In view of the fact that there is a lot of biomedical research data, rapidly accumulating to relevant repositories, there is an urgent need these data to be delivered, as soon as possible, to the specific scientific audience interesting in it. Unfortunately, the current database technologies often isolate data rather than making it easily and freely accessible. A considerable effort by the information scientists is needed to process the resources that meet the scientific query criteria as well as to index and present them as useful metadata. Taking into account that biomedical data are mostly hidden from the public eye, often stored in not indexed databases or libraries and inaccessible by standard search engines, the retrieval, storing, annotating, and qualification of health information remain major challenges. The evolution of the World Wide Web from a collection of unstructured and predominantly human readable data into the Semantic Web of knowledge with meaningful relationships between resources and machine readable data will significantly improve our ability to conduct bioinformatics analyses and to make better clinical decisions that positively affect healthcare outcomes. To this end novel semantic web services arise, which depend on markup ontologies in order to make biological and clinical data logical analysis computational and reasonable processed through the utilization of appropriate algorithms. Herein, we discuss the use of these technologies for the efficient and reliable retrieval of meaningful biomedical data from the relevant resources and repositories.