million annual investment in Xenopus research. The Goal of this proposal is to maintain and expand Xenbase.
Our Aims, developed through extensive input from the community are:
Aim1 Maintain Xenbase and continue curation of Xenopus research data Aim 2 Develop support for Xenopus models of human diseases Aim 3 Enhance support for new data types, bioinformatics tools and data sharing infrastructure

Public Health Relevance

Research with animal models such as the frog Xenopus, is essential for understanding of health and human development. In the post genomic are with vast amounts of diverse data being generated bioinformatics resources are necessary to integrate and translate this information into a meaningful synthesis. This proposal aims to maintain and improve Xenbase the Xenopus Model organism database, a critical resource for all research in this valuable system.

National Institute of Health (NIH)
Eunice Kennedy Shriver National Institute of Child Health & Human Development (NICHD)
Biotechnology Resource Grants (P41)
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Special Emphasis Panel (ZHD1)
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Coulombe, James N
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Cincinnati Children's Hospital Medical Center
United States
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Patrushev, Ilya; James-Zorn, Christina; Ciau-Uitz, Aldo et al. (2018) New methods for computational decomposition of whole-mount in situ images enable effective curation of a large, highly redundant collection of Xenopus images. PLoS Comput Biol 14:e1006077
Karimi, Kamran; Wuitchik, Daniel M; Oldach, Matthew J et al. (2018) Distinguishing Species Using GC Contents in Mixed DNA or RNA Sequences. Evol Bioinform Online 14:1176934318788866
Karimi, Kamran; Fortriede, Joshua D; Lotay, Vaneet S et al. (2018) Xenbase: a genomic, epigenomic and transcriptomic model organism database. Nucleic Acids Res 46:D861-D868
James-Zorn, Christina; Ponferrada, Virgilio; Fisher, Malcolm E et al. (2018) Navigating Xenbase: An Integrated Xenopus Genomics and Gene Expression Database. Methods Mol Biol 1757:251-305
Vize, Peter D; Zorn, Aaron M (2017) Xenopus genomic data and browser resources. Dev Biol 426:194-199
Session, Adam M; Uno, Yoshinobu; Kwon, Taejoon et al. (2016) Genome evolution in the allotetraploid frog Xenopus laevis. Nature 538:336-343
Deans, Andrew R; Lewis, Suzanna E; Huala, Eva et al. (2015) Finding our way through phenotypes. PLoS Biol 13:e1002033
Vize, Peter D; Liu, Yu; Karimi, Kamran (2015) Database and Informatic Challenges in Representing Both Diploid and Tetraploid Xenopus Species in Xenbase. Cytogenet Genome Res 145:278-82
Grant, Ian M; Balcha, Dawit; Hao, Tong et al. (2015) The Xenopus ORFeome: A resource that enables functional genomics. Dev Biol 408:345-57
James-Zorn, Christina; Ponferrada, Virgillio G; Burns, Kevin A et al. (2015) Xenbase: Core features, data acquisition, and data processing. Genesis 53:486-97

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