After the completion of the Human Genome Project, a new, post genomic era, is beginning to analyze and interpret the huge amount of genomic information. Information methods and techniques from areas such as database integration, information retrieval, knowledge discovery in databases (KDD) and decision support systems (DSS) are needed. These systems should take into account idiosyncratic differences between these two interacting fields, medicine and biology. Their correspondent medical informatics (MI) and bioinformatics (BI) should also interact and there is a need for a point to support the communication. Biomedical ontologies can be used to enhance biomedical information systems, providing a knowledge sharing framework. However, ontology tools are still in its infancy and there is a need of standards, services, automatic management tools, etc... to be able to properly apply this technology environment. Nevertheless, ontologies are just the technical framework the most important issue is the content and the use policy.