The 2010 DOE Systems Biology Knowledgebase Implementation Plan describes scientific objectives the Knowledgebase will support in microbial, plant, and metacommunity research areas. Microbial scientific objective 1, Reconstruct and Predict Metabolic Networks to Manipulate Microbial Function, has a number of workflows with various intermediate goals and timelines. One example workflow illustrated in this figure, includes:
1. Generation of automatic genomic annotations for automated inference of a draft metabolic network.
2. A reconstruction and simulation engine that automatically generates a list of gaps (e.g., missing enzymes or transporters) and inconsistencies (e.g, functions without context or “dangling” compounds). Such a list has significant scientific value because it identifies open research problems, missing knowledge, and important experiments.
3. Existing and newly developed software tools that attempt to fill in gaps and impose consistency on annotations (e.g., negate “weak” functional assignments not supported by the functional context).
4. A modified set of annotations, as well as additional assumptions about boundary conditions and pathways (e.g., based on experimental physiological data), used to guide hypotheses and experimental designs.
5. Incorporation of experimental data to validate or disprove parts of the metabolic network.
Credit or Source: Office of Biological and Environmental Research of the U.S. Department of Energy Office of Science. science.energy.gov/ber
U.S. DOE. 2010. DOE Systems Biology Knowledgebase Implementation Plan. U.S. Department of Energy Office of Science (p. 15) ( website)