Abstract. The call for a "focus on content" in ontology research by Nicola Guarino and Mark Musen in their launching statement of the journal Applied Ontology has quite some implications and ramifications. We reflectively discuss ontology engineering as a scientific discipline, and we put this into the wider perspective of debates in other fields. We claim and argue that ontology is a new scientific method for theory formation. This positioning allows for stronger concepts and techniques for theoretical, empirical and practical validation that in our view are now needed in the field. A prerequisite for this is an emphasis on ontology as a (domain) content oriented concept, rather than as primarily a computer representation notion. We propose that taking domain theories and the associated substantive or content reference of ontologies really seriously as first-class citizens, will actually increase the contribution of ontology engineering to the development of scientific metho...