Data and Text Mining Data-Driven Extraction of Relative Reasoning Rules to Limit Combinatorial Explosion in Biodegradation Pathway Prediction

Motivation: The University of Minnesota Pathway Prediction System (UM-PPS) is a rule-based expert system to predict plausible biodegradation pathways for organic compounds. However, iterative application of these rules to generate biodegradation pathways leads to combinatorial explosion. We use data from known biotransformation pathways to rationally determine biotransformation priorities (relative reasoning rules) to limit this explosion. Results: 112 relative reasoning rules were identified and implemented. In one prediction step, i.e., per one generation predicted, the use of relative reasoning decreases predicted biotransformations by over 25 % for 50 compounds used to generate the rules and by about 15 % for an external validation set of 47 xenobiotics, including pesticides, biocides, and pharma