1. Abstraction and Visualization to Support Access to NPO’s Structure and Content Michael Halper, Vladimir Ventura, Yehoshua Perl SABOC New Jersey Institute of Technology Newark, NJ 07102

2. Overview Abstraction Networks (“AbNs”) for Ontologies Two example AbNs: – Area taxonomy – Partial-area taxonomy BLUOWL: taxonomy-based software tool Application to the NPO Conclusions 2

3. Ontology Excerpt 3 IS-A wave speed Parameter length unit unit of measurement wave parameter wavelength wave amplitude speed of sound wave has_unit_of_measure unit of velocity wavelength of sound frequency of sound wave frequency unit wave frequency amplitude of sound wave

4. Abstraction Networks (“AbNs”) An abstraction network (“AbN”) is derived from an ontology’s content and structure and provides a compact (summarization) view AbNs group “similar” concepts together and represent them using a single node Nodes are organized into a hierarchy 4

5. Area and Partial-Area Taxonomies Area taxonomy summarizes structurally similar concepts Partial-area taxonomy refines the area taxonomy into hierarchically related groups of concepts Will review derivation using examples from NPO 5

6. Area Taxonomy Derivation An area is a set of concepts that share the same relationship structure (structurally similar) 6 Areas

7. Partial-Area Taxonomy Derivation Root: A concept with no parents in its area Partial-area: A root + all its descendants in the area (structurally similar and clustered similarly) 7 Root

8. Overlapping Concepts Partial-areas are not necessarily disjoint A concept residing in two or more partial- areas is called an overlapping concept 8 overlapping

9. Overlapping Metrics 9 LevelArea Name# overlapping 3has_function, part_of, participates_in1 3has_function, has_quality, participates_in18 4has_function, has_part, has_quality, participates_in6 6has_component_part, has_function, has_part, has_quality, has_role, participates_in3 6 has_output_participant, has_participant, negatively_regulates, positively_regulates, realizes, regulates1

10. Applications of Taxonomies QA (inconsistency detection and improved modeling) Summarization Navigation Proposed: – Support of ontology development – Support of various biomedical applications where similar concepts need to be identified 10

11. Taxonomy-Based Software Tool BLUOWL Automatic generation of a variety of taxonomy views Concept-level browsing based on those views Aids for QA guidelines 11

12. NPO Taxonomies Based on the inferred view of the NPO Relationships (object properties) defined in terms of domains And/or relationships defined as restrictions on concepts 12

13. Conclusions Taxonomies are useful tools for getting a high-level view of NPO while ignoring minutiae BLUOWL automatically generates the taxonomies and permits customized browsing BLUOWL was demonstrated on the NPO Plan to work next on ChEBI 13