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What is an Ontology?

What is an Ontology?. AmphibiaTree 2006 Workshop Saturday 8:45 – 9:15 A. Maglia. Outline. What is an ontology Elements of an ontology Other ways of representing data Examples. In philosophy…. The study of being or existence

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What is an Ontology?

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  1. What is an Ontology? AmphibiaTree 2006 Workshop Saturday 8:45–9:15 A. Maglia

  2. Outline • What is an ontology • Elements of an ontology • Other ways of representing data • Examples

  3. In philosophy… • The study of being or existence • Describes the basic categories and relationships of being to define entities and types of entities • Study of the conceptions of reality • Nouns are entities or collections of objects or events

  4. In computer science… • A data model that represents a domain, the objects in that domain, and the relations between them • A form of knowledge representation about the world or some part of it

  5. Informally… • A set of definitions of formal vocabulary • Includes an agreement to use a vocabulary in ways that are consistent (but not complete) with respect to the theory specified by the ontology

  6. A working definition… • A formal vocabulary, in the form of a knowledge representation, that describes the basic categories of being by defining entities, types of entities, and the relationships among them

  7. Elements of an Ontology • Instances (Individuals) • Classes • Attributes (properties) • Relationships • Hierarchical structure

  8. Instances • Also called Individuals • The most basic components of an ontology • The actual, concrete objects (e.g., animals, bones, cars, etc.) • An ontology does not require the inclusion of instances, but a main purpose of an ontology is to provide a means of classifying individuals, even if those instances are not explicitly part of the ontology

  9. Examples of Instances • Instance: David Cannatella • an instance of Homo sapiens • Instance: KU103854 • an instance of Dermophis mexicanus • Instance: Jayhawk Room • an instance of a meeting room • Instance: Maglia’s car • An instance of a Toyota Prius

  10. Classes • Also called Concepts • Abstract groups, sets, or collections of objects. • May contain individuals, other classes, or a combination of both

  11. Examples of Classes • Class: Vehicle • Class: Car • Class: Toyota • Class: Hybrid • Class: Prius

  12. Attributes • Also called Properties • Features, characteristics, or parameters that objects can have and share • Objects in the ontology are described by assigning attributes to them

  13. Example of Attributes • Class: Prius • Attribute: Number_of_doors: Value: four • Attribute: Engine: Value: hybrid synergy • Instance: Maglia’s car • Attribute: Name: Value: Maglia’s car • Attribute: Color: Value: Silver • Attribute: Registration_state: Value: Missouri

  14. Relationships • Ways that objects interact with one another • An attribute whose value is another object in the ontology • Most important type is subsumption: is_a

  15. Examples of Relationships • Instance: Maglia’s car • Relationship: is_a: Class: Prius • Relationship: is_same_color_as: Instance: Leopold’s car • Relationship: is_slower_than: Instance: Trueb’s car • Class: Prius • Relationship: is_a: Class: Toyota • Relationship: is_smaller_than: Class: 4-Runner

  16. Hierarchical structure • Inherent in classification system • Defined by relationships among classes • Attributes of superclasses are inherited by subclasses • Most commonly used are is_a and part_of

  17. Is_a classification Class: Vehicle Class: Truck Class: Car Class: Honda Class: Toyota Class: Gasoline Class: Hybrid Class: Prius

  18. Part_of classification Class: Vehicle Class: Frame Class: Engine Class: Electrical system Class: Transmission Class: Sprockets Class: Bearings

  19. Problems with Partonomies • Inheritance of properties from superclass that may not hold • Can lead to paradoxes, including self-reference, infinity, circular definitions, and confusion of levels of reasoning • Class: Transmission • Class: Sprockets • Class: Hybrid • Class: Prius vs.

  20. Other ways to represent knowledge • Controlled Vocabulary: classes only, no attributes, no relationships, no hierarchy • Anatomical Dictionary: classes and attributes, no hierarchy, no relationships • Taxonomy: classes, hierarchy, and relationships, no attributes

  21. Examples • Gene Ontology • Mouse Anatomical Dictionary • Dinosaur Anatomy Dictionary • Foundational Model of Anatomy • ZFIN: Anatomical Dictionary

  22. Gene Ontology Ontology with both is_a and part_of

  23. Mouse Anatomical Dictionary Taxonomy with both is_a and part_of

  24. Dinosaur Anatomy Dictionary Anatomical dictionary

  25. ZFIN: Anatomical Ontology Partonomy (= ontology with part_of hierarchy)

  26. Foundational Model of Anatomy Domain ontology (is_a hierarchy)

  27. Amphibian Anatomical Ontology • Do we need one? • Should it be an ontology, partonomy, other? • How should it to look and feel?

  28. Domain and Scope • What is the domain that it will cover? • For what are we going to use the ontology? • For what types of questions should the information in the ontology provide answers? (i.e., competency questions) • Who will use it?

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