Protégé Short Course
Hands-On Training<br>Protégé Short Course<br>June 23–25, 2026<br>Stanford, California, USA
This two-and-a-half day Protégé Short Course provides a comprehensive introduction to ontology development<br>and the OWL 2 Web Ontology Language using the Protégé toolset. Most of the course is hands-on.<br>Participants will learn how to navigate the latest version of the Protégé and WebProtégé toolsets,<br>which support the full OWL 2 standard.
The course is taught by members of the Protégé team. Enrollment is limited to ensure optimal<br>learning experiences.
Target audience members include everyone who wishes to develop or enhance their skills for building<br>OWL ontologies using Protégé. The course can benefit both beginners with no prior experience and<br>intermediate users of Protégé Desktop or WebProtégé.
Topics<br>✓ Steps in the ontology development process<br>✓ Semantic Web technologies, e.g., OWL and RDF<br>✓ OWL 2 language, reasoning, and querying<br>✓ Collaborative ontology development<br>✓ Import from spreadsheets and other data sources
Detailed topic list<br>Introduction to Ontologies and Ontology Engineering<br>Knowledge Representation on the Web: Motivation and examples<br>Definitions of ontology<br>Rationale for ontologies: why build ontologies, example applications and usage<br>Basic components of an ontology<br>Introduction to course running example<br>Knowledge Engineering Techniques: defining domain and scope, competency questions, card sorting, identifying domain terms<br>Ontology modeling approaches: generic and application ontologies, ontology design patterns<br>Testing ontologies: competency questions as tests, validation strategies
Introduction to Protégé<br>The Protégé user interface: tabs, views, lists and sections
Introduction to OWL<br>Where OWL fits into the Knowledge Representation landscape<br>Basic OWL terminology: Classes, Object Properties, Data Properties, Annotation Properties, Individuals, Datatypes, Literals, Complex Class Expressions, Axioms<br>Entailment, Inference and Automated Reasoning<br>OWL Profiles (OWL2EL, OWL2QL and OWL2RL)<br>The Resource Description Framework (RDF)<br>OWL Syntaxes and the relationship to RDF
Hands on OWL<br>Entities and entity naming strategies<br>Classes: declarations, owl:Thing, owl:Nothing<br>SubClassOf axioms, class hierarchies and terminology<br>Entailment, reasoning, and automated computation of class hierarchies<br>Annotation assertions for metadata: literals, language tags, referencing external information, working with SKOS and Schema.org<br>Representing relationships at the class level: object properties, SomeValuesFrom (existential restrictions), property hierarchies, HasValueFrom<br>Transitive property axioms<br>Functional properties<br>Combining complex class expressions: IntersectionOf (And), UnionOf (Or), OneOf (Enumerations)<br>Class definitions: EquivalentClasses axioms, primitive and defined classes<br>Negation in OWL: ComplementOf (Not), disjoint classes axioms<br>Negation of complex class expressions, AllValuesFrom (universal restrictions), and the duality with SomeValuesFrom<br>Representing relationships at the instance level: individuals, PropertyAssertion axioms, property chains, domain and range axioms<br>Data properties and data ranges<br>Understanding the Open World Assumption (OWA)
Who tends to attend
Enrollment is capped to keep the group small enough for meaningful interaction<br>with the instructors and with each other. The mix varies from year to year, but<br>cohorts typically draw an international audience and tend to include:
✓ Biomedical and life-science researchers building or applying ontologies for clinical, disease, phenotype, drug, or data-harmonization work.<br>✓ Knowledge engineers and ontologists designing, maintaining, or integrating ontologies and knowledge graphs.<br>✓ Industry professionals applying ontologies to practical problems — including Silicon Valley tech companies, and across pharma, biotech and healthcare; finance and insurance; software and AI; and government, defense and standards bodies.<br>✓ Graduate students and postdoctoral researchers seeking formal training in ontology development.<br>✓ Librarians, terminologists, and standards staff working on controlled vocabularies and terminology services also join from time to time.
Past cohorts have included participants from universities, research institutes,<br>industry, government agencies, and international organizations such as the<br>World Health Organization (WHO).
The result is a rich and unique experience. Participants learn content, and<br>learn it in a way, that is hard to find anywhere else — the combination of<br>instructors, materials, hands-on modeling work, and the format of the course is<br>not easily replicated through online tutorials, books, or self-study.
Much of that value comes from the mix of people in the room. Working alongside<br>peers from different disciplines and sectors deepens understanding of the<br>material, broadens the range of real-world modeling problems and approaches<br>participants encounter, and helps attendees build professional contacts...