Data integration across multiple disciplines is a key requirement for virtual observatories. We have designed and implemented a virtual observatory for the areas of solar, solar-terrestrial, and space physics that leverages semantic technologies. Our work provides an implemented demonstration of ontology-enabled semantic interoperability. We have encoded an ontology in OWL covering topics of importance to atmospheric and solar researchers. This ontology is used to inform our virtual observatory services. Our goal was to provide semantically-enabled search and analysis functionalities that access a virtual repository of scientific data. The target user community includes a broad range of scientific researchers over a wide array of data sources. We have implemented a number of use cases that demonstrate semantic integration across various solar atmospheric data sets and the impacts of solar activity on the atmosphere. The implementation is deployed and two scientific user communities are migrating over to full usage in October, 2006.