Download - A Practical Introduction to Ontologies & OWL
BioHealthInformaticsGroup
O p en G A L E N
A Practical Introduction to Ontologies & OWL
Session 1: Primitive Classes in OWL
Nick Drummond & Matthew Horridge
Copyright © 2005, The University of Manchester
Overview
► Pizzas – Card Sorting
► Protégé Introduction
► Subsumption
► Creating a Class Hierarchy
► Consistency
► Disjointness
► Relationships & Properties
► Restrictions
► Polyhierarchies - Issues
Copyright © 2005, The University of Manchester
Our Domain
►Pizzas have been used in Manchester tutorials for years.
►Pizzas were selected as a domain for several reasons:► They are fun
► They are internationally known
► They are highly compositional
► They have a natural limit to their scope
► They are fairly neutral
►Although arguments still break out over representation
►Even pizzas can do this - its an inevitable part of knowledge modelling
►ARGUING IS NOT BAD!
Copyright © 2005, The University of Manchester
You are the Expert
►Most often it is not the domain expert that formalises their knowledge – because of the complexity of the modelling it is normally a specialist “knowledge engineer”Hopefully, as tools get easier to use, this will change
►Having access to experts is critical for most domains
►Luckily, we are all experts in Pizzas, so we just need some material to verify our knowledge…
Copyright © 2005, The University of Manchester
Reference Materials
►Having references to validate decisions, and act as provenance can be useful for maintaining an ontology
►Mistakes, omissions and intentions can be more easily traced if a reference can be made
► When building, we highly recommend documenting your model as you go – keeping provenance information is a good way of doing this
►We have provided you with a pizza menu and several cards with ingredients on
Copyright © 2005, The University of Manchester
Our Ontology
► When building an ontology we need an application in mind – ontologies should not be built for the sake of it
► Keep the application in mind when creating concepts – this should help you scope the project
► The PizzaFinder application has been developed so that you can plug your ontology in at the end of the day and see it in action
Let us know your ideas for extending the application
Copyright © 2005, The University of Manchester
Our Application
www.co-ode.org/downloads/pizzafinder/
Copyright © 2005, The University of Manchester
Exercise 1: Card Sorting
Copyright © 2005, The University of Manchester
Card Sorting - Issues
► different viewpoints
► Tomato – Vegetable or Fruit?
► culinary vs biological
► Ambiguity
► words not concepts
► Missing Knowledge
► What is peperonata?
► multiple classifications (2+ parents)
► lots of missing categories (superclasses?)
► competency questions
► What are we likely to want to “ask” our ontology?
► bear the application in mind
Copyright © 2005, The University of Manchester
OWL Constructs
Person Country
Class (concept)
Animal
Individual (instance)
Belgium
Paraguay
China
Latvia
Elvis
Hai
Holger
Kylie
S.Claus
Rudolph
Flipper arrow = relationship
label = Property
lives_in
lives_in
lives_in
has_pet
has_pet
has_
pet
Copyright © 2005, The University of Manchester
OWL Constructs:Classes
Eg Mammal, Tree, Person, Building, Fluid, Company
► Classes are sets of Individuals
► aka “Type”, “Concept”, “Category”
► Membership of a Class is dependent on its logical description, not its name
► Classes do not have to be named – they can be logical expressions – eg things that have colour Blue
► A Class should be described such that it is possible for it to contain Individuals (unless the intention is to represent the empty class)
► Classes that cannot possibly contain any Individuals are said to be inconsistent
Copyright © 2005, The University of Manchester
OWL Constructs: Properties
Eg hasPart, isInhabitedBy, isNextTo, occursBefore
► Properties are used to relate Individuals
► We often say that Individuals are related along a given property
► Relationships in OWL are binary:
Subject predicate Object
Individual a hasProperty Individual b
nick_drummond givesTutorial Manchester_ProtegeOWL_tutorial_29_June_2005
► N-ary relationships can be modelled with workarounds in OWL, but this design pattern will not be discussed today
Copyright © 2005, The University of Manchester
OWL Constructs: Individuals
Eg me, you, this tutorial, this room
► Individuals are the objects in the domain
► aka “Instance”, “Object”
► Individuals may be (and are likely to be) a member of multiple Classes
Copyright © 2005, The University of Manchester
…
► Is a knowledge modelling environment
► Is free, open source software
► Is developed by Stanford Medical Informatics
► Has a large user community (approx 30k)
Copyright © 2005, The University of Manchester
► core is based on Frames (object oriented) modelling
► has an open architecture that allows other modelling languages to be built on top
► supports development of plugins to allow backend / interface extensions
► now supports OWL through the Protégé-OWL plugin
So let’s have a look…
…
Copyright © 2005, The University of Manchester
Protégé-OWL
Copyright © 2005, The University of Manchester
Class Hierarchy Subsumption hierarchy
Structure as asserted by the ontology engineer
owl:Thing is the root class
Copyright © 2005, The University of Manchester
Subsumption
► Superclass/subclass relationship, “isa”
► All members of a subclass can be inferred to be members of its superclasses
owl:Thing: superclass of all OWL Classes
B
A
• A subsumes B
• A is a superclass of B
• B is a subclass of A
• All members of B are also members of A
Copyright © 2005, The University of Manchester
Class EditorClass annotations (for class metadata)
Class name and documentation
Properties “available” to
Class
Disjoints widget
Conditions Widget
Class-specific tools (find usage etc)
Copyright © 2005, The University of Manchester
Exercise 2: Create Class Hierarchy
Before you start:
► If you are borrowing a laptop, please take a note of the number on the top cover
► Please save all files to:My Documents\ontologies
► Because you will be needing your work again tomorrow
Copyright © 2005, The University of Manchester
Exercise 2: Create Class Hierarchy
► You will notice that we use naming conventions for our ontology entities
► Typically, we use CamelNotation with a starting capital for Classes
► Use whatever conventions you like
► It is helpful to be consistent – especially when trying to find things in your ontology
Copyright © 2005, The University of Manchester
Saving OWL Files
1. Select File Save Project AsA dialog (as shown) will pop up
2. Select a file directly by clicking the button on the top rightYou will notice that 2 files are created.pprj – the project file
this just stores information about the GUIand the workspace
.owl – the OWL filethis is where your ontology is stored inRDF/OWL format
3. Select OK
OWL = easy to make mistakes = save regularly
Copyright © 2005, The University of Manchester
Loading OWL files
1. If you only have an OWLfile:
- File New Project- Select OWL Files as the type- Tick Create from existing sources- Next to select the .owl file
2. If you’ve got a valid project file*:- File Open Project- select the .pprj file
* ie one created on this version of Protégé - the s/w gets updated once every few days, so don’t count on it unless you’ve created it recently– safest to build from the .owl file if in doubt
Copyright © 2005, The University of Manchester
Consistency Checking
► We’ve just created a class that doesn’t really make sense
► What is a MeatyVegetableTopping?
► We’d like to be able to check the logical consistency of our model
► This is one of the tasks that can be done automatically by software known as a Reasoner
► Being able to use a reasoner is one of the main advantages of using a logic-based formalism such as OWL (and why we are using OWL-DL)
Copyright © 2005, The University of Manchester
Reasoners
► Reasoners are used to infer information that is not explicitly contained within the ontology
► You may also hear them being referred to as Classifiers
► Standard reasoner services are:► Consistency Checking
► Subsumption Checking
► Equivalence Checking
► Instantiation Checking
► Reasoners can be used at runtime in applications as a querying mechanism (esp useful for smaller ontologies)
► We will use one during development as an ontology “compiler”. A well designed ontology can be compiled to check its meaning is that intended
Copyright © 2005, The University of Manchester
Reasoners and Protégé
► Protégé-OWL supports the use of reasoners implementing the DIG interface
► This means that the reasoner you choose is independent of the ontology editor, so you can choose the implementation you want depending on your needs (eg some may be more optimised for speed/memory, others may have more features)
► These reasoners typically set up a service running locally or on a remote server – Protégé-OWL can only connect to reasoners over an http:// connection
Copyright © 2005, The University of Manchester
Accessing the Reasoner
Classify taxonomy
(and check consistency)
Just check consistency
(for efficiency)
Compute inferred types
(for individuals)
Copyright © 2005, The University of Manchester
Reasoning about our Pizzas
► When we classify an ontology we could just use the “Check Consistency” button but we’ll get into the habit of doing a full classification as we’ll be doing this later
► The reasoner dialog will pop up while thereasoner works
► When the reasoner has finished, you will see an inferred hierarchy appear, which will show any movement of classes in the hierarchy
► If the reasoner has inferred anything about our model, this is reported in the reasoner dialog and in a separate results window
► inconsistent classes turn red► moved classes turn blue
Copyright © 2005, The University of Manchester
Disjointness
► OWL assumes that classes overlap
MeatTopping VegetableTopping
= individual
► This means an individual could be both a MeatTopping and a VegetableTopping at the same time
► We want to state this is not the case
Copyright © 2005, The University of Manchester
Disjointness
► If we state that classes are disjoint
MeatTopping VegetableTopping
= individual
► This means an individual cannot be both a MeatTopping and a VegetableTopping at the same time
► We must do this explicitly in the interface
Copyright © 2005, The University of Manchester
ClassesTab: Disjoints Widget
Add siblings as disjoint
Add new disjoint Remove disjoint siblings
List of disjoint classes
Copyright © 2005, The University of Manchester
Exercise 3: Add Disjoints
► Run a reasoner locally on your machine
► Your reasoner may be found at…
Copyright © 2005, The University of Manchester
Why is MeatyVegetableTopping Inconsistent?
► We have asserted that a MeatyVegetableTopping is a subclass of two classes we have stated are disjoint
► The disjoint means nothing can be a MeatTopping and a VegetableTopping at the same time
► This means that MeatyVegetableTopping can never contain any individuals
► The class is therefore inconsistent
► This is what we expect!
► It can be useful to create classes we expect to be inconsistent to “test” your model – often we refer to these classes as “probes” – generally it is a good idea to document them as such to avoid later confusion
Copyright © 2005, The University of Manchester
Other Inconsistencies?
► Your ontology is likely to have several classes with multiple parents
► We call this a tangle
► As we have seen, a class cannot have 2 disjoint parents – it will be inconsistent
► To remove other inconsistencies you will have to be careful about where your disjoints are – remove disjoints between multiple parents by hand
► This is obviously an awkward thing to manage – we will later show you how to manage your tangle to simplify these issues
Copyright © 2005, The University of Manchester
What have we got?
► We’ve created a tangled graph (not a tree – multiple parents) of mostly disjoint classes
► Disjoints are inherited down the subsumption hierarchyeg something that is a TomatoTopping cannot be a Pizza because its superclass, PizzaTopping, is disjoint from Pizza
► You should now be able to select every class and see its siblings in the disjoints widget (if it has any)
Copyright © 2005, The University of Manchester
What are we missing?
► This is not a semantically rich model
► Apart from “is kind of” (subsumption) and “is not kind of” (disjoint), we currently don’t have any other information of interest
► We want to say more about Pizza Individuals, such as their relationship with other Individuals
Pizza PizzaTopping
= individual
Copyright © 2005, The University of Manchester
Relationships in OWL
► In OWL-DL, relationships can only be formed between Individuals or between an Individual and a data value.(In OWL-Full, Classes can be related, but this cannot be reasoned with)
► Relationships are formed along Properties
► We can restrict how these Properties are used:► Globally – by stating things about the Property itself
► Or locally – by restricting their use for a given Class
Copyright © 2005, The University of Manchester
OWL Properties
► Object Property – relates Individuals
► Datatype Property – relates Individuals to data (int, string, float etc)
► Annotation Property – for attaching metadata to classes, individuals or properties
Copyright © 2005, The University of Manchester
Properties Tab: Property Browser
Note that Properties can be in a hierarchy, although we are not going to be using this feature today
Copyright © 2005, The University of Manchester
Creating Properties
not used today:
- New Datatype Property (String, int etc)
New Object Property:
Associates an individual to another individual
Delete Property
- New Annotation Properties for metadata
- New SubProperty – ie create “under” the current selection
Copyright © 2005, The University of Manchester
Creating Properties
► We tend to name properties using camelNotation with a lowercase letter to begin
► We often create properties using 2 standard naming patterns:► has… (eg hasColour)
► is…Of (eg isTeacherOf) or other suffixes (eg …In …To)
► This has several advantages:► It is easier to find properties
► It is easier for tools to generate a more readable form(see tooltips on the classes in the hierarchy later)
► Inverses properties typically follow this patterneg hasPart, isPartOf
► Our example hasBase fits into this(we will not create the inverse in this tutorial)
Copyright © 2005, The University of Manchester
Associating Properties with Classes
► We now have a property we want to use to describe Pizza individuals
► To do this, we must go back to the Pizza class and add some further information
► This comes in the form of Restrictions
► We create Restrictions using the Conditions widget
► Conditions can be any kind of Class – you have already added Named superclasses in the Conditions Widget. Restrictions are a type of Anonymous Class
Copyright © 2005, The University of Manchester
Conditions Widget
Conditions asserted by the ontology engineer
Add different types of condition
Definition
of the class
(later)
Description
of the class
Conditions inherited from superclasses
Copyright © 2005, The University of Manchester
Conditions TypesLogical (Anonymous) Classes
Add Named Superclass
Create Restriction (next)
Create Class Expression
Copyright © 2005, The University of Manchester
Creating Restrictions
Restriction
Type
Restricted Property
Filler
Expression
Syntax
check
Expression
Construct
Palette
Copyright © 2005, The University of Manchester
What does this mean?
► We have created a restriction: hasBase PizzaBaseon Class Pizza as a necessary condition
► “If an individual is a member of this class, it is necessary that it has at least one hasBase relationship with an individual from the class PizzaBase”
Pizza PizzaBase
hasBase
hasBase
hasBase
hasBase
► “Every individual of the Pizza class must have at least one base from the class PizzaBase”
Copyright © 2005, The University of Manchester
What does this mean?
► We have created a restriction: hasBase PizzaBaseon Class Pizza as a necessary condition
Pizza PizzaBase
hasBase
hasBase
hasBase
hasBase
► “There can be no individual, that is a member of this class, that does not have at least one hasBase relationship with an individual from the class PizzaBase”
Copyright © 2005, The University of Manchester
hasBase PizzaBase
Why?
► We have created a restriction: hasBase PizzaBaseon Class Pizza as a necessary condition
PizzaBase
hasBase
hasBase
hasBase
hasBase
hasBase
hasBase
► Each Restriction or Class Expression describes the set of all individuals that satisfy the condition
Copyright © 2005, The University of Manchester
Pizza
Why? Necessary conditions
► We have created a restriction: hasBase PizzaBaseon Class Pizza as a necessary condition
► Each necessary condition on a class is a superclass of that class
PizzaBase
hasBase
hasBase
hasBase
hasBase
hasBase
hasBase
hasBase PizzaBase
► ie The restriction hasBase PizzaBase is a superclass of Pizza
► As Pizza is a subclass of the restriction, all Pizzas must satisfy the restriction that they have at least one base from PizzaBase
Copyright © 2005, The University of Manchester
Exercise 4: Properties & Restrictions
Copyright © 2005, The University of Manchester
Restriction Types
Existential, someValuesFrom “Some”, “At least one”
Universal, allValuesFrom “Only”
hasValue “equals x”
Cardinality “Exactly n”
Max Cardinality “At most n”
Min Cardinality “At least n”
Copyright © 2005, The University of Manchester
Primitive Classes
► All classes in our ontology so far are Primitive
► We describe primitive pizzas
► Primitive Class = only Necessary Conditions
► They are marked as plain orange circles in the class hierarchy
We condone building a disjoint tree of primitive classes
Copyright © 2005, The University of Manchester
Polyhierarchies
► By the end of this tutorial we intent to create a VegetarianPizza
► Some of our existing Pizzas should be types of VegetarianPizza
► However, they could also be types of SpicyPizza or CheeseyPizza
► We need to be able to give them multiple parents in a principled way
► We could just assert multiple parents like we did with MeatyVegetableTopping (without disjoints)
BUT…
Copyright © 2005, The University of Manchester
Asserted Polyhierarchies
We believe asserting polyhierarchies is bad
let the reasoner do it!
►We lose some encapsulation of knowledge► Why is this class a subclass of that one?
►Difficult to maintain► Adding new classes becomes difficult because all subclasses may
need to be updated► Extracting from a graph is harder than from a tree
Copyright © 2005, The University of Manchester
Summary
You should now be able to:
► extract Knowledge (and act as an expert)
► identify components of the Protégé-OWL Interface
► create Primitive Classes
► create Properties
► create some basic Restrictions on a Class using Existential qualifiers