Pathway data was obtained from the Resource Description Framework (RDF) format of WikiPathways with the semantic query language SPARQL. The RDF data is generated daily; for this study, data from November 2020 was used (archived at 10.5281/zenodo.5776229). For the metabolic reactions, we defined key:value pairs between the source and target metabolites for each reaction using identifiers from Wikidata. Other relevant properties retrieved were enzyme names and identifiers related to the reaction, literature references related to the pathway or the reaction, and pathway and disease ontologies. These reactions and their additional properties were queried with three subscripts to avoid query timeouts (which can happen with large amounts of data) and have been adapted to run either on the SPARQL endpoint of WikiPathways (containing the pathway models which have undergone peer review by the WikiPathways curation team from the LIPID MAPS, Reactome, and WikiPathways pathway model collection) or on Blazegraph (which can also contain models without peer review).