The Neo4j data model is constructed in the following format:

Class 3 consist out of 7 individual steps, marked as A-G. Please execute these classes in this order.

• FillNeo4jDb_3A_All.java : Removes existing data, and adds data from Wikipathways (curated and uncurated), Reactome and LipidMaps pathways (integrated here).

• FillNeo4jDb_” 3B / 3C / 3D “ updates the interaction data with the WikiPathways (3B), Reactome (3C) and Lipid Maps (3D) data.

• The combined Data Analysis Collection is loaded through scripts 3B2 / 3C2 / 3D2.

• FillNeo4jDb_3E_Side Relabels the interactions between side metabolites, and removes interactions from main to side metabolites (and vice versa).

• FillNeo4jDb_3F_CHEBIHMDB adds the identifier links from ChEBi and HMDB to Wikidata (the main identifier of the network).

• FillNeo4jDb_3G_DatabaseInfo provided some queries on the final data in Neo4j, to show the Node and interaction size.