1. Introduction to Protégé AmphibiaTree 2006 Workshop Sunday 8:45–9:15 J. Leopold & A. Maglia

2. Ontology Language Ontology must be expressed in a formal language so that expressions can be interpreted and processed by a computer An ontology language needs to allow specification of terms, relationships, properties

3. OBO Open Biomedical Ontologies Flat-file structure with “identifiers” specific to biomedical terminology (especially genes and proteins)

4. OBO File Format

5. View/Edit in OBO-Edit

6. Critique of OBO Good: –Made specifically for biological applications –Restricted set of functions and relationships, prevents logical inconsistencies Bad: –Domain-specific, not a perfect fit for anatomy –Too restrictive, hard to represent diversity

7. OWL Ontology Web Language Semantic markup language (like XML)

8. OWL File Format

9. View/Edit in Protégé

10. Critique of OWL Good: –Generalized language for all ontologies –Easy to represent anatomy –Easy to represent diversity Bad: –Very powerful, easy to create logical inconsistencies