SemBiosphere: A Semantic Web Approach to Recommending Microarray Clustering Services
SemBiosphere: A Semantic Web Approach to Recommending Microarray Clustering Services
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DOI：
10.1142/9789812701626_0018
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发表时间：
2005-12
影响因子：
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通讯作者：
Kevin Y. Yip;Peishen Qi;Martin H. Schultz;D. Cheung;K. Cheung
中科院分区：
文献类型：
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作者：
Kevin Y. Yip;Peishen Qi;Martin H. Schultz;D. Cheung;K. Cheung
聚类是分析微阵列数据的流行方法。鉴于可用的聚类算法数量众多，很难确定最适合特定任务的算法。定位、下载、安装和运行算法也很困难。本文描述了一个匹配系统 SemBiosphere，它解决了这两个问题。它根据一些最小的用户需求输入和数据属性推荐聚类算法。本体是用 OWL（一种富有表现力的本体语言）开发的，用于描述算法是什么、它们如何执行以及如何调用它们。这使得机器能够“理解”算法并提出建议。该算法可以由不同的团队以不同的语言实现，并在地理分布的站点的不同平台上运行。通过使用基于 XML 的 Web 服务，它们都可以以相同的标准方式进行调用。目前的聚类服务是由Biosphere系统的非语义Web服务改造而来，其中包括多种已应用于微阵列基因表达数据分析的算法。新的算法可以毫不费力地集成到系统中。 SemBiosphere 系统和完整的聚类本体可以通过 http://yeasthub2.gersteinlab 访问。组织/sembiosphere/。
Clustering is a popular method for analyzing microarray data. Given the large number of clustering algorithms being available, it is difficult to identify the most suitable ones for a particular task. It is also difficult to locate, download, install and run the algorithms. This paper describes a matchmaking system, SemBiosphere, which solves both problems. It recommends clustering algorithms based on some minimal user requirement inputs and the data properties. An ontology was developed in OWL, an expressive ontological language, for describing what the algorithms are and how they perform, in addition to how they can be invoked. This allows machines to "understand" the algorithms and make the recommendations. The algorithm can be implemented by different groups and in different languages, and run on different platforms at geographically distributed sites. Through the use of XML-based web services, they can all be invoked in the same standard way. The current clustering services were transformed from the non-semantic web services of the Biosphere system, which includes a variety of algorithms that have been applied to microarray gene expression data analysis. New algorithms can be incorporated into the system without too much effort. The SemBiosphere system and the complete clustering ontology can be accessed at http://yeasthub2.gersteinlab. org/sembiosphere/.