1. A method for analyzing metabolomics data using a storage medium for storing data and one or a plurality of computer processors for processing data and making calculations, comprising: a. retrieving chemical structures of said metabolites; b. converting said chemical structures of said metabolites into structure data of said metabolites including one or a plurality of structure variables; c. summarizing said structure variables into one or a plurality of summary structure variables; d. analyzing the relative or absolute concentration levels of said metabolites with or without other input data to derive one or a plurality of original test statistics for said metabolites; and e. integrating said structure variables or said summary structure variables with said original test statistics of said metabolites to derive new test statistics for said metabolites, whereby said structure data is incorporated to improve the evaluation of said metabolites in said metabolomics data.