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Systems Biology Knowledgebase for a New Era in Biology

A Genomics:GTL Report from the May 2008 Workshop

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To promote development of a data and information management system, or knowledgebase, DOE’s Office of Biological and Environmental Research (OBER) hosted a workshop May 28–30, 2008, in Washington, D.C. Experts from scientific disciplines relevant to DOE missions and from the enabling technologies (e.g., bioinformatics, computer science, database development, and systems architecture) met to determine the opportunities and requirements for developing and managing this knowledgebase for OBER’s Genomics:GTL program (GTL).

Workshop participants defined the proposed GTL Knowledgebase, or GKB, as an informatics resource that would focus on DOE science-application areas yet also be widely and easily applicable to all systems biology research. Also discussed were requirements for effective development of data capabilities for systems biology that could be applied specifically to plants and microbes (i.e., bacteria, archaea, fungi, and protists—unicellular eukaryotes such as microalgae) as well as to three areas of science related to DOE missions: (1) researching and developing biofuels, (2) advancing fundamental understanding of the global carbon cycle, and (3) understanding and using biological systems for environmental remediation. Participants were organized into working groups based on four knowledgebase themes: data, metadata, and information; data integration; database architecture and infrastructure; and community and user issues.

The workshop highlighted DOE’s unique and extensive data-management needs as a foundation of mission-inspired systems biology research. These needs require a principal GTL data resource, the GKB, with critical links to complementary systems supported by other agencies and community organizations worldwide. This knowledgebase would facilitate a new level of scientific inquiry by serving as a central component for the integration of modeling, simulation, experimentation, and bioinformatic approaches. The GKB also would be a primary resource for data sharing and information exchange among the GTL community. Furthermore, not only would the GKB allow scientists to expand, compute, and integrate data and information program wide, it also would drive two classes of work: experimental design and modeling and simulation. Integrating data derived from computational predictions and modeling, as envisioned in the knowledgebase project, would increase data completeness, fidelity, and accuracy. These advancements in turn would greatly improve modeling and simulation, leading to new experimentation, analyses, and mechanistic insight. Scientists’ ever-increasing exploitation of the dynamic linkages among data integration, experimentation, and modeling and simulation—aided by the GKB—will advance efforts to achieve a predictive understanding of the functions of biological systems. The knowledgebase, therefore, must serve multiple roles, including (1) a repository of data and results from high-throughput experiments; (2) a collection of tools to derive new insights through data synthesis, analysis, and comparison; (3) a framework to test scientific understanding; (4) a heuristic capability to improve the value and sophistication of further inquiry; and (5) a foundation for prediction, design, manipulation, and, ultimately, engineering of biological systems to meet national needs in bioenergy, environmental remediation, and carbon cycling.

Suggested citation for this report: 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 (http://genomicsgtl.energy.gov/compbio/).

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