The biomedical domain experiences rapid growth of knowledge in various subfields. Most of this knowledge is expressed through natural text which poses some challenges regarding processing such large quantities of information and more importantly, learning from it. Biomedical ontologies have been developed to counter this challenge among many others. In this paper, we go over fundamental notions of ontologies, followed by a review of some of the most used biomedical ontologies, and finally discuss some of their applications and challenges regarding knowledge discovery from biomedical data.