Xenbase: Core features, data acquisition, and data processing. Issue 8 (16th July 2015)

• Record Type: Journal Article
• Authors: James‐Zorn, Christina; Ponferrada, Virgillio G.; Burns, Kevin A.; Fortriede, Joshua D.; Lotay, Vaneet S.; Liu, Yu; Brad Karpinka, J.; Karimi, Kamran; Zorn, Aaron M.; Vize, Peter D.; Vize, Peter; Westerfiled, Monte
• Is Part Of: Genesis. Volume 53:Issue 8(2015:Aug.)
• Page Start: 486
• Page End: 497
• Publication Date: 2015-07-16
• Subjects: Developmental genetics -- Periodicals; Genetics -- Periodicals; Developmental biology -- Periodicals; Embryology -- Periodicals; Genetic regulation -- Periodicals; 576.5
• DOI: 10.1002/dvg.22873
• Languages: English
• ISSNs: 1526-954X

Abstract

<abstract abstract-type="main"> <title>Summary</title> <p>Xenbase, the <italic>Xenopus</italic> model organism database (<ext-link ext-link-type="uri" xlink:href="http://www.xenbase.org" xlink:type="simple" xmlns:xlink="http://www.w3.org/1999/xlink">www.xenbase.org</ext-link>), is a cloud‐based, web‐accessible resource that integrates the diverse genomic and biological data from <italic>Xenopus</italic> research. <italic>Xenopus</italic> frogs are one of the major vertebrate animal models used for biomedical research, and Xenbase is the central repository for the enormous amount of data generated using this model tetrapod. The goal of Xenbase is to accelerate discovery by enabling investigators to make novel connections between molecular pathways in <italic>Xenopus</italic> and human disease. Our relational database and user‐friendly interface make these 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 these data through high‐quality gene expression curation and data integration, by providing bioinformatics tools optimized for <italic>Xenopus</italic> experiments, and by linking <italic>Xenopus</italic> data to other model organisms and to human data. Xenbase draws in data via pipelines that download data, parse the content, and save them into appropriate files and database tables. Furthermore, Xenbase makes these data accessible to the broader biomedical community by continually providing annotated data updates to organizations such as NCBI, UniProtKB, and Ensembl. Here, we describe our bioinformatics, genome‐browsing tools, data acquisition and sharing, our community submitted and literature curation pipelines, text‐mining support, gene page features, and the curation of gene nomenclature and gene models. genesis 53:486–497, 2015. © 2015 Wiley Periodicals, Inc.</p> </abstract>