Knowledge modeling and the semantic dimension of information plays an increasingly central role in the network economy today. Theoretical research and actual implementations bring up unexpected problems and issues and there is, moreover, an increasing need for solid theoretical foundations for practical applications of ontologies, based on philosophy, linguistics, artificial intelligence and logic. The fifth International workshop Formal Ontology Meets Industry (FOMI 2011), held in Delft, the Netherlands in July 2011, brings together researchers and practitioners involved in this field, without the restrictions of their usual domains of work: business, medicine, engineering, finance, law, biology, geography, electronics, and many more. The nine papers presented here are divided into three sections: Philosophical Foundations of FOMI, Methodological Approaches, and finally, Data Integration. Subjects covered in part one include defining the general notion of technical artifacts in formal ontologies and a philosophy inspired schema to describe applied ontologies. Part two includes a paper on the context and methodological approach for the support of ontology-based annotations and meta data management of clinical trial resources, as well as a presentation of two formal approaches to similarity, the geometric model and feature matching model. In part three, there is a proposal to apply ontologies for Linked Open Data to monitor operational behavior, particularly supply chain risk analysis; this section also includes a description of Gellish, a formal ontological language. IOS Press is an international science, technical and medical publisher of high-quality books for academics, scientists, and professionals in all fields. Some of the areas we publish in: • Biomedicine • Oncology • Artificial intelligence • Databases and information systems • Maritime engineering • Nanotechnology • Geoengineering • All aspects of physics • E-governance • E-commerce • The knowledge economy • Urban studies • Arms control • Understanding and responding to terrorism • Medical informatics • Computer Sciences