The volume of publicly available data in biomedicine is constantly increasing. However, this data is stored in different formats on different platforms. Integrating this data will enable us to facilitate the pace of medical discoveries by providing scientists with a unified view of this diverse information. Under the auspices of the National Center for Biomedical Ontology, we have developed the Resource Index—a growing, large-scale index of more than twenty diverse biomedical resources. The resources include heterogeneous data from a variety of repositories maintained by different researchers from around the world. Furthermore, we use a set of 200 publicly available ontologies, also contributed by researchers in various domains, to annotate and to aggregate these descriptions. We use the semantics that the ontologies encode, such as different properties of classes, the class hierarchies, and the mappings between ontologies in order to improve the search experience for the Resource Index user. Our user interface enables scientists to search the multiple resources quickly and efficiently using domain terms, without even being aware that there is semantics under the hood.