Structuring the Life Science Resourceome for Semantic Systems Biology: Lessons from the BioGateway Project

The application of Semantic Web technologies in the life sciences for data integration is still nascent. We have recently built BioGateway, an RDF store that integrates all the candidate OBO Foundry ontologies with other resources such as SWISS-PROT. In the course of developing BioGateway, we faced challenges that are common to other projects that involve large datasets in diverse formats. We present a detailed analysis of the obstacles that had to be solved in creating BioGateway. In doing so, we demonstrate the potential of a comprehensive application of Semantic Web technologies to global biomedical data. The time is ripe for launching a community effort aiming at a wider acceptance and application of Semantic Web technologies in the life sciences domain. We make a public call for the creation of a forum that strives to implement a truly semantic life science foundation of a type of Systems Biology that we named Semantic Systems Biology.