The results were concatenated into one file for each pathway collection, to avoid redundancy within the reaction data. All unique key:value pairs received a unique internal identifier, to create a bipartite graph connecting the source and target metabolite through a reaction node. 4.14.0), 64-bit, Linux (Ubuntu 18.04), see github.com/cyneo4j/DSMN. Documentation on setting up the code in Eclipse, downloading and starting Neo4j, and loading data into Neo4j are available in the documentation of this repository, as well as the extended documentation website: cyneo4j.github.io/DSMN. The nodes in the network were built from Wikidata, with ChEBI and HMDB added to the final network as "Mapping" Nodes, to allow easy integration with other identifier types commonly used in the metabolomics community.