The Foundational Model of Anatomy ontology is implemented in Protégé, which is a frame-based system developed by members of Stanford Center for Biomedical Informatics Research. Protégé is an authoring and editing environment for knowledge bases (ontologies). The authors of the FMA use Protégé to enter and modify data in a MySQL database with a specific relational database schema. Although Protégé can also serve for viewing the FMA, we provide a less complex and faster web browser, the Foundational Model Explorer (FME) for accessing the FMA.

Protégé represents information about an anatomical class in an object called frame. In the FME, for each class selected in the left pane of the display, the corresponding frame will be displayed in the right pane. Frames that represent an anatomical class include a set of slots, and these slots are filled with one or more values. For example, because physical state is an attribute of Heart, the value for the physical state slot in the frame Heart is solid, whereas for the same slot in the frame Blood, is liquid. The set of slots that constitute the frame of a particular class fully describe or characterize that class.

A key feature of Protégé is the discipline and system it imposes on the configuration of these frames. The frames constitute the mechanism for inheritance, and hence, the creation of the class hierarchy; i.e., the taxonomy. By extension, the frames also serve to support inference and can therefore be used to enforce the economy and consistency of the knowledge entered.