This paper presents current progress in the development of Ontological Framework on top of the data integration environment which is a part of the Biomedical Informatics Research Network (BIRN; http://www.nbirn.net) project which is sponsored by the National Institutes of Health (NIH). The goal is the development of a ontological framework for biomedical research that support advance data acquisition, data storage, data integration, data visualization and other computing and information processing services over the Internet. Ontologically enabled data integration system performs semantic integration of data sources distributed over multiple research centers. It enables researchers to perform analyses based on larger and broader semantically relevant datasets than would be available from any single institution’s data. This paper describes the system architecture, capabilities of the semantically based data integration and a new way to animate semantics of texts. Also, it demonstrates a way to represent ontology through holographic reduced representation (HRR) and describe ontological confabulation as a way to optimize semantics browsing.