Furthermore, pathways only describe a (sub)section of relevant biochemical interactions biased toward well-known reactions which might miss specific metabolites originating from plants or the microbiome . The choice of database(s) used for annotation impacts the results found with regard to enrichment analysis and predictive modeling (for all -omics data types) . Different methods exist to execute pathway analysis for metabolomics, which can be classified as over-representation analysis , functional class scoring , pathway topology analysis , and network enrichment analysis . This last method surpasses the boundaries of a pathway model, by comparing all relationships present in a chemical reaction network for overlap between metabolites of interest and metabolites present in the network. Merging information from different resources into one larger network aids in understanding metabolic changes which affect multiple processes. These networks are also known as graphs, which entail the mathematical representation of a network.