Open Bioinformatics Grid (OBIGrid) was established in 2002 for sharing the bioinformatics environment including computational resources, public databases, and bioinformatics application tools over the Internet. Grid is one of the most attractive cyber infrastructures for achieving scalability in the computation power and data storage necessary for bioinformatics. Grid also plays the role of ?Ba?, the basis of virtual organizations in which people share time and place to work together. ?Ba? can extend beyond the boundaries of current grid computing by utilizing web service technologies for sharing databases, tools, and knowledge distributed all over the world.

However, many issues regarding the widespread use of the web services have been raised, such as the semantic gap between bioinformatics workflows and the application programming interfaces provided by web services. The key to solving such issues is the bioinformatics ontology employed to establish interoperability among biological databases and bioinformatics application tools used by the web services. This paper proposes a design of bioinformatics ontology based on triadic relations among input-output data, commands, and databases, and demonstrates its feasibility in the automatic generation of bioinformatics workflows.