1. Building Ontologies with Protégé-2000
Mark A. Musen, M.D., Ph.D.
Stanford Medical Informatics
Stanford University

2. Conceptual building blocks for building intelligent systems
Domain ontologies
Characterization of concepts and relationships in an application area, providing a domain of discourse
Problem-solving methods
Abstract algorithms for achieving solutions to stereotypical tasks (e.g., constraint satisfaction, classification, planning, simulation)

4. What Protégé-2000 offers
Ontology editor for defining classes of concepts (e.g., esophagus)
Automated generation of tools for building knowledge bases that define instances of concepts (e.g., Cornelius’ esophagus)
Knowledge-visualization systems
Lots of user-contributed “plug ins”
Ability to archive ontologies and knowledge bases in a variety of formats

5. Digital Anatomist Foundational Model of Anatomy
Material Physical
Anatomical Entity
Anatomical
Spatial Entity
Anatomical Structure
Body Substance
Body
Part
Organ
System
Organism
Cell
Subdivision
Component
Tissue

6. Is-a Classes of anatomical structures Parts of the heart Part-of
Spatial Entity
Anatomical
Structure
Organ
Organ
Part
Body
Space
Anatomical
Feature
Viscus
Organ
Subdivision
Organ
Component
Organ
Cavity
Internal
Feature
Hollow
Viscus
Cardiac
Chamber
Heart
Parts of the heart
Organ Cavity
Subdivision
Cavity
of Heart
Right
Atrium
Wall
of Heart
Cavity of
Right Atrium
Fossa
Ovalis
Wall of
Right Atrium
Myocardium
Is-a
Part-of
Sinus
Venarum
Myocardium
of Right Atrium SA
Node

7. The Ontology in Protégé-2000

8. Visualizing relationships with JAMBALAYA
Hierarchy (nested graph) based on is-a and instance-of relationships. The user can zoom in and explore any of the subclasses in more detail (see next slide).

10. No hierarchical relationships, just a few slot types visible and a spring layout done on those arc types
To help the user explore structures (see filter panel for arc types not filtered).
Classes are blue, instances are white.

11. Protégé Uses Open Knowledge-Base Connectivity (OKBC) model
Classes define concepts in the domain
Slots define attributes of classes
Facets put constraints on values of classes (e.g., type, cardinality, defaults)
Protégé may exchange knowledge with any other OKBC-compatible server (e.g., Ontolingua, LOOM, Ocelot)

12. Additional features of Protégé’s knowledge model
Metaclasses allow developers to define special-purpose facets of base classes that are “instances” of the metaclasses
Protégé axiom language (PAL) allows developers to specify complex semantic constraints using logic

13. Metaclasses allow developers to define new template slots (e. g
Metaclasses allow developers to define new template slots (e.g., as in GO)

14. Evaluation of constraints can point out semantic errors

15. OntoViz tab: Another visualization plug-in that uses AT&T’s GraphViz system

16. PROMPT: A plug in that allows users to compare and merge different versions of ontologies

17. Building intelligent systems with Protégé-2000
Build a domain ontology
Protégé-2000 generates a custom-tailored GUI for acquisition of content knowledge
Elicit content knowledge from application specialists
Map domain ontology to appropriate problem-solving methods for automation of particular tasks

18. Building knowledge bases: The Protégé methodology
Domain ontology
to provide domain
of discourse
Knowledge-acquisition tool
for entry of detailed content

19. In Protégé-2000, ontologies can define an overarching structure for a domain knowledge base

20. Forms allow entry of instances and are generated directly from the ontology

21. Sometimes diagrams are more intuitive than forms are
Developers can use diagrams for entry of complex relationships
Forms and diagrams can be freely mixed based on the requirements of the ontology

22. Protégé-2000 supports special-purpose “plug ins”
Widgets to acquire and display special information
Tabs that provide enhanced functionality
Access to UMLS and WordNet
Access to problem solvers (e.g., JESS, Prolog)
Access to visualization systems
Tabs that support entire knowledge-based applications

24. Current “back ends” for reading and writing knowledge
Relational databases (via JDBC)
CLIPS
OKBC
XML (using DTDs)
XML (using XML Schema)
Resource Description Framework (RDF/S)
DAML+OIL (in progress)

25. Protégé-2000 is
Available under an open-source license and freely downloadable from our Web site
Used by more than 1000 investigators around the world
Supported by Stanford Medical Informatics and by the Protégé-2000 user community

26. The Protégé community keeps growing
9.4 new downloads each day (mean)
4133 registered users as of July 1, 2002
877 people subscribe to our “protege-discussion” mailing list