Mastering Ontology Engineering with Protégé and the Executable Ontology Architecture (EKA)

A New Resource for Learning Ontology Engineering with Protégé and the Pizza Tutorial

A while ago, Xiaoqi “Yasen” Zhao contacted me about an eBook he was developing based on the Pizza ontology tutorial and Protégé. I reviewed an early version and thought it was a great addition to the materials to help developers understand and utilize semantic web technology. We had some very interesting discussions about knowledge graphs, property graphs and many other issues.

The project has grown considerably since then. What began as an extension of the Pizza tutorial has become a multi-volume series called *Mastering Ontology Engineering with Protégé and Pizza.owl*. It is available on GitHub at https://github.com/yasenstar/protege_pizza

It starts with the fundamentals—classes, properties, restrictions, reasoning, and the RDF representation underlying an OWL ontology—and then expands into knowledge graphs, semantic governance, and Yasen's concept of Executable Knowledge Architecture.

One aspect of the project that I particularly like is its emphasis on learning by doing. Ontology engineering is difficult to learn just by reading definitions of terms such as class, axiom, domain, range, and Open World Assumption (OWA). The Pizza ontology has been useful for so long because it gives people a domain that is immediately understandable, allowing them to concentrate on the modeling concepts rather than first becoming experts in some complicated application domain. This also addresses one of the most common problems I see when people try to develop ontologies. Some people feel that drawing boxes and arrows on a white board or a diagramming tool is the same as defining an ontology. It isn't. I believe the power of OWL is that the foundational concepts from set theory and logic are intuitive to most people and with a bit of effort it is easy to understand how to utilize those concepts to defne a coherent model. However, it does take some effort and without that effort boxes and arrows are just boxes and arrows, they aren't models.

Yasen has built on that approach to create a model he developed called the Executable Knowledge Architecture (EKA). EKA is a practical framework for transforming human knowledge into machine-readable, machine-reasonable, and ultimately machine-executable intelligence.

The framework is represented as: EKA = (K, R, Θ, Φ, Γ)

K = Knowledge

R = Reasoning & Rules

Θ = Triggers

Φ = Actions / Execution

Γ = Governance

EKA provides an architectural bridge between:

• Ontology Engineering

• Knowledge Graphs

• Semantic Governance

• AI Systems

• Agent Architectures

• Executable Intelligence

EKA is similar to Domain Driven Design (Evans, 2003) which is a design approach specific to Microservices (Fowler & Lewis, 2014) and Data Products (Dehghani, 2022) (Dehghani, 2020) (Strengholt, 2023). EKA is a design approach for Semantic Knowledge Graphs and AI (LLM, Agentic AI) systems.

The eBook has detailed step-by-step ontology snapshots, extensive written material, and accompanying video tutorials. The GitHub repository also makes much of the source material available openly, so readers can examine the models and experiment with them directly. For people who have used the Pizza tutorial and want a hands-on resource that continues beyond the introductory material into broader architectural questions, I think Yasen's project is quite valuable. It's one more strong contribution to the long history of open source code and training materials started by people such as Matthew Horridge and Holger Knublauch who created the original Pizza tutorial.

References

Dehghani, Z., 2020. Data Mesh Principles and Logical Architecture. [Online] Available at: https://martinfowler.com/articles/data-mesh-principles.html[Accessed 16 2 2026].

Dehghani, Z., 2022. Data Mesh. Sebastopol, California, USA: O'Reilly.

Evans, E., 2003. Domain-Driven Design: Tackling Complexity in the Heart of Software. San Francisco, CA, USA: Addison-Wesley.

Fowler, M. & Lewis, J., 2014. Microservices: A Definition of This New Architectureal Term. [Online] Available at: https://martinfowler.com/articles/microservices.html[Accessed 16 2 2026].

Strengholt, P., 2023. Data Management at Scale: Modern Data Architecture with Data Mesh and Data Fabric. Sevastapol(CA): O'Reilly Media.