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Example Workflow for Integrating Phenotypic and Experimental Data and Metadata to Predict Biomass Properties from Genotype

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The 2010 DOE Systems Biology Knowledgebase Implementation Plan describes scientific objectives the Knowledgebase will support in microbial, plant, and metacommunity research areas. An example workflow for plant scientific objective 1, Integrate Phenotypic and Experimental Data and Metadata to Predict Biomass Properties from Genotype, is illustrated in this figure and proceeds from upper left to lower right. A user designs an experiment employing a Knowledgebase interface (upper left oval). The data to be collected (yellow box surrounded by data and metadata in green) is determined in part by instrumentation and also by the user based on the specific objective. Data would be checked for errors and for conformance to controlled vocabularies. One or more analysis modules shown as blue rectangles following the decision points (orange diamonds) would be selected. These modules themselves may be multicomponent pipelines for reducing data dimensionality, extracting features, genotyping, or other specific goals. Results would be incorporated into the Knowledgebase. As the database grows, potential for comparison across experiments would expand and further enable systems-based approaches (brown oval, lower right).

Credit or Source: Office of Biological and Environmental Research of the U.S. Department of Energy Office of Science. science.energy.gov/ber

Citation(s):

U.S. DOE. 2010. DOE Systems Biology Knowledgebase Implementation Plan. U.S. Department of Energy Office of Science (p. 39) ( website)

Biological and Environmental Research Information System, Oak Ridge National Laboratory, genomicscience.energy.gov/ and genomics.energy.gov/.