As new biomedical technologies are developed, the amount of publically available biomedical data continues to increase. To help manage these vast and disparate data sources, researchers have turned to the Semantic Web. Specifically, ontologies are used in data annotation, natural language processing, information retrieval, clinical decision support, and data integration tasks. The development of software applications to perform these tasks requires the integration of Web services to incorporate the wide variety of ontologies used in the health care and life sciences. The National Center for Biomedical Ontology, a National Center for Biomedical Computing created under the NIH Roadmap, developed BioPortal, which provides access to one of the largest repositories of biomedical ontologies. The NCBO Web services provide programmtic access to these ontologies and can be grouped into four categories; Ontology, Mapping, Annotation, and Data Access. The Ontology Web services provide access to ontologies, their metadata, ontology versions, downloads, navigation of the class hierarchy (parents, children, siblings) and details of each term. The Mapping Web services provide access to the millions of ontology mappings published in BioPortal. The NCBO Annotator Web service “tags” text automatically with terms from ontologies in BioPortal, and the NCBO Resource Index Web services provides access to an ontology-based index of public, online data resources. The NCBO Widgets package the Ontology Web services for use directly in Web sites. The functionality of the NCBO Web services and widgets are incorporated into semantically aware applications for ontology development and visualization, data annotation, and data integration. This overview will describe these classes of applications, discuss a few examples of each type, and which NCBO Web services are used by these applications.