Figure 1

Rule-based mediation in the context of SBML model annotation. Non-OWL formats are first converted into syntactic ontologies. Here, both UniProtKB and BioGRID data are in XML: UniProtKB has its own schema, while BioGRID uses PSI-MIF. These formats are converted into syntactic ontologies via the XMLTab. BioPAX, the format used for Pathway Commons, is already in OWL and needs no conversion. Next, the instances present in the syntactic ontologies are mapped to the core ontology using SWRL. Finally, querying is performed using SQWRL queries using only core ontology concepts. Information is then passed through a final syntactic ontology (MFO) into an SBML model.