Through high quality curation we aim to integrate the wealth of Xenopus data into a single easily accessible computer framework that accelerates research, and facilitates the translation of this large amount of information into meaningful knowledge. The data in Xenbase must be comprehensive, accurate and up to date. Xenbase contains many different data types including; genomes and gene models, DNA, RNA and protein sequences, gene names and symbols, gene expression patterns, gene function, anatomy, orthology, reagents (MOs and antibodies), investigator information, phenotypes and disease associations. This data comes from the published literature, direct community submissions and from other databases (e.g. NCBI, JGI, OMIM). In order for the information in Xenbase to be computer readable, we index and annotate data using ontologies and standardized procedures that are the accepted best practices as shared across major model organism databases (MODs). This allows Xenopus data to be compared to other animals and to human disease gene and phenotypes. The majority of the curation effort is to read and annotate the published Xenopus literature. Xenbase contains a corpus of ~46,000 Xenopus papers, mirroring PubMed, but to date only about 10% of these have been curated, primarily for gene expression patterns. Preliminary analysis indicate that ~11,000 uncurated papers are likely to contain valuable high priority data and about 1,300 new Xenopus papers are published each year. In the Curation Component we will annotate this Xenopus research data.

Agency
National Institute of Health (NIH)
Institute
Eunice Kennedy Shriver National Institute of Child Health & Human Development (NICHD)
Type
Biotechnology Resource Grants (P41)
Project #
5P41HD064556-08
Application #
9380970
Study Section
Special Emphasis Panel (ZHD1)
Project Start
Project End
Budget Start
2017-12-01
Budget End
2018-11-30
Support Year
8
Fiscal Year
2018
Total Cost
Indirect Cost
Name
Cincinnati Children's Hospital Medical Center
Department
Type
DUNS #
071284913
City
Cincinnati
State
OH
Country
United States
Zip Code
45229
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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
Karpinka, J Brad; Fortriede, Joshua D; Burns, Kevin A et al. (2015) Xenbase, the Xenopus model organism database; new virtualized system, data types and genomes. Nucleic Acids Res 43:D756-63
Karimi, Kamran; Vize, Peter D (2014) The Virtual Xenbase: transitioning an online bioinformatics resource to a private cloud. Database (Oxford) 2014:
Segerdell, Erik; Ponferrada, Virgilio G; James-Zorn, Christina et al. (2013) Enhanced XAO: the ontology of Xenopus anatomy and development underpins more accurate annotation of gene expression and queries on Xenbase. J Biomed Semantics 4:31
James-Zorn, Christina; Ponferrada, Virgilio G; Jarabek, Chris J et al. (2013) Xenbase: expansion and updates of the Xenopus model organism database. Nucleic Acids Res 41:D865-70

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