Exploiting functional context in biology: Reconsidering classification of bacterial life

Abstract

Ontologies are built in various domains such as biology, chemistry, and business. Ontologies as knowledge bases have great potential to serve as providers of context for analytics not only to yield more relevant results but also to provide meaning in explaining results. Simply put, analysis without context ignores the underlying meaning in data. In this paper, we discuss one important example, how traditional classification of organisms in biology can become obsolete given the tremendous amount of genetic data now being analyzed under the lens of gene ontologies. Gene ontologies provide a functional context to how organisms operate and perform the functions of life. Ontologies such as gene ontologies encapsulate collective intelligence of scientists based on many decades of work. In this paper, we put forth a vision of contextual analytics in the field of genetics powered with big data and describe blueprints of an new approach to classification. There are many dimensions to biological function. We demonstrate how the cellular processes of interest can provide the context for classification of thousands of organisms based on their functional potential.