Semantic Query and Reasoning Among Gene Ontology Annotations

As by far the most famous bio-ontology, Gene Ontology is widely used for annotations of gene products coming from different organisms. However, there exist some shortcomings in RDF file provided by GO consortium: (1) GO term-centric view of annotation data. The requirements are intractable when attempting to retrieve GO annotations based on big volume dataset. (2) Lack of richer semantic relationships between the pairs of terms coming from three independent GO subontologies. (3) Not supporting GOSlim. By encoding heterogeneous original data with uniform RDF format, creating additional ontology mappings, and introducing a set of reasoning rulebases, we proposed a Semantic Web model GORouter. Furthermore, we chose Oracle NDM as native RDF repository and used table function RDFMATCH to combine the result of RDF query with traditional relational data, seamlessly. Finally, we attempt to provide a mixture semantic query and reasoning solution.