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

Nucleic Acids Res. 2011 Jul;39(Web Server issue):W406-11. doi: 10.1093/nar/gkr200. Epub 2011 Apr 12.


The University of Minnesota Pathway Prediction System (UM-PPS, 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.

Publication types

  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Biotransformation*
  • Computer Graphics
  • Databases, Factual*
  • Environmental Microbiology
  • Knowledge Bases
  • Organic Chemicals / metabolism
  • Software


  • Organic Chemicals