Ontological Integration of Data Models for Cell Signaling Pathways by Defining a Factor of Causality Called `Signal'

Abstract

Databases have collected masses of information concerning cell signaling pathways that includes information on pathways, molecular interactions as well as molecular complexes. However we have no general data model to represent comprehensive properties of cell signaling pathways, so that this type of information has been represented by two di#erent data models that we call `binary relation' and `state transition'. The disagreement between the existing models derives from lack of consensus about a factor of causality in reactions in cell signaling pathways, which is often called `signal'. We developed an ontology named CSNO (Cell Signaling Networks Ontology) based on device ontology