PROTG: OWL Tutorial
Acep Irham Gufroni
Semantic Web 2016
(adapted from : Presentation by the COODE and HyOntUse Projects
by Photchanan Ratanajaipan )
OWL Tutorial : Overview
Session 1: Interface basics
Session 2: Defining a vegetarian pizza
Session 3: Case Study
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Session 1: Interface Basics
Review: OWL Basics
Intro: Protg-OWL
Interface: Creating Classes
Concept: Disjointness
Interface: Creating Properties
Concept: Describing Classes
Interface: Creating Restrictions
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Review of OWL
OWL
is a W3C standard Web Ontology Language
comes in 3 flavours (lite, DL and full)
we are using OWL DL (Description Logic)
DL = decidable fragment of First Order Logic (FOL)
is generally found in RDF/XML syntax
is therefore not much fun to write by hand
So, we have tools to help us
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OWL Constructs
Person
Country
Elvis
Belgium
Holger
Paraguay
Kylie
= class (concept)
Latvia
S.Claus
China
Hai
= property (relationship)
= individual (instance)
Flipper
Animal
Rudolph
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Get Protg-OWL
Logon to Windows
1. Go to: http://protege.stanford.edu/download/registered.html
2. Download full Protg
3. Install the software
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Starting Protg-OWL
Run Protg.exe
1. Select New Project
2. Select OWL/RDF Files
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Protg OWL plugin
Protg tabs
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Protg OWL plugin: Tabs
Used in this tutorial
Changing the GUI
Populating the model
Top-level functionality
Extensions (visualisation)
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Classes Tab
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ClassesTab: Asserted Class Hierarchy
Subsumption hierarchy (superclass/subclass)
Structure as asserted by the ontology engineer
Create and Delete classes (actually subclasses!!)
Everything is a subclass of owl:Thing
Search for class
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ClassesTab: Class Editor
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ClassesTab: Class Editor
Class annotations (for class metadata)
Class name and documentation
Switch view
to show
Properties
available to
Class
Disjoints
widget
Conditions Widget
Class-specific tools (find usage etc)
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Create Classes
Start with your empty ontology
1. Click the Create subclass button
(this is above the class hierarchy)
A new class will be created as a subclass of owl:Thing
2. Type in a new name DomainConcept over the default
(press enter updates the hierarchy)
3. Req. for later labs: document your class using the rdfs:comment field
4. Create another class called Pizza by clicking the Create sibling class
You will notice that Pizza has been created as a subclass of
DomainConcept as this was the class selected when the button was
pressed. You can also right-click any class and select Create Class
5. Create two more subclasses of DomainConcept called PizzaTopping
and PizzaBase.
Any mistakes, use the Delete Class button next to Create Class
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Disjointness
OWL assumes that classes overlap
Pizza
PizzaTopping
= individual
This means an individual could be both a Pizza and
a PizzaTopping at the same time
We want to state this is not the case
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Disjointness
If we state that classes are disjoint
Pizza
PizzaTopping
= individual
This means an individual cannot be both a Pizza
and a PizzaTopping at the same time
We must do this explicitly in the interface
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ClassesTab: Disjoints Widget
Add siblings as disjoint
Add new disjoint
List of disjoint classes
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Remove disjoint siblings
Make Classes Disjoint
Start with your existing ontology
1. Select the Pizza class
You will notice that the disjoints widget is empty
2. Click the Add all siblings button
The Add siblings to disjoints dialog pops up
3. Select the Mutually between all siblings option and OK
PizzaTopping and PizzaBase appear in the disjoints widget
4. Select the PizzaTopping class
Pizza and PizzaBase are already in the disjoints widget
5. Note that the same applies for PizzaBase
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Save Your Work
OWL = easy to make mistakes save regularly
1. Select File Save
A dialog (as shown) will pop up
2. Select a file using a file selector by clicking the button on the top right
You will notice that there are 2 files created
.pprj the project file
this just stores information about the GUI
and the workspace
.owl the OWL file
this is where your ontology is stored in
RDF/OWL format
3. Select OK
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Create PizzaToppings
Start with your existing ontology
1. Create subclasses of PizzaTopping:
CheeseTopping
VegetableTopping
MeatTopping
2. Make these subclasses all disjoint from one another
(remember to chose Mutually between all siblings when prompted)
3. Create subclasses of CheeseTopping:
MozzarellaTopping, ParmesanTopping
4. Make these subclasses all disjoint from one another
5. Create subclasses of VegetableTopping and make them disjoint:
TomatoTopping, MushroomTopping
6. Save to another file using File Save As
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What have we got?
Weve created a tree of disjoint classes
Disjoints are inherited down the tree
e.g. 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
(except DomainConcept) and see its siblings in the
disjoints widget
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What are we missing?
This is not a semantically rich model
Apart from is kind of and is not kind of, we currently dont
have any other information of interest
We want to say more about Pizza individuals, such as their
relationship with other individuals
We can do this with properties
Pizza
PizzaTopping
= individual
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Properties Tab
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Properties Tab: Property Browser
Properties can be in a hierarchy
Search for property
SuperProperties of the current selected
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Properties Tab: Property Browser
Delete Property
New Object Property:
Associates an individual to another individual
not used today:
- New Datatype Property (String, int etc)
- New Annotation Properties for metadata
- New SubProperty ie create under the current selection
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Create a Property
Start with your existing ontology
1. Switch to the Properties tab
There are currently no properties, so the list is blank
2. Create a new Object property using the button in the
property browser
3. Call the new Property hasTopping
4. Create another Object Property called hasBase
5. Save under a new filename
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Associating Properties with Classes
We now have two properties 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 (which are a
type of Condition)
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ClassesTab: 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
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Create a Restriction
Start with your existing ontology
1. Switch to the OWL Classes tab
2. Select Pizza
Notice that the conditions widget only contains one item,
DomainConcept with a Class icon.
Superclasses show up in the conditions widget in this way
3. Click the Create Restriction button
A dialog pops up that we will investigate in a minute
4. Select hasBase from the Restricted Property pane
5. Leave the Restriction type as someValuesFrom
6. Type PizzaBase in the Filler expression editor, then Click OK
A restriction has been added to the Conditions widget
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What does this mean?
We have created a restriction: hasBase PizzaBase
on Class Pizza as a necessary condition
Pizza
PizzaBase
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
Every individual of the Pizza class must have at least one base from the
class PizzaBase
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What does this mean?
We have created a restriction: hasBase PizzaBase
on Class Pizza as a necessary condition
Pizza
PizzaBase
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
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Restrictions Popup
Restricted Property
Restriction Type
Filler Expression
Expression
Construct
Palette
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Syntax check
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
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Another Existential Restriction
Start with your existing ontology
1. Make sure Pizza is selected
2. Create a new Existential (SomeValuesFrom) Restriction with the
hasTopping property and a filler of PizzaTopping
When entering the filler, you have 2 shortcut methods rather than typing
the entire classname:
1) enter a partial name and use Tab to
autocomplete
2) use the select Class button
on the editor palette
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Create a Universal Restriction
Start with your existing ontology
1. Create 2 disjoint subclasses of PizzaBase
called ThinAndCrispy and DeepPan
2. Create a subclass of Pizza called RealItalianPizza
3. Create a new Universal (AllValuesFrom) Restriction on RealItalianPizza
with the hasBase property and a filler of ThinAndCrispy
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What does this mean?
We have created a restriction: hasBase ThinAndCrispy
on Class RealItalianPizza as a necessary condition
RealItalianPizza
ThinAndCrispy
If an individual is a member of this class, it is necessary that it must only
have a hasBase relationship with an individual from the class
ThinAndCrispy
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What does this mean?
We have created a restriction: hasBase ThinAndCrispy
on Class RealItalianPizza as a necessary condition
DeepPan
RealItalianPizza
ThinAndCrispy
No individual of the RealItalianPizza class can have a base from a class
other than ThinAndCrispy
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Universal Warning Trivial Satisfaction
If we had not already inherited: hasBase PizzaBase
from Class Pizza the following could hold
RealItalianPizza
ThinAndCrispy
Trivially satisfied
by this individual
If an individual is a member of this class, it is necessary that it must only
have a hasBase relationship with an individual from the class
ThinAndCrispy, or no hasBase relationship at all
ie Universal Restrictions by themselves do not state at least one
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Summary
You should now be able to:
identify components of the Protg-OWL
Interface
create Primitive Classes
create Properties
create some basic Restrictions on a Class
using Existential and Universal qualifiers
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More exercises:
Create a MargheritaPizza
Start with your existing ontology
1. Create a subclass of Pizza called NamedPizza
2. Create a subclass of NamedPizza called MargheritaPizza
3. Create a restriction to say that:
Every MargheritaPizza must have at least one topping from
TomatoTopping
4. Create another restriction to say that:
Every MargheritaPizza must have at least one topping from
MozzarellaTopping
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More exercises:
Create other pizzas
Start with your existing ontology
1. Add more topping ingredients as subclasses of
PizzaTopping
Use the hierarchy, but be aware of disjoints
2. Create more subclasses of NamedPizza
3. Create a restrictions on these pizzas to describe their
ingredients
4. Save this for the next session
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OWL Tutorial: Session II
adapted from
Presentation by the COODE and
HyOntUse Projects
by
Photchanan Ratanajaipan
OWL Tutorial : Overview
Session 1: Interface basics
Session 2: Defining a vegetarian pizza
Page 44
Session 2: Vegetarian Pizza
Issue: Primitive Classes & Polyhierarchies
Advanced: Reasoning
Advanced: Creating Defined Classes
Union Classes: Covering Axioms
Example: Creating a Vegetarian Pizza
Issue: Open World Assumption
Union Classes: Closure
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Loading OWL files from scratch
Run Protg.exe
1. If youve only got an
OWL file:
Select OWL Files as the
Project Format, then Build
to select the .owl file
2. If youve got a valid project file*:
Select OWL Files as the Project Format, and then Open Other to find the .pprj
file (if youve already opened it, it will be in Open Recent)
3. Open C:\Protg_3.0_beta\examples\pizzas\pizzas2_0.owl
* ie one created on this version of Protg - the s/w gets updated once every few days, so dont
count on it unless youve created it recently safest to build from the .owl file if in doubt
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Primitive Classes
All classes in our ontology so far are Primitive
We describe primitive pizzas
Primitive Class = only Necessary Conditions
They are marked as yellow in the class hierarchy
We condone
building a
disjoint tree of
primitive
classes
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Describing Primitive Pizza Classes
Start with pizzas2_0.owl
1. Create a new pizza under NamedPizza
either choose from the menu or make it up
2. Create a new Existential (SomeValuesFrom) Restriction with
the hasTopping property and a filler from PizzaTopping (eg
HamTopping)
3. Add more Restrictions in the same way to complete the
description
each restriction is added to an intersection
so a Pizza must have toppingA and must have toppingB etc
see MargheritaPizza for an example
4. Create another pizza that has at least one meat ingredient
remember disjoints
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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
CheeseLoversPizza
We need to be able to give them multiple parents
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Vegetarian Pizza attempt 1
Start with pizzas2_1.owl
1. Create a new pizza called
VegetarianPizza under Pizza
make this disjoint from its siblings as we have been doing
2. Select MargheritaPizza
you will notice that it only has a single parent, NamedPizza
3. Add VegetarianPizza as a new parent using the conditions
widget Add Named Class button
notice that MargheritaPizza now occurs in 2 places in the asserted hierarchy
we have asserted that MargheritaPizza has 2 parents
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Reasoning
Wed like to be able to check the logical consistency
of our model
Wed also like to make automatic inferences about
the subsumption hierarchy. A process known as
classifying
i.e. Moving classes around in the hierarchy based on their
logical definition
Generic software capable of these tasks are known as
reasoners (although you may hear them being referred to as Classifiers)
RACER, Pellet are reasoners
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Running Racer
Run racer.exe
A cmd window will open and two service enabled
messages will appear in the ouput
NB. Alternative DIG reasoners like FaCT, Pellet can also be
used
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Running Racer
Racer is now ready for use as an http server
using a standard interface called DIG
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Running Pellet
Run pellet dig
A cmd window will open, pellet is now ready for use
as an http server using a standard interface called
DIG
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You can set the reasoner URL from
Preferences setting
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Classifying
Classify taxonomy (and check consistency)
Compute inferred types (for individuals)
Just check consistency (for efficiency)
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Reasoning about our Pizzas
Start with pizzas2_2.owl
1. Classify your ontology
You will see an inferred hierarchy appear, which will
show any movement of classes in the hierarchy
You will also see a results window appear at the bottom
of the screen which describes the results of the reasoner
MargheritaPizza turns out to be
inconsistent why?
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Why is MargheritaPizza inconsistent?
We are asserting that a MargheritaPizza is a
subclass of two classes we have stated are disjoint
The disjoint means nothing can be a NamedPizza
and a VegetarianPizza at the same time
This means that the class of MargheritaPizzas can
never contain any individuals
The class is therefore inconsistent
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Attempting again
Start with your current ontology
1. Close the inferred hierarchy
and classification results pane
2. Remove the disjoint between VegetarianPizza and
its siblings
When prompted, choose to remove only between this class and its siblings
3. Re-Classify your ontology
This should now be accepted by the reasoner with no inconsistencies
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Asserted Polyhierarchies
We believe asserting polyhierarchies is bad
We lose some encapsulation of knowledge
Difficult to maintain
let the reasoner do it!
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Defined Classes
Have a definition. That is at least one Necessary
and Sufficient condition
Are marked in orange in the interface
Classes, all of whose individuals satisfy this
definition, can be inferred to be subclasses
Reasoners can perform this inference
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Describing a MeatyPizza
Start with pizzas2_3.owl, close the reasoner panes
1. Create a subclass of Pizza called MeatyPizza
Dont put in the disjoints or youll get the same problems as before
In general, defined classes are not disjoint
2. Add a restriction to say:
Every MeatyPizza must have at least one meat
topping
3. Classify your ontology
What happens?
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Defining a MeatyPizza
Start with pizzas2_4.owl, close the reasoner panes
1. Click and drag your hasTopping MeatTopping restriction
from Necessary to Necessary & Sufficient
The MeatyPizza class now turns orange, denoting that it is now a defined class
2. Click and drag the Pizza Superclass from Necessary to
Necessary & Sufficient
Make sure when you release you are on top of the existing restriction otherwise
you will get 2 sets of conditions.
You should have a single orange
icon on the right stretching across
both conditions like this
3. Classify your ontology
What happens?
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Reasoner Classification
The reasoner has been able to infer that anything
that is a Pizza that has at least one topping from
MeatTopping is a MeatyPizza
Therefore, classes fitting this
definition are found to be
subclasses of MeatyPizza, or are
subsumed by MeatyPizza
The inferred hierarchy is updated
to reflect this and moved classes
are highlighted in blue
Page 64
How do we Define a Vegetarian Pizza?
Nasty
Define in words?
a pizza with only vegetarian toppings?
a pizza with no meat (or fish) toppings?
a pizza that is not a MeatyPizza?
More than one way to model this
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Defining a Vegetarian Topping
Start with pizzas2_5.owl
1. Create a subclass of PizzaTopping
called VegetarianTopping
2. Click Create New Expression in the Conditions Widget
Type in or select each of the top level PizzaToppings that are not meat
or fish (ie DairyTopping, FruitTopping etc) and between each, type the
word or
the or will be translated into a union symbol
3. Press Return when finished
you have created an anonymous class described by the expression
4. Make this a defined class by moving both conditions from the
Necessary to the Necessary & Sufficient conditions
5. Classify your ontology
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Class Constructors: Union
AKA disjunction
This OR That OR TheOther
(This That TheOther)
Set theory
Commonly used for:
Covering axioms (like VegetarianTopping)
Closure
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Covering Axioms
Covered class that to which the condition is added
Covering classes those in the union expression
A covering axiom in the Necessary & Sufficient Conditions means:
the covered class cannot contain any instances from a class other than
one of the covering classes
Gender
Gender Female
Female
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Male
Male
In this example, the class Gender is covered
by Male or Female
All individuals in Gender must be individuals
from Male or Female
There are no other types of Gender
Vegetarian Pizza attempt 2
Start with pizzas2_6.owl
1. Select MargheritaPizza and remove
VegetarianPizza from its superclasses
2. Select VegetarianPizza and create a restriction to say that it
only has toppings from VegetarianTopping
3. Make this a defined class by moving all conditions from
Necessary to Necessary & Sufficient
Make sure when you release you are on top of the existing restriction otherwise
you will get 2 sets of conditions.
You should have a single orange icon on the right stretching across both
conditions
4. Classify your ontology
What happens?
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Open World Assumption
The reasoner does not have enough information to
classify pizzas under VegetarianPizza
Typically several Existential restrictions on a single
property with different fillers like primitive pizzas
Existential should be paraphrased by amongst
other things
Must state that a description is complete
We need closure for the given property
This is in the form of a Universal Restriction with a
Union of the other fillers using that property
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Closure
Example: MargheritaPizza
All MargheritaPizzas must have:
at least 1 topping from MozzarellaTopping and
at least 1 topping from TomatoTopping and
only toppings from MozzarellaTopping or TomatoTopping
The last part is paraphrased into
no other toppings
The union closes the hasTopping property on
MargheritaPizza
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Closing Pizza Descriptions
Start with pizzas2_7.owl
1. Select MargheritaPizza
2. Create a Universal Restriction on the hasTopping property
with a filler of TomatoTopping
MozzarellaTopping
Remember, you can type or to achieve this, or you can use the expression
palette
3. Close your other pizzas
Each time you need to create a filler with the union of all the classes used on the
hasTopping property (ie all the toppings used on that pizza)
4. Classify your ontology
Finally, the defined class VegetarianPizza should subsume any classes that only
have vegetarian toppings
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Summary
You should now be able to:
Use Defined Classes allow a polyhierarchy to
be computed
Classify and check consistency using a
Reasoner
Create Covering Axioms
Close Class Descriptions to cope with Open
World Reasoning
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Viewing our Hierarchy Graphically
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OWLViz Tab
View Asserted Model
View Inferred Model
Polyhierarchy
tangle
Page 75
Your Pizza Finder
Once you have a pizza ontology you are
happy with, you can plug it in to the
PizzaFinder
Instructions available on line at
Page 76
Other Exercises:
Create a ProteinLoversPizza
Start with pizzas2_8.owl
Create a new subclass of Pizza
Define this as:
Any Pizza that has at least one MeatTopping and at least
one CheeseTopping and at least one FishTopping
If you dont have any pizzas that will classify under
this, create one which should (SicilianaPizza should)
Classify to check that it works
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Other Exercises:
Define RealItalianPizza
Start with pizzas2_9.owl
Convert RealItalianPizza to a defined class
Add information to your pizzas to allow some of
them to classify under this one
Classify
remember to check your disjoint if you have problems
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Others
Show RDF/XML source code
OWLViz Tab
Protg OWL Reasoner API
http://protege.stanford.edu/plugins/owl/api/Reasoner
APIExamples.html
Ontology Development
GiftMe The Gift Recommendation System
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Thank You
Feedback on tutorial appreciated
Original of PowerPoint slides available from
- http://www.cs.man.ac.uk/~drummond/cs646
Software / resources / community at:
http://www.co-ode.org/
http://protege.stanford.edu/
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