For approaches like the ones we have presented to be more widely adopted, several aspects must be improved. First, it is essential to establish richer metadata collection mechanisms at the public mass spectrometry repository level. The ReDU framework represents a fundamental advancement in this sense to constructing a KG should be further standardized. This standardization will require strengthening the current data processing workflow through sounder data validation processes and the development of simplified user interfaces to facilitate data deposition. We would like to underline that in the current work, we have employed a series of tools and strategies commonly used in our labs for the peak-picking (i.e., MzMine) and metabolite annotation stage (i.e., Sirius, taxonomically informed metabolite annotation using the ISDB-LOTUS). These tools are, however, not the only ones available and the ENPKG workflow should be adapted in the future to handle better the output of other peak-picking (e.g., XCMS or asari), metabolite annotation strategies (e.g., MSDial) or chemical taxonomies (e.g. ChemOnt from ClassyFire) .