The EMP Ontology (EMPO) is built upon existing ontologies and is used to assign samples to habitats in a hierarchical framework that captures major axes of microbial community diversity. Version 2 (Shaffer et al., 2022) is the current EMPO, superseding Version 1 of EMPO (Thompson et al., 2017). Version 2 adds an additional level of distinction and is comprised of five fields: empo_0 (level 0: root), empo_1 (level 1: Free-living, Host-associated, Control), empo_2 (level 2: Free-living (non-saline), Free-living (saline), Host-associated (non-saline), Host-associated (saline)), empo_3 (level 3: host taxon or phase), and empo_4 (microbial environment). A text file describing the ontology can be downloaded here.