The current models and tools are not directly suited to solve the issues raised above. Existing tools such as the MetaboNetworks toolbox , or biochem4j do combine metabolic pathway knowledge in larger networks or graphs. These approaches help to overcome the data sparseness in metabolomics pathway models and allow users to focus only on the paths between the metabolites of interest. Issues with these tools are the requirement to use proprietary software, lack of methods for reproducibility of obtained results, missing provenance of pathway models and reaction mechanisms, using only one database to retrieve metabolic reactions from, ignoring the directionality of reactions, unsuited for integration of other omics data, or being discontinued or not maintained.