The University of Minnesota Pathway Prediction System: multi-level prediction and visualization

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.