The program itself is frame-based and is made up of the following components:

1. Knowledge base- Consists of frames that represent classes, slots, facets, instances and constraints.
2. Classes are concepts in the domain of discourse. They are abstract conceptual entities in the domain (e.g., the concept of an ACE Inhibitor), or named collections of instances (e.g., sets of Guidelines).
3. Slots- Binary-relationships that describe properties or attributes of classes (e.g., the eligibility criteria in the Guideline class).
4. Facets- Describe properties of slots (e.g., the data type of the eligibility criteria slot).
5. Instances of classes have specific slot values (e.g., in EON, hypertension_guideline is an instance of the Guideline class).
6. Constraints specify additional relationships among instances

A primary feature of Protégé-2000 is its ability to automatically generate a GUI form for each class based on the class definition. Domain experts can use these forms to enter instances of classes. Besides the forms, complex special-purpose user-interface widgets can also be added to the system as plug-ins to simplify knowledge acquisition (e.g., a diagram widget to encode clinical algorithms). There is also a notion of a Project, which contains configuration information and form layout information. Configuration information includes descriptions of all the user-interface widgets that have been added to the project and a list of other projects that have been included by the current project. .