title: Improving infrastructure for pathway prediction.
abstract: The UM-BBD Pathway Prediction System (UM-PPS, http://umbbd.msi.umn.edu/predict/) predicts microbial catabolism of organic compounds. We improved UM-PPS infrastructure to improve pathway prediction results. We added the ability to allow relative reasoning and variable aerobic likelihood. One relative reasoning entry decreased choices 75% with no loss of sensitivity. Variable aerobic likelihood gives more accurate likelihood for rules triggered by substrates with certain chemical structures. Predictions are improved.
authors.affiliation: Health Informatics Division, Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis, MN, 55455, USA.
authors.forename: Junfeng
authors.initials: J
authors.lastname: Gao
authors.forename: Lynda B M
authors.initials: LB
authors.lastname: Ellis
mesh_terms: D000465:Algorithms; D001420:Bacteria, Aerobic / Q000378:metabolism*; D003198:Computer Simulation; D008660:Metabolism; D008910:Minnesota; D008954:Models, Biological; D009930:Organic Chemicals / Q000378:metabolism*; D015398:Signal Transduction / Q000502:physiology*
chemical_list: D009930:Organic Chemicals