During the last two years, the INFOGENMED project, an EU-funded project for integrating heteregeneous clinical and genomic databases, has been developed and completed. This project has used biomedical ontologies in issues such as database mapping and integration. Within the framework of INFOGENMED, we have developed various tools for mapping and querying databases over Internet using the UMLS, Gene Ontology and HGNC. Any other ontology could be easily added to the system, providing a valuable aid to both systems administrators and users. Although these domain ontologies present various constraints that must be considered by informaticians, they provide a powerful foundation for various information-related tasks in biomedicine. In this direction, ontologies present potential uses for biomedical informatics research, in areas such as data integration, information retrieval, data mining, decision support and others. These advances should also contribute to advance medicine and biology.

Recent approaches to developing biomedical ontologies with more formal and logical basis could be valuable to enhance their characteristics and capabilities, providing a fundamental tool for biomedical research and practice. In this sense, supporting research on ontological development and engineering should be a priority in future plans of funding agencies. While this need is true, ontologies should be not considered as an universal solution for the problems that medical informaticians, bioinformaticians and now, biomedical informaticians, have faced in various decades of research and professional work. The complexity of many biomedical and informatics issues cannot be only addressed in terms of methodological representation and conceptualization, as it has been shown since the pioneering work on medical expert systems during the 70s.