1. Stanford Medical Informatics
The Protégé System Collaborative Expedition Workshop NSF, October 19, 2004
Holger Knublauch
Stanford Medical Informatics

2. Ontologies Formal models of a domain Shared (internet, between groups)
Common modeling constructs
Classes
Properties
Logic / Meaning
Individuals
Can be used to define domain-
specific modeling languages

3. Web Ontology Language (OWL)
W3C Standard
Based on RDF(S)
Ontologies are shared on the web
Explicit support for linking ontologies
Built-in reasoning support based on Description Logics
Rule-based extension SWRL

4. Protégé Open-Source ontology editing tool
Developed at Stanford Medical Informatics with help from community
Evolves since the 1980s
In routine use around the world
Traditional domain: Biomedicine
General-purpose tool and platform

6. Protégé and OWL Core System (since 1990s) OWL Plugin (since 2003)
Generic metamodel (OKBC)
Configurable
Open platform with “Plugins”
OWL Plugin (since 2003)
OWL Full metamodel
Optimized user interface
Built-in reasoning access
Several thousand users

7. OWL Plugin Background OWL Plugin started in 2003
Major sources of Funding: NLM, NCI
Goals (Achievements):
Comprehensive support for OWL DL & Full
Editing and visualizing OWL/RDF ontologies
Integration of DL reasoners (classification)
Open platform for Semantic Web community

8. Ontology Development
Person
Organization
Event
TerroristEvent

9. OWL Plugin Scope RDF (Schema) OWL DL OWL Full Semantic Web
Including Metaclasses
Richer use of annotation properties
Semantic Web
Multiple namespaces
Multiple files with owl:imports

10. Classes / Logic View

11. Classes / Properties View

12. Editing Properties

13. Editing Individuals

14. Configuring Forms

15. Classifying Individuals

16. An Open-Source Platform
Available for free
Transparent behavior / semantics
Flexible “Plugin” mechanism
New user interface components
New file formats
New reasoners
... (your application here)
80+ plugins publicly available

17. Visualization / OWLViz (1)

18. Visualization / OWLViz (2)

19. Visualization / TGViz

20. Visualization / ezOWL

21. Visualization / Jambalaya (1)

22. Visualization / Jambalaya (2)

23. Input - Output Formats Default: CLIPS Text files
Available backend plugins
OWL / RDF
OWL Databases
RDF
XML / XML Schema
UML (OWL-UML bridge work in progress)

24. Database Export / OntoBase

25. Database Export / RDF Stores
Protege to Jena Database format
Protege to Joseki RDF Server
Sesame RDF Database (RDF Plugin)

26. Other Plugins / OWL Wizard

27. Other Plugins / Prompt

28. Multi-User Mode Client-Server setup
Central database
Clients with user interface
Changes are synchronized immediately
Scalable

29. Protégé Web Browser

30. Experience Thousands of users (20,000+ registrations)
Very active community
OWL Plugin getting increasingly stable
Has been used to edit ontologies with tens of thousands of concepts
Foundational Model of Anatomy
UMLS import/reference tab
Pilot at National Cancer Institute

31. Summary An open-source ontology tool platform
De-facto standard OWL editor
Comprehensive OWL / RDF support
Configurable visual editors
Built-in reasoning capabilities
Many plugins for visualization etc.
We are happy to collaborate (on extensions, applications, etc)