First, all metabolic reaction participants were uploaded to Neo4j, converting source and target metabolites (key:value pairs) to nodes in the graph model (labeled ":Metabolites"); the metabolites were annotated solely with a Wikidata identifier . Since a product of one reaction can be the substrate of a new reaction, nodes were merged with each other in the graph database for entries with identical Wikidata identifiers. Second, another set of nodes was created for all reactions (one per key:value pair) by their unique internal identifier (labeled ":Reaction"). Directed edges were used to connect the source metabolite node to the corresponding reaction node, and from the reaction node to the target metabolite (labeled ":AllInteractions"). All metadata (references, ontologies, provenance) were loaded onto the edges. Third, the protein nodes and their connection to the reaction nodes are created. This process was repeated for the other three sources of reaction data: LIPID MAPS, Reactome, and the WikiPathways curated collection. Additional edges were added between the substrate:product combinations belonging to the LIPID MAPS, Reactome, and the WikiPathways collection (since only one relationship type per edge could be defined). Last, a label for the reactions combining these three databases was created, ":AnalysisInteractions" (disregarding unapproved models).