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Protégé

Protégé. Version 4.0 beta. Protégé. Free, open-source ontology editor and knowledge-base framework Based on Java, is extensible, and provides a plug-and-play environment Supported by a strong community of developers and academic, government and corporate users. Protégé Version 4.0 beta.

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Protégé

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  1. Protégé Version 4.0 beta

  2. Protégé • Free, open-source ontology editor and knowledge-base framework • Based on Java, is extensible, and provides a plug-and-play environment • Supported by a strong community of developers and academic, government and corporate users

  3. ProtégéVersion 4.0 beta • Pure OWL Framework • Supports both OWL1.1 and OWL 2.0 • Direct connection with OWL Reasoners • Pellet • FaCT++

  4. Protégé 4.0 betaMore information • Homepage • http://protege.stanford.edu/ • Download • http://protege.stanford.edu/download/protege/4.0/installanywhere/ • Documentation • http://protegewiki.stanford.edu/index.php/Protege4UserDocs • Plugins • http://code.google.com/p/co-ode-owl-plugins/downloads/list?can=3

  5. Protégé 4.0 betaOverview

  6. Ontology Design With Protégé 4.0 beta

  7. Ontology Concepts • Classes • Sets that contain individuals • Thing • Class representing the set containing all individuals • All classes are subclasses of Thing • Properties • Binary relations between two individuals (Object Property) or one individual and a datatype (Datatype Property) • Individuals • Represent objects within the Ontology (members of classes)

  8. Ontology concepts The Unique Name Assumption • OWL does not use the Unique Name Assumption (UNA) • This means that different names may refer to the same individual • E.g. the names “Matt” and “Matthew” may refer to the same individual (or they may not) • Cardinality restrictions rely on ‘counting’ distinct individuals • Therefore it is important to specify that either “Matt” and “Matthew” are the same individual, or that they are different individuals

  9. Ontology conceptsDisjoint • OWL Classes are assumed to ‘overlap’ • Individuals of a class A can also be individuals of class B • Therefore one cannot assume that an individual is not a member of a particular class simply because it has not been asserted to be a member of that class • To ‘separate’ a group of classes • One must make them disjoint from one another • If A is disjoint from B, then an individual of class A cannot also be an individual of class B

  10. Ontology conceptsOpen Vs Close World Assumption • The information contained within the ontology is incomplete • It is assumed there can always be more information • Something does not hold unless it is explicitly stated • E.g. The information on the Semantic Web • The information contained within the ontology is complete • It is assumed the information available is everything • Something does not hold by not been stated • E.g. The information within a Database Open World Assumption Close World Assumption

  11. Classes

  12. ClassesCreate Pizza Ontology classes • Pizza • PizzaBase • PizzaTopping Make all sibling classes disjoint from each other

  13. ClassesPizza Base classes • Select PizzaBase as root class • Add classes • ThinAndCrispyBase • DeepPanBase Using the Tools->“Create class Hierarchy…”

  14. ClassesPizza Toppings classes • CheeseTopping • MozzarellaTopping • ParmezanTopping • MeatTopping • HamTopping • PepperoniTopping • SalamiTopping • SpicyBeefTopping • SeafoodTopping • AnchovyTopping • TunaTopping • VegetableTopping • OliveTopping • OnionTopping • PepperTopping • TomatoTopping Using the Tools->“Create class Hierarchy…” Meaning: All individuals that are members of the class TomatoTopping are members of the class VegetableTopping and members of the class PizzaTopping…

  15. PropertiesObject & Datatype Properties • Object Properties • Relationships between two individuals • Correspond to relationships in UML • Datatype Properties • Relationships between an individual and data values • Correspond to attributes in UML

  16. PropertiesOverview • Domain and Range • Properties link individuals from the domain to individuals or datatypes from the range • Characteristics • Specify the meaning of properties • Restrictions • Explained latter • Super Properties • Properties can be further refined as sub-properties inheriting the domain, range, characteristics and restrictions

  17. PropertiesOWL 1.1 characteristics • Functional (single valued properties) • There can be at most one individual (range) that is related to the domain individual via the property. • e.g. A person only has one mother. • Inverse Functional • The inverse property is functional (which does not mean that the property is functional).

  18. PropertiesOWL 1.1 characteristics • Transitive: P(A,B) and P(B,C) -> P(A,C) • If a property P is transitive, and the property relates individual A to individual B, and also individual B to individual C, • Then we can infer that individual A is related to individual C via property P. • Notes • If a property is transitive then its inverse property should also be transitive • If a property is transitive then it cannot be functional. • e.g. An ancestor of a person’s father is also his ancestor. • Symmetric: P(A,B) -> P(B,A) • If a property P is symmetric, and the property relates individual A to individual B • Then individual B is also related to individual A via property P. • e.g. Two sibling persons are siblings with each other.

  19. PropertiesOWL 2.0 additional characteristics • Antisymmetric: P(A,B) -> ∼P(B,A) • If a property P is antisymmetric, and the property relates individual A to individual B then individual B cannot be related to individual A via property P • e.g. If a person is parent of its child, then its child never can be a parent of that person. • Reflexive: P(A,A) • A property P is said to be reflexive when the property must relate individual A to itself • e.g. A Person always knows herself. • Irreflexive • If a property P is irreflexive, it can be described as a property that relates an individual A to individual B, where individual A and individual B are not the same. • e.g. A Person cannot be father of himself.

  20. Object Properties

  21. Object PropertiesOverview • Domain • Classes of Individuals • Range • Classes of Individuals • Characteristics that can be applied • Functional • Inversed Functional • Transitive • Symmetric • Antisymmetric • Reflexive • Irreflexive • Inverted Properties • If some property links individual A to individual B then its inverse property will link individual B to individual A • E.g. hasIngredient versus isIngredientOf

  22. Object PropertiesCreate some Object Properties • hasIngredient • hasTopping • hasBase • isIngredientOf • isToppingOf • isBaseOf Pizza Ingredients Ingredients that make up the Pizza

  23. Object PropertiesExample • Maintain hasIngredient domain and range as Thing • Since hasIngredient is to be set as transitive • Thus the domain and range must be compatible • Specify the range for hasTopping to PizzaTopping • Specify the range for hasBase to PizzaBase • Make isIngredientOf properties inverse of hasIngredient • Make the hasIngredient property transitive • A ingredient of an ingredient, is also an ingredient of a Pizza • Make the hasBase property functional • A Pizza has only one base Domain & Ranges Property Characteristics

  24. Datatype Properties

  25. Datatype PropertiesOverview • Domain • Classes of Individuals • Range • XML Schema Datatype value (http://www.w3.org/TR/xmlschema-2/) • RDF literal • XML literal • Characteristics that can be applied • Functional • Cannot have Inverted Properties

  26. Datatype PropertiesXML Schema Datatype

  27. Datatype PropertiesAdd datatype properties • Create a hasCalorificContentValuedatatype property with integer as range • Create a hasBaseProperty for PizzaBase (domain) • Create a hasWidthdatatype sub-property of hasBaseProperty with integer as range • Create a hasThicknessdatatype sub-property of hasBaseProperty with float as range • Change characteristics to Functional of the datatype properties • hasCalorificContentValue • hasWidth • hasThickness

  28. Individuals

  29. IndividualsDescription & Property Assertions • Type • Specifies the class(es) which it is an instance • Same Individuals • Relation between two individuals which are “clones” of each other • Different Individuals • Relation between two individuals independent individuals • Object Property Assertions • Specify relations over a given object property • Data Property Assertions • Specify relations over a given datatype property Description Property Assertions

  30. IndividualsAdd some individuals • Create a class called Country and populate it with some individuals • Italy, America, England, France, and Germany • Create example pizza individuals • “Example-Margherita” with calorific value of 263 (integer) • “QuattroFormaggio” with calorific value of 723 (integer) • Create a MozzarellaTopping individual

  31. RestrictionsDefinition • A restriction describes an anonymous (unnamed) class • The set of subclasses and individuals that satisfy the given restriction • Applies to • Classes • Object Properties • Datatype Properties

  32. Restrictions Restriction Types • Quantifier Restrictions • Effectively puts constraints on the relationships that the individual participates in by • Specifying that at least one kind (existential) of relationship must exist, or • e.g. Pizza hasTopping some TomatoTopping • Specifying the only kinds (universal) of relationships that can exist (if they exist) • e.g. Pizza hasBase only PizzaBase • Cardinality Restrictions • Specify the number of relationships that an individual may participate in for a given property • Comes in three flavors: Min, Max and Exact • Value Restrictions (covered latter) • Specifies a object property relation to a specific individual

  33. RestrictionsAdd restrictions • Specify that Pizza only has one PizzaBase • Add a cardinality restriction to Pizza on hasBase to exactly one PizzaBase • Add to the superclasses section “hasBase exactly 1 PizzaBase” • Specify that Pizza has at least one PizzaTopping • Add an existencial restriction to Pizza on hasTopping to PizzaToppings • Add to the superclasses section “hasTopping some PizzaTopping” • Create a value restriction to specify that MozzarellaTopping has Italy as its country of origin • Create hasCountryOfOrigin object property with Country as range • Add to the superclass section “hasCountryOfOrigin value Italy”

  34. Restrictions Necessary Vs Necessary & Suficcient • If an individual is a member of class A it must satisfy the conditions (necessary) • One-way implication • Restrictions in the “superclass” section • Used for checking Consistency! • If an individual is a member of the class A it must satisfy the conditions (necessary) • And if any individual satisfies these conditions then it must be a member of class A (sufficient) • Two-way implication • Restrictions in the “equivalent class” section • Used for assertion (Classification)! Necessary Necessary & Sufficient

  35. Restrictions Covering Axiom • A covering axiom consists of two parts • The class that is being ‘covered’ • The class is equivalent to one of its subclasses • The classes that form the covering • All subclasses must be disjoint

  36. Value PartitionsCreate a value partition • Create a ValuePartition to represent the spiciness of pizza toppings • Create a subclass of Thing called “Spiciness” • Create three new classes (Hot, Medium, and Mild) as subclasses of “Spiciness” • Make all subclasses disjoint • Create an object property called hasSpiciness with Spiciness as range • Create a Covering Axiom for Spiciness • Add to the “equivalent classes” section “Hot or Medium or Mild”

  37. Enumerated ClassesDefinition & Example • Classes that are defined as the precisely listing of the individuals that are the members of the class • e.g. Days of the week (Monday, Tuesday, Wednesday, Thursday, Friday, Saturday and Sunday) • Make Country an enumerated class • At the restriction to the equivalent class section • Add “{America, England, France, Germany, Italy}”

  38. Ontology DesignCommon Mistakes • Some of the common mistakes made when modelling have been enumerated • They include: • Misuse of property domain and range • Misunderstanding of intersections and other constructs • Not understanding the Open World Assumption • Misuse/lack of disjoints • See OWL Pizzas: Common errors & common patterns http://www.co-ode.org/resources/papers/

  39. Using a Reasoner With Protégé 4.0 beta

  40. ReasonerDefinition • A piece of software able to infer logical consequences from a set of asserted facts or axioms

  41. ReasonerUsed for • Consistency checking • Test whether a class could have instances • Classification • A classifier takes a class hierarchy and places a class in the class hierarchy • Task of turning implicit definitions already present in the hierarchy as explicit

  42. ReasonerProtégé 4.0 beta support • Built-in support • Pellet (http://clarkparsia.com/pellet) • FaCT ++(http://owl.man.ac.uk/factplusplus/) • Connection to external reasoners through a DIG interface

  43. ReasonerPellet vsFaCT++ • Open-source Java OWL DL reasoner • Support expressivity of SROIQ(D) • Supports SWRL rules • Available through AGPL version 3 licence • Latest version is 2.0.0 rc5 • Support in Protégé for 1.5 version • New generation and C++ implementation of FaCT • Support expressivity of SROIQ(D) • No support for Rules • Available through GNU publiclicense • Latest version is 1.2.3 • Support in Protégé for 1.2.3 version Pellet FaCT++

  44. ReasonerSelecting and running a Reasoner • Selecting… • Go to the “reasoner” menu and select “Pellet” as your reasoner • Running… • In the same menu, click “Classify…” • or simply type Ctrl-R

  45. Run reasoner…Quick Overview of the new assertions • Object Properties • Both isBaseOf and isToppingOf assume the range of its inverted properties as their domain • The domain of a property is the range of its inverted property (and vice-versa) • Datatype Properties • Both hasWidth and hasThickness inherit the hasBaseProperty domain • Individuals • Individual “MozarellaTopping_1” inherits the object property hasCountryOfOrigin with “Italy” as range

  46. ConsistencyInconsistent Classes • Add a Probe Class called ProbeInconsistentTopping which is a subclass of both CheeseTopping and VegetableTopping • Classify… • Inconsistency detected since subclasses of PizzaTopping are Disjoint. • Remove the disjoint statement between CheeseTopping and VegetableTopping to see what happens • Classify… • Consistent! • Remember to add disjoint statement at the end and remove Probe Class

  47. ClassificationCreate some named Pizza classes • Create a subclass of Pizza called “NamedPizza” • Create Margherita, Americana, American hot and Soho pizzas as subclasses of named pizza • Margherita Pizza with toppings Mozzarella and Tomato (add to the “superclasses” section “hasTopping some TomatoTopping”) • AmericanaPizza with toppings Mozzarella, Tomato and Pepperoni • AmericanHotPizza with toppings Mozzarella, Tomato, Pepperoni and Pepper • SohoPizza with toppings Mozzarella, Tomato, Olive and Parmesan • Make named pizzas disjoint

  48. ClassificationExistencial Restriction • Create a cheesy pizza class for pizzas with cheese topping • Create a subclass of Pizza called “CheesyPizza” • Add to the “equivalent classes” section “Pizza and hasTopping some CheeseTopping” • Classify… • AmericanPizza, AmericanHotPizza, MargheritaPizza and SohoPizza are now subclasses of CheesyPizza.

  49. Classification Universal Restrictions • Create a vegetarian pizza that only has cheese and vegetable toppings • Create a subclass of Pizza called “VegetarianPizza” • Add to the “equivalent classes” section “Pizza and hasTopping only (CheeseTopping or VegetableTopping)” • Classify… • Why aren’t MargheritaPizza and SohoPizza classified as VegetarianPizza?

  50. Classification Universal Restrictions • Remember “Open World Assumption” • We have stated that Margherita pizza has toppings that are kinds of mozzarella and also kinds of tomato, • but we did not explicitly say that a margherita pizza only has these kinds of toppings, • it is assumed that a margherita pizza could have other toppings… • Solution • Add a Closure Axiom for all the Existential Axioms

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