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Tripal: a construction toolkit for online genome databases

机译:三重:在线基因组数据库的构建工具包

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摘要

As the availability, affordability and magnitude of genomics and genetics research increases so does the need to provide online access to resulting data and analyses. Availability of a tailored online database is the desire for many investigators or research communities; however, managing the Information Technology infrastructure needed to create such a database can be an undesired distraction from primary research or potentially cost prohibitive. Tripal provides simplified site development by merging the power of Drupal, a popular web Content Management System with that of Chado, a community-derived database schema for storage of genomic, genetic and other related biological data. Tripal provides an interface that extends the content management features of Drupal to the data housed in Chado. Furthermore, Tripal provides a web-based Chado installer, genomic data loaders, web-based editing of data for organisms, genomic features, biological libraries, controlled vocabularies and stock collections. Also available are Tripal extensions that support loading and visualizations of NCBI BLAST, InterPro, Kyoto Encyclopedia of Genes and Genomes and Gene Ontology analyses, as well as an extension that provides integration of Tripal with GBrowse, a popular GMOD tool. An Application Programming Interface is available to allow creation of custom extensions by site developers, and the look-and-feel of the site is completely customizable through Drupal-based PHP template files. Addition of non-biological content and user-management is afforded through Drupal. Tripal is an open source and freely available software package found at
机译:随着基因组学和遗传学研究的可用性,可负担性和规模的增加,提供在线访问所得数据和分析的需求也随之增加。定制的在线数据库的可用性是许多研究人员或研究社区的需求。但是,管理创建此类数据库所需的信息技术基础结构可能会干扰主要研究工作,或者可能导致成本过高。 Tripal通过将流行的Web内容管理系统Drupal与Chado的功能相融合来简化站点开发,Chado是一种社区衍生的数据库架构,用于存储基因组,遗传和其他相关生物数据。 Tripal提供了一个接口,可将Drupal的内容管理功能扩展到Chado中存储的数据。此外,Tripal还提供了基于Web的Chado安装程序,基因组数据加载程序,基于Web的生物数据编辑,基因组特征,生物学库,受控词汇表和种群集合。还提供Tripal扩展,该扩展支持NCBI BLAST,InterPro,《京都议定书》的基因和基因组百科全书以及基因本体分析的加载和可视化,以及将Tripal与流行的GMOD工具GBrowse集成的扩展。应用程序编程接口可用于允许站点开发人员创建自定义扩展,并且站点的外观可通过基于Drupal的PHP模板文件完全自定义。通过Drupal提供了非生物内容和用户管理功能。 Tripal是一个开源软件,可从以下网站免费获得软件包:

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