Ontologies enjoy increasing popularity among bioinformatics researchers who seek assistance in coping with the rapid upgrowth of biological data to be handled and related information to be considered. While communities of committed ontology pioneers drive the development and optimisation of ontologies for a wide range of relevant domains, the amble adoption of ontologies in bioinformatics research is still decelerated by technological, managerial and communication barriers. This paper contains a brief review of current trends, challenges and perspectives in ontology research and practice in bioinformatics.