Pathway-rules-based phenotype predictions
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This approach uses explicit logic-based ‘pathway rules’ to assign binary phenotypes. These rules combine (1) expert curators’ knowledge regarding the gene composition of various metabolic pathway variants contained in the mcSEED database with (2) a decision tree method to identify patterns of gene representation in reference genomes corresponding to an intact functional pathway variant (and a respective binary phenotype value denoted as ‘1’). A total of 106 functional pathway-specific decision trees was generated (Rpart