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. Four fields are used: empo_0 (level 0: root), empo_1 (level 1: Free-living, Host-associated, Control, or Unknown), empo_2 (level 2: Saline, Non-saline, Animal, Plant, or Fungus), and empo_3 (level 3: most specific habitat name).

The network diagram below shows the relationships between EMPO classes, which are linked to ENVO and other ontology classes. A VUE file and text file describing the ontology can be downloaded here.

The table below shows examples of how different sample types are classified under the EMPO system.

empo_1 empo_2 empo_3 Examples
Free-living Non-saline Water (non-saline) fresh water from lake, pond, river (<5 psu)
Free-living Non-saline Sediment (non-saline) sediment from lake, pond, river (<5 psu)
Free-living Non-saline Soil (non-saline) soil from forest, grassland, tundra, desert, etc.
Free-living Non-saline Surface (non-saline) biofilm from wet (<5 psu) or dry surface, wood, dust, microbial mat
Free-living Non-saline Subsurface (non-saline) deep or subsurface environment
Free-living Non-saline Aerosol (non-saline) aerosolized dust or liquid
Free-living Saline Water (saline) salt water from ocean, sea, estuary, mangrove, coral reef (>5 psu)
Free-living Saline Sediment (saline) sediment from ocean, sea, estuary, mangrove, beach (>5 psu)
Free-living Saline Hypersaline (saline) water from hypersaline sample or brine (>50 psu)
Free-living Saline Surface (saline) biofilm from wet or underwater surface or microbial mat (>5 psu)
Free-living Saline Aerosol (saline) seaspray or other aerosolized saline material (>5 psu)
Host-associated Animal Animal distal gut feces, stool
Host-associated Animal Animal proximal gut gut intestine, gizzard, crop, lumen, mucosa
Host-associated Animal Animal secretion saliva, breast milk, vaginal secretion
Host-associated Animal Animal surface skin, sebum, mucus, slime
Host-associated Animal Animal corpus tissue of sponge, coral, gill, siphon, carcass, etc. or whole small animal
Host-associated Plant Plant secretion pollen, sap
Host-associated Plant Plant surface leaf or kelp surface biofilm
Host-associated Plant Plant rhizosphere plant root system, may include some soil
Host-associated Plant Plant corpus tissue of leaf, stem, fruit, algae
Host-associated Fungus Fungus corpus tissue of mushroom or other fungi
Host-associated Fungus Fungus surface biofilm of mushroom
Control Negative Sterile water blank sterile water blank used as negative control for extraction, PCR, and sequencing
Control Positive Single strain known single strain used as positive control
Control Positive Mock community known mixed community used as positive control
Unknown Contradictory Unknown (contradictory) unknown sample type because other metadata is contradictory
Unknown Missing Unknown (missing) unknown sample type because metadata is unavailable