Khatri Purvesh, Bhavsar Pratik, Bawa Gagandeep, Draghici Sorin
Department of Computer Science, Wayne State University, 431 State Hall, Detroit, MI 48202, USA.
Nucleic Acids Res. 2004 Jul 1;32(Web Server issue):W449-56. doi: 10.1093/nar/gkh409.
The Onto-Tools suite is composed of an annotation database and five seamlessly integrated web-accessible data mining tools: Onto-Express (OE), Onto-Compare (OC), Onto-Design (OD), Onto-Translate (OT) and Onto-Miner (OM). OM is a new tool that provides a unified access point and an application programming interface for most annotations available. Our database has been enhanced with more than 120 new commercial microarrays and annotations for Rattus norvegicus, Drosophila melanogaster and Carnorhabditis elegans. The Onto-Tools have been redesigned to provide better biological insight, improved performance and user convenience. The new features implemented in OE include support for gene names, LocusLink IDs and Gene Ontology (GO) IDs, ability to specify fold changes for the input genes, links to the KEGG pathway database and detailed output files. OC allows comparisons of the functional bias of more than 170 commercial microarrays. The latest version of OD allows the user to specify keywords if the exact GO term is not known as well as providing more details than the previous version. OE, OC and OD now have an integrated GO browser that allows the user to customize the level of abstraction for each GO category. The Onto-Tools are available online at http://vortex.cs.wayne.edu/Projects.html.
Onto-Tools套件由一个注释数据库和五个无缝集成的可通过网络访问的数据挖掘工具组成：Onto-Express（OE）、Onto-Compare（OC）、Onto-Design（OD）、Onto-Translate（OT）和Onto-Miner（OM）。OM是一个新工具，为大多数可用注释提供统一的访问点和应用程序编程接口。我们的数据库通过120多种新的商业微阵列以及针对褐家鼠、黑腹果蝇和秀丽隐杆线虫的注释得到了增强。Onto-Tools经过重新设计，以提供更好的生物学见解、更高的性能和用户便利性。OE中实现的新功能包括支持基因名称、LocusLink ID和基因本体（GO）ID，能够为输入基因指定倍数变化，链接到KEGG通路数据库以及详细的输出文件。OC允许比较170多种商业微阵列的功能偏差。OD的最新版本允许用户在不知道确切的GO术语时指定关键词，并且比以前的版本提供更多详细信息。OE、OC和OD现在有一个集成的GO浏览器，允许用户为每个GO类别自定义抽象级别。Onto-Tools可在http://vortex.cs.wayne.edu/Projects.html在线获取。
