Xenbase: Core features, data acquisition, and data processing
Xenbase: Core features, data acquisition, and data processing
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DOI：
10.1002/dvg.22873
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发表时间：
2015-08-01
期刊：
影响因子：
1.5
通讯作者：
Vize, Peter D.
中科院分区：
文献类型：
--
作者：
James-Zorn, Christina;Ponferrada, Virgillio G.;Vize, Peter D.
Xenbase，非洲爪蟾模式生物数据库（），是一个基于云的，网络访问的资源，集成了来自非洲爪蟾研究的各种基因组和生物学数据。非洲爪蟾蛙是用于生物医学研究的主要脊椎动物模型之一，Xenbase是使用该模型四足动物生成的大量数据的中央存储库。Xenbase的目标是通过使研究人员能够在非洲爪蟾和人类疾病的分子途径之间建立新的联系来加速发现。我们的关系数据库和用户友好的界面使这些数据易于查询，并允许调查人员快速查询和链接不同的数据类型，否则将是困难的，耗时的，或不可能的。Xenbase还通过高质量的基因表达管理和数据整合，提供针对非洲爪蟾实验优化的生物信息学工具，并将非洲爪蟾数据与其他模式生物和人类数据联系起来，提高了这些数据的价值。Xenbase通过下载数据、解析内容并将其保存到相应文件和数据库表中的管道来绘制数据。此外，Xenbase通过不断向NCBI、UniProtKB和Ensembl等组织提供注释数据更新，使更广泛的生物医学界可以访问这些数据。在这里，我们描述了我们的生物信息学，基因组浏览工具，数据获取和共享，我们的社区提交和文献管理管道，文本挖掘支持，基因页面功能，以及基因命名和基因模型的管理。创世纪53：486-497，2015。(c)2015年威利期刊公司
Xenbase, the Xenopus model organism database (), is a cloud-based, web-accessible resource that integrates the diverse genomic and biological data from Xenopus research. Xenopus 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 Xenopus 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 Xenopus experiments, and by linking Xenopus 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. (c) 2015 Wiley Periodicals, Inc.