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Phases in Knowledgebase Development and Functionality

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Living systems are extremely complex, and thus investigating their properties requires multiple experimental tools. Integrating diverse types of data generated by these different tools represents a major challenge in efforts to understand and predict biological function. Further complicating this challenge is the advent of high-throughput technologies, such as transcriptional profiling and mass spectrometry-based proteomics, that can generate enormous amounts of data. Storing and managing these high-throughput data continue to be significant issues, but a more pressing and difficult problem involves interpreting and integrating the data with current biological knowledge. Much of this problem arises because knowledge in a given field is dispersed among individual investigators or found within a generally unstructured literature. Biology, unlike mathematics, lacks a formal language to describe and codify biological understanding and relationships. Therefore, most of our knowledge of biological systems is descriptive and qualitative in nature, a level of understanding insufficient for building predictive models of biological processes. Effective approaches for data integration and analysis need to be developed to successfully exploit biological systems to address energy and environmental challenges. DOE's Genomic Science program is beginning to address these needs with its Systems Biology Knowledgebase.

This table shows three phases of technology development from less to more mature (lower left to upper right, respectively). The state of technology development for the biological systems (microbes, plants, and metacommunities) addressed in the 2010 DOE Systems Biology Knowledgebase Implementation Plan is in different stages of maturity. Technologies for microbial research and analysis currently are well into Phase I. Upon implementing this plan, the Microbial Scientific Objectives will move fully into Phase II. Though technologies are less mature for plant and metacommunities, deploying the implementation plan will result in substantial progress in Phase I and Phase II.

Credit or Source: Office of Biological and Environmental Research of the U.S. Department of Energy Office of Science.


U.S. DOE. 2009. U.S. Department of Energy Office of Science Systems Biology Knowledgebase for a New Era in Biology: A Genomics:GTL Report from the May 2008 Workshop, DOE/SC-113, U.S. Department of Energy Office of Science. (p. vii) (website)

US DOE. 2009. New Frontiers in Characterizing Biological Systems: Report from the May 2009 Workshop, DOE/SC-0121, US Department of Energy Office of Science. (p. 33) (website)

U.S. DOE. 2010. DOE Systems Biology Knowledgebase Implementation Plan. U.S. Department of Energy Office of Science (p. vii) ( website)

Prepared by the Biological and Environmental Research Information System, Oak Ridge National Laboratory, and