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Referenced Taxonomies are ontology hierarchies that hold non-resource classes used as values to describe resource attributes. In the data, the IRIs of referenced taxonomy classes are used directly as the objects of RDF triples about a resource instance. Instances of referenced taxonomy classes are not created in the eagle-i data.

A hierarchy becomes a referenced taxonomy when its root is annotated as belonging to the referenced taxonomy class group, and a referenced taxonomy IRI is present. The root of a referenced taxonomy hierarchy can be defined as the range of a property used to collect data about a resource type that is the domain of that property. This axiom in the ontology tells the application to present a field for the resource based on the property, and shows the reference taxonomy rooted at the class indicated as the range in a pick list for entering values of this property in the SWEET UI. 

Referenced taxonomies can live in the ero.owl core, or in the extended ontologies. For example, the 'technique' referenced taxonomy lives in ero.owl and is used to record methods related to a given resource, while the 'material anatomical entity' referenced  taxonomy that lives in the uberon.owl extended ontology file is used to record the origin of things like 'cell lines' or 'biological specimens'. "Core Reference Taxonomies" are those that live in the core ero.owl file (e.g. 'technique', 'organization', 'data format specification', 'measurement scale'). "Extended Reference Taxonomies" are those that live in an extended ontology file  (Uberon, GO, MP, Pato, DOID), e.g. 'life cycle stage', 'material anatomical entity', 'disease'.

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