Nucleic Acids Research · 2011 · 110 citations · 17 references
Life SciencesBiochemistryBioinformaticsMetabolismMicrobial MetabolismPathway AnalysisBiotransformation PathwaysMetabolic Pathway AnalysisPathway DatabasesPathway EngineeringPathway VisualizationBiotransformationBiotransformation ModelingDirected Acyclic Graph VisualizationKnowledge Base ArchitectureMetabolic Pathway DatabasesMetabolic Pathway ModelingMetabolic Route PredictionPathway Knowledge Bases
The University of Minnesota Pathway Prediction System (UM-PPS, http://umbbd.msi.umn.edu/predict/) is a rule-based system that predicts microbial catabolism of organic compounds. Currently, its knowledge base contains 250 biotransformation rules and five types of metabolic logic entities. The original UM-PPS predicted up to two prediction levels at a time. Users had to choose a predicted product to continue the prediction. This approach provided a limited view of prediction results and heavily relied on manual intervention. The new UM-PPS produces a multi-level prediction within an acceptable time frame, and allows users to view prediction alternatives much more easily as a directed acyclic graph.
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