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Tripal v1.1: a standards-based toolkit for construction of online genetic and genomic databases

机译:Tripal v1.1:用于构建在线遗传和基因组数据库的基于标准的工具包

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摘要

Tripal is an open-source freely available toolkit for construction of online genomic and genetic databases. It aims to facilitate development of community-driven biological websites by integrating the GMOD Chado database schema with Drupal, a popular website creation and content management software. Tripal provides a suite of tools for interaction with a Chado database and display of content therein. The tools are designed to be generic to support the various ways in which data may be stored in Chado. Previous releases of Tripal have supported organisms, genomic libraries, biological stocks, stock collections and genomic features, their alignments and annotations. Also, Tripal and its extension modules provided loaders for commonly used file formats such as FASTA, GFF, OBO, GAF, BLAST XML, KEGG heir files and InterProScan XML. Default generic templates were provided for common views of biological data, which could be customized using an open Application Programming Interface to change the way data are displayed. Here, we report additional tools and functionality that are part of release v1.1 of Tripal. These include (i) a new bulk loader that allows a site curator to import data stored in a custom tab delimited format; (ii) full support of every Chado table for Drupal Views (a powerful tool allowing site developers to construct novel displays and search pages); (iii) new modules including ‘Feature Map', ‘Genetic', ‘Publication', ‘Project', ‘Contact' and the ‘Natural Diversity' modules. Tutorials, mailing lists, download and set-up instructions, extension modules and other documentation can be found at the Tripal website located at http://tripal.info. Database URL: http://tripal.info/
机译:Tripal是一个免费的开放源代码工具包,用于构建在线基因组和遗传数据库。它旨在通过将GMOD Chado数据库架构与流行的网站创建和内容管理软件Drupal集成,促进社区驱动的生物网站的开发。 Tripal提供了一套用于与Chado数据库进行交互并在其中显示内容的工具。这些工具被设计为通用的,以支持将数据存储在Chado中的各种方式。 Tripal的先前发行版支持生物体,基因组库,生物种群,种群集合和基因组特征,它们的比对和注释。而且,Tripal及其扩展模块为常用文件格式(例如FASTA,GFF,OBO,GAF,BLAST XML,KEGG继承文件和InterProScan XML)提供了加载程序。为生物数据的通用视图提供了默认的通用模板,可以使用开放的“应用程序编程接口”自定义默认模板,以更改数据的显示方式。在这里,我们报告了Tripal v1.1发行版中的其他工具和功能。其中包括:(i)一个新的批量加载器,它允许站点管理员导入以自定义制表符分隔格式存储的数据; (ii)对每个Chado表的Drupal Views完全支持(一种强大的工具,允许站点开发人员构建新颖的显示和搜索页面); (iii)新模块,包括“功能图”,“遗传”,“出版物”,“项目”,“联系”和“自然多样性”模块。可以在Tripal网站http://tripal.info上找到教程,邮件列表,下载和设置说明,扩展模块和其他文档。数据库URL:http://tripal.info/

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