Connecting ontologies for the representation of biological pathways

Significant effort has been put into the creation of a multitude of large, publicly available pathway databases. Most make their content available in at least one of several standard representation formats, but there are limitations to existing pathway representation formats, including underutilization of a common set of biomedical ontologies. To address this limitation, we developed an approach to representing biological pathways that relies on the use of ontologies from the Open Biomedical Ontologies (OBO) Foundry, including the Relation Ontology (RO), and adheres to the logical principles of ontology development advocated by the Foundry. To demonstrate the utility of this representation approach, we have curated comprehensive pathway representations for the signal transduction pathways initiated by seven of the mouse Toll-like receptors (TLR). Current efforts include the development of approaches for utilizing these representations for pathway analysis.