The United States Patent Office (USPTO) reaction dataset and a 151,306 subset of the Synthetically Accessible Virtual Inventory (SAVI) containing 1.75B reactions was used to generate the reaction knowledge graph. Reactions were extracted from the data sources in the format of extended RXSMILES strings. This gave rise to 2,090,546 reactions and 1,408,610 substances . However, due to a noncanonical ordering of substances and additionally some individual substance SMILES also have multiple representations and are not canonicalized . Therefore, we deduplicated the knowledge graph according to the procedure described in section "Reaction Deduplication", in SI. This resulted in a total number of 1,248,813 unique reactions (146,250 unique SAVI reactions) and 1,408,610 unique substances, which constitute the deduplicated knowledge graph. RXSMILES includes the reagents in between the reactants and products. The information of substance-compound associations ("Fragment grouping" ) were determined using the "f:a.b,x.y" (zero-indexed) terms of the extensions. The unique keys of reaction and substance nodes are reaction identifier (rxid) and InChI-Key , respectively.