The data integration pipeline. The integration starts by generating an Upper Level Ontology, which is then linked with the different ontologies: GO (Biological Process, Molecular Function and Cellular Component fragments), the MI ontology and the Biorel ontology, forming a seed ontology. Mouse, human and rat-specific data are integrated from Gene Ontology Annotation files and IntAct. Next, these species-specific ontologies are merged and additional data is integrated including protein information (UniProt), pathway annotations (KEGG), basic information for genes (NCBI) and orthology relations for proteins (orthAgogue). The final ontology is available in OBO and RDF formats.