The original data formats are all converted to the native PathVisio pathway model language (GPML), which is subsequently converted to a semantic model (RDF). Three different queries are executed to retrieve the metabolic reaction data from the RDF data.

The data cleanup consisted out of merging metabolic reactions based on the combination of unique Wikidata identifiers for the source and target metabolites, for each reaction. Alos, a unique reaction ID was added for each unique source-target combination.