The structures.sdffile containing all structures in the HMDB was downloaded from http: //www.hmdb.ca/downloads on 10 September 2017. Queries for alkynes and internal alkynes were performed with the Python package rdkit using SMARTS queries [#6]C#C[#6]for internal alkynes and C#Cfor all alkynes. A Jupyter notebook 30 performing these queries is provided in the Supporting Information. The source (e.g. plant, fungal, animal, or drug) of alkynes was determined for each parsed structure by manual search. This information is provided as an excel file in the Supporting Information. The structures were clustered using rdkit's default fingerprinting algorithm.