The contributions gathered here demonstrate how categorical ontology can provide a basis for linking three important basic sciences: mathematics, physics, and philosophy. Category theory is a new formal ontology that shifts the main focus from objects to processes. The book approaches formal ontology in the original sense put forward by the philosopher Edmund Husserl, namely as a science that deals with entities that can be exemplified in all spheres and domains of reality. It is a dynamic, processual, and non-substantial ontology in which all entities can be treated as transformations, and in which objects are merely the sources and aims of these transformations. Thus, in a rather surprising way, when employed as a formal ontology, category theory can unite seemingly disparate disciplines in contemporary science and the humanities, such as physics, mathematics and philosophy, but also computer and complex systems science.