The NMDC Ontology (NMDCO) is used by the National Microbiome Data Collaborative (NMDC, https://microbiomedata.org) to annotate multi-omic microbiome metadata. It merges a number of ontologies relevant to the NMDC (such as the plant and environment ontologies) into a single ontology. The ontology can be download from Github at https://github.com/microbiomedata/nmdc-ontology.