Gene expression profiling data provide useful information for the investigation of biological function and process. However, identifying a specific expression pattern from extensive time series gene expression data is not an easy task. Clustering, a popular method, is often used to classify similar expression genes, however, genes with a ‘desirable’ or ‘user-defined’ pattern cannot be efficiently detected by clustering methods. To address these limitations, we developed an online tool called GEsture. Users can draw, or graph a curve using a mouse instead of inputting abstract parameters of clustering methods. GEsture explores genes showing similar, opposite and time-delay expression patterns with a gene expression curve as input from time series datasets. We presented three examples that illustrate the capacity of GEsture in gene hunting while following users’ requirements. GEsture also provides visualization tools (such as expression pattern figure, heat map and correlation network) to display the searching results. The result outputs may provide useful information for researchers to understand the targets, function and biological processes of the involved genes.

The semantic web is a second generation of the Web and is a vision of information that is understandable by computers. The Semantic Web provides a common framework that allows data to be shared and reused across application, enterprise, and community boundaries. Ontologies are used to define the concepts in the domain of discourse and their relationships and as such provide the formal vocabulary applications use to exchange data. Besides the Web, the technologies developed for the Semantic Web have proven to be useful also in other domains, especially when data is exchanged between applications from different parties. The software engineering community has developed various tools to support the specification, development, and maintenance of software. Many of these tools use proprietary data formats to store artifacts which hamper interoperability. Software engineering is one of these domains in which recent research shows that Semantic Web technologies are able to reduce the barriers of proprietary data formats and enable interoperability. In this paper, we present Semantic Web technologies and their application in software engineering or ontologies developed for software engineering, review the current efforts on applying the Semantic Web techniques on different software engineering aspects, and present the benefits of their applications. We discuss the current status of ontologies for software entities, bug reports, or change requests, as well as semantic representations for software and its documentation. This way, architecture, design, code, or test models can be shared across application boundaries enabling a seamless integration of engineering results.

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