Interactive web service system for exploration of biological pathways.

ABSTRACT

OBJECTIVE: Existing bioinformatics databases such as KEGG (Kyoto Encyclopedia of Genes and Genomes) provide a wealth of information. However, they generally lack a user-friendly and interactive interface. METHODOLOGY: The study proposes a web service system for exploring the contents of the KEGG database in an intuitive and interactive manner. In the proposed system, the requested pathways are uploaded from the KEGG database and are converted from a static format into an interactive format such that their contents can be more readily explored. The system supports two basic functions, namely an exhaustive search for all possible reaction paths between two specified genes in a biological pathway, and the identification of similar reaction sequences in different biological pathways. RESULTS: The feasibility of the proposed system is evaluated by means of an initial pilot study involving 10 students with varying degrees of experience of the KEGG website and its operations. The results indicate that the system provides a useful learning tool for investigating biological pathways. CONCLUSION: A system is proposed for converting the static pathway maps in KEGG into interactive maps such that they can be explored at will. The results of a preliminary trial confirm that the system is straightforward to use and provides a versatile and effective tool for examining and comparing biological pathways.