1. BioHealth Informatics Group Advanced OWL Tutorial 2005 Design Patterns Robert Stevens

2. Advanced OWL Tutorial Design Patterns in ontology making ►Design Pattern: common solution for a frequent modelling problem. ►Better ontologies: ►More consistent style. ►Better structured (easily extensible). ►Knowledge domain better captured. ►Overcoming language limitations. ►Neater. ►In this tutorial: value partitions, n-ary relationships, lists, normalisation, exceptions. ►Protégé wizards: value partition, list. ►To learn more: Semantic Web Best Practices and Deployment Working Group: http://www.w3.org/2001/sw/BestPractices/

3. BioHealth Informatics Group Advanced OWL Tutorial 2005 Value Partitions

4. Advanced OWL Tutorial Value Partitions ►Used to model descriptive features of things. ►Makes certain descriptive properrties explicit. ►The features are constrained to have certain values (e.g. Size: small, medium, large). ►OWL elements: ►Feature (Size): property (has_size) or class (Size). ►Values: classes or individuals. ►The values it can have are constrained by the range of the property. ►Using classes allows to make subpartitions (e.g. very large, moderately large). ►http://www.w3.org/TR/swbp-specified-values/

5. Advanced OWL Tutorial Value Partitions ►The feature to be partitioned is covered: defined by the union of its subclasses, the subclasses being disjoint: Size ≡ Small ∪ Medium ∪ Large Size SmallMedium Large IsA Human has_size

6. Advanced OWL Tutorial How to model amino acids? Amino acid hasPolarity Polar Polarity Non-polar isA Polarity ≡ Polar ∪ Non-polar

7. Advanced OWL Tutorial How to model amino acids? Amino acid hasWaterProperty HydrophobicHydrophilic isA waterProperty waterProperty ≡ Hydrophilic ∪ Hydrophobic

8. BioHealth Informatics Group Advanced OWL Tutorial 2005 Bio-ontologies Tutorial Day 2 30 th November 2005 University of Manchester

9. Advanced OWL Tutorial N-ary relationships ►Properties are binary (Individual - Individual). ►Impossible to express a property that links more than one individual at the same time. ►Impossible to express different features of the same property, e.g: Christine has breast tumor with high probability. ►Binary relation: Christine - breast tumor. ►Feature of the relation has: high probability. ►http://www.w3.org/TR/swbp-n-aryRelations/

10. Advanced OWL Tutorial N-ary relationships ►Solution: make a new class that represents the relation ►http://www.w3.org/TR/swbp-n-aryRelations/ has_diagnosis diagnosis_value diagnosis_probability Christine diagnosis_relation Tumor High

11. Advanced OWL Tutorial N-ary relationships ►In our case: Chromosome TransportInMitosis has_cytoskeletal_transport is_transported_from NucleusAxes is_transported_by is_transported_to Spindle Centrosome