The transformation reaction information used in this study was the Metabolism and Metabolites section of PubChem with HSDB as the data source. This source was selected since it was the largest data source in the Metabolism and Metabolites sections and also has high reliability, as the information was manually curated over 40 years by a scientific review panel. The text excerpts are text-mined by PubChem using LeadMine and an internal synonym dictionary to extract all chemical names and link them to their PubChem compound identifiers (CIDs). The HSDB excerpts with accompanying markup and CIDs are available as a JavaScript Object Notation (JSON) file. This JSON file was processed in R to extract the chemical names together with the CID and other information. Other chemical identifiers, such as Simplified Molecular-Input Line-Entry System (SMILES), were added. The resulting file was exported as a .csv together with the original text and source descriptions. The code to create this file is available on GitLab .