The course covers advanced topics in conceptual modelling, data management, integration and analysis, all of which have applications in data-intensive disciplines such as biology, biomedicine and others. The aims of the course is to provide an in-depth understanding of the state of the art in formal ontologies, including their role in integrating and analyzing data. While Knowledge Representation and Reasoning (CS 213) introduced basic logic formalisms that can be used to express knowledge. Examples include the theories for mereological (parthood) relations, or theories of space and time and the consequences of selecting a particular theory in formalized knowledge bases. The Course is split in two parts, the first focusing on concrete applications with examples taken from the biomedical domain, the second focusing on the theoretical framework underlying formal ontologies and their role in information systems.