PNNL

Abstract

The new systems approach to biology has created a great need for innovative database technologies. Biologists need new ways to integrate large scale data and concepts they form about the data during experimental and computational research. The Heuristic Entity Relationship Building Environment (HERBE) is a new prototypical architecture fusing data management technologies with knowledge management components. This hybrid approach enables the scientist to manage both their concepts and related data in a synchronized fashion. HERBE is currently being used for microbial research and in this paper we will describe how HERBE is used to capture microbial protein concepts grouped by organism, how the microbial proteins are reengineered into a combined knowledge on multiple microbial organisms, and how the data associated with the organisms can be mined. This paper also describes how the scientist’s evolving knowledge can be annotated by connecting the biologist’s knowledge to community resources such as the Gene Ontology.