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Journal of Information Science and Engineering, Vol. 22 No. 1, pp. 19-29 (January 2006)

GOBU: Toward an Integration Interface for Biological Objects

Wen-Dar Lin, Yun-Ching Chen, Jan-Ming Ho and Chung-Der Hsiao*
Institute of Information Science
*Institute of Cellular and Organismic Biology
Academia Sinica
Taipei, 115 Taiwan

In the present post-genomic era, many annotation catalogs are being created for annotating biological objects, for example, structural families, functional annotations, or expression levels in microarray experiments. Given a set of biological objects, one of the most important biological research goals is to find meaningful correspondences between annotations from different catalogs. For catalogs with linear structures, e.g., real numbers like expression levels, this problem can be solved by using computational methods. However, for catalogs with complex structures, e.g., functional annotations organized in a directed acyclic graph structure, this problem may be complicated for computer scientists, because these structures usually involve biological domain knowledge. Thus, it is necessary to have an interface that can help biologists discover important biological knowledge from these complex structures. In this paper, we propose the Gene Ontology Browsing Utility (GOBU), a Java-based software program, for integrating biological annotation catalogs under an extendable architecture that uses the Gene Ontology and a user-defined hierarchy as two main catalogs. GOBU is an OpenSource project hosted on OSSF and available at http://gobu.OpenFoundry.org/.

Keywords: gene ontology, annotation, data integration, bioinformatics, user interface

Full Text () Retrieve PDF document (200601_02.pdf)

Received June 15, 2005; accepted October 10, 2005.
Communicated by Kwei-Jay Lin.