None of the 240 articles examined, or their associated SI files, included a unique, citable, and persistent identifier for any compound, even though SMILES, InChIs and InChIKeys are widely supported in software handling chemical information such as databases, inventories, laboratory information management systems (LIMS) and electronic lab noteboooks (ELNs). Systematic naming of organic compounds using International Union of Pure and Applied Chemistry (IUPAC) nomenclature was widely used. Although syntax analysis could be considered an option for parsing these names, this would rely on their provision in a machine-readable text format and compound naming was provided in the PDF format of the supporting files for all manuscripts. The lack of structure identifiers highlights the culture change that is required to reverse the loss of machine-readable compound identifiers when data are prepared for publication.