Protégé training
Gary Polhill
Craigiebuckler, Aberdeen, AB15 8QH, UK
Overview
• Obtaining, installing & community
• Creating and loading ontologies
• Creating classes, properties,
restrictions & individuals
• Using the reasoner
• Diagramming
Overview
• Obtaining, installing & community
• Creating and loading ontologies
• Creating classes, properties,
restrictions & individuals
• Using the reasoner
• Diagramming
Obtaining
• Protégé [Ontology development tool]
– http://protege.stanford.edu/download/download.html
– Version 3.1 beta
• Graphviz [Diagram support tool]
– http://www.graphviz.org/Download.php
– Version 2.2.1
• Racer [DL reasoner]
–
http://www.racer-systems.com/products/download/education.phtml
– Version 1-8-0
– Version 1-7-24?
Licences (Protégé and Graphviz)
• Protégé
– Mozilla Public Licence
• http://www.mozilla.org/MPL/
– You are licensed to “use, reproduce, modify,
display, perform, sublicense, and distribute” it
• Graphviz
– Common Public Licence
• http://www.graphviz.org/Download.php
– You are licensed to “reproduce, prepare
derivative works of, publicly display, publicly
perform, distribute and sublicense” it
Racer licence
• Racer 1-8-0
– Educational proprietary licence
•
http://www.racer-systems.com/products/download/edu-license.phtml
– Requires registration
– Install and use one copy on one computer
– Limited time (180 days, possibly negotiable…)
• 990EUR cost for single workstation non-network licence
– In publications for which Racer is used, name:
• RacerPro Software
• Racer Systems GmbH & Co. KG -- licensor
• http://www.racer-systems.com/ -- licensor website
• Racer 1-7-24
– Not available any more, and not supported
– Non-commercial licence
Possible alternative to Racer: FaCT
• FaCT
– http://www.cs.man.ac.uk/~horrocks/FaCT/
•
•
•
•
Released under GNU GPL
Lisp based
Description logic reasoner for SHF & SHIQ
Requires Tomcat to talk to Protégé
– Use FaCT DIG Servlet version
• Doesn’t talk to Protégé very well!
– Some loss of functionality
Installation of Protégé
• Run the install_protege.exe script
• Follow the installation wizard
• Accept all default options, except:
Basic+OWL
might be OK
(not tested)
Choose
Components
Everything
Installation of Graphviz & Racer
• Graphviz
– Run graphviz-2.2.1.exe
– Accept all the default options
– Never need to run it
• Racer 1.7.24
– Doesn’t really need installing…
– Extract the executable from the zip file
• racer-1-7-24-windows.zip
– Copy it to the Desktop
• … or somewhere you will remember
– Run it when you need it
Racer: Exercise
• Check that you can run Racer
– Copy it from the CD to the computer
• You need to have write permission to the folder that Racer lives in
– Double click it to run
Exit by
closing the
window
Port number for
HTTP service
Running Protégé
• Start > Programs > Protege_3.1_beta
> Protege
• Command tool interface opens with
diagnostic messages
• GUI opens with utility to open recent
projects or create a new one
Protégé community
• Various mailing lists
– http://protege.stanford.edu/community/lists.html
– protege.discussion/general
• High volume, for general Protégé usage queries, not OWL
– protege.owl
• High volume, for OWL specific Protégé usage queries
– protege.beta
• Low volume, announces new beta releases of Protégé
– protege.users/announce
• Low volume, announces new full releases and
conferences, etc.
Overview
• Obtaining, installing & community
• Creating and loading ontologies
• Creating classes, properties,
restrictions & individuals
• Using the reasoner
• Diagramming
Create a new project wizard
Create from existing sources
1
3
OWL Files
OWL DL
2
4
Project components
• A Protégé project has two parts
– Project file (with .pprj suffix)
• Contains details about the settings for the use of
Protégé
• Can be version specific (i.e. a .pprj file for version 3.1
may not open in version 3.0 and vice versa)
– OWL file (with .owl suffix)
• The ontology
• You can create a Protégé project from an
existing OWL file by checking the ‘Create
from existing sources’ box in step 1
Loading an ontology
• Select recently used projects from
window at startup
• File > Open Project…
• File > Open Recent Project > project
• If you tell Windows that .pprj files
belong to Protégé
– Double click the .pprj file from Explorer
Protégé: Exercise
• Start Protégé
• Create a new project
– Not from an existing source
– OWL Files
– Don’t import any ontologies
– Default namespace
– OWL-DL
Overview
• Obtaining, installing & community
• Creating and loading ontologies
• Creating classes, properties,
restrictions & individuals
• Using the reasoner
• Diagramming
Working in Protégé
• Creating anything is called an
assertion
• Think of it as creating some axioms
• You need to be clear about what each
kind of assertion means
Creating classes
Create
Sibling
Class of…
Create
Subclass of…
…selected
class
Tools > Quick OWL >
Create multiple classes
(Wizard)
Classes tab
Comment
Class name
Metadata
Properties
Hierarchy
Conditions
Disjoints
Classes: Naming Conventions
• No mandatory conventions…
• Class names begin with uppercase
• Separate words in class names using
CamelStyle or Using_Underscores
• Regexp for ASCII characters
– [A-Za-z£$_][-A-Za-z0-9£$_.]*
• Unicode characters can also be used
– Edit > Insert Unicode Characters…
– Protégé’s default font doesn’t have very many
Classes: Meanings
• Individuals can belong to many classes
• Classes can have many superclasses
• Classes are not assumed to be disjoint
– You can make them disjoint
A
B
– By doing so you assert that
• No individuals belong to classes A and B
• Subclass means necessary implication
– If A and B are classes, and A is a subclass of B you
assert that
A B
C
• All individuals belonging to A belong to B
• (…and all individuals not belonging to B don’t belong to A)
• Note that if B is disjoint with C, then no individual
belonging to A can belong to C.
Classes: Exercise
• Create the following class hierarchy
– Man & Woman should be disjoint
Different kinds of property
• Datatype property
– String, Integer, etc.
• Object property
– Relates one class of objects (domain) to
another (range)
• Annotation property
– For different kinds of metadata
– Can be object or datatype!
Creating Properties
Properties tab
Datatype property
Object property
Subproperty
Annotation datatype
and object properties
Properties tab (object properties)
Name
Comment
Metadata
Property
hierarchy
Property
Characteristics
Multiple
superproperties
Inverse
Domain
Range
Properties tab (datatype property)
• As per object,
except…
Range is a datatype
Datatype properties
can’t be symmetric,
transitive, or have an
inverse
You can specify a
set of values the
property can take
Creating properties from the Classes tab
Create new
datatype property
(domain this class)
Create new
object property
(domain this class)
Add this class to
domain of existing
property
Properties: Naming Conventions
• Again, no strict naming conventions
• Lower case initial letter
• Begin with ‘has’ or ‘is’
– Facilitates English Prose Tooltip Generator (see later)
– … but not worth it if too awkward
• Same ASCII regexp as Classes
• If different classes have a similar property name
(e.g. age)
– Use class domain in property name if a union domain is
not appropriate
• E.g. if range is a different type
• hasPersonAge (10, 34, 57), hasHistoryAge (Victorian)
Properties: Meanings 1
• Domain & Range
– Be careful…
• These do not stipulate restrictions!
• Any individual asserted or inferred to be on the ‘left hand side’ of
the property will be inferred to be a member of the domain class
• Any individual asserted or inferred to be on the ‘right hand side’ of
the property will be inferred to be a member of the range class
– Multiple classes for the domain and range are interpreted to be
a union class
– OWL class expressions can be used for the range of a property
(e.g. intersection of two classes)
– OWL allows this for domains, too, but not in Protégé
• Subproperty
– If property P is a subproperty of Q, and P(x, y) is asserted or
inferred, then Q(x, y) may be asserted or inferred
– Datatype properties may not be subproperties of object
properties, and vice versa
Properties: Meanings 2
• Property Characteristics
– Inverse
• If P is the inverse of Q and P(x, y), then Q(x, y)
– Symmetric
• If P is symmetric and P(x, y), then P(y, x)
– Transitive
• If P is transitive and P(x, y) and P(y, z) then P(x, z)
• A transitive property must have a transitive inverse
– Functional
•
•
•
•
Aka feature or single valued property
The right hand side may only be one individual
If more than one individual is found they are inferred to be the same
A transitive property cannot be functional
– Inverse functional
• The left hand side may only be one individual
• If more than one individual is found they are inferred to be the same
• An inverse functional property has a functional inverse (and vice versa)
Other information about Properties
• Annotation properties
– Metadata
– Can be applied to Classes, Properties (datatype or
object), and Individuals
– Restrictions in OWL-DL
• Property value must be a literal, URI, or individual
• Cannot be used in property axioms (e.g. cannot be
subproperty or have a subproperty)
• Cannot have a domain or range
• Classes as property range
– Not possible in OWL-DL – OWL-Full only
– A rare requirement
Properties: Exercise
• Create datatype properties
– hasAge (integer)
– hasSex (“Male” or “Female”)
• Create object properties
– hasAncestor, hasParent, hasMother, hasFather
– isAncestorOf, isParentOf, isMotherOf, isFatherOf
– hasSpouse, hasHusband, hasWife
• Ensure property characteristics are appropriately set
–
–
–
–
Domain and range
Subproperty
Inverse
Transitive, Symmetric, Functional, Inverse Functional
Creating Restrictions
Create
restriction
on any
property
Create
expression
Select
property and
create
restriction
Right click
property and
select
restriction to
create
Create Restriction Window
Property to be
restricted
Restriction
expression
tool
Type of
restriction
Restriction
expression
Keep this
guy happy!
Different kinds of restriction
• Quantifier restriction (Object property)
– Existential
• “At least one” “some” “some values from”
• e.g. (Husband class) ∃ hasWife Woman
– Universal
• “Only” “all values from”
• e.g. (Person class) ∀ hasFather Man
• hasValue restriction (Datatype property)
– e.g. (Man class) hasSex ∋ “Male”
• Cardinality restriction (Object property)
– Exact cardinality
– Minimum cardinality
– Maximum cardinality
Other kinds of restriction
• Union classes
– e.g. hasDifficultChildren (Toddler ⊔ Teenager)
• Intersection classes
– e.g. hasSingleParent (Parent ⊓ Divorcee)
• Negation
– e.g. Bachelor class: ¬(∃ hasWife Woman)
• Expressions can have arbitrary complexity
– … but probably a good idea to keep it simple
• Use intermediate classes
Restrictions: Meanings 1
• A restriction actually defines an anonymous class
– When used to describe classes, they define an anonymous
superclass
• Existential restrictions
– Beware the Open World Assumption!
• Only says that at least one of the relationships an individual has is
with a member of the specified class …
• … so the individual could have that relationship also with a
member of a different class
• Universal restrictions
– Beware!
• Only says that all relationships an individual has must be with
members of the specific class …
• … includes individuals who have NO relationship of this kind with
ANY individual
– Often used with existential restrictions (closure axiom)
Restrictions: Meanings 2
• hasValue restrictions
– Can be used with object properties to point to a specific
individual
• e.g. hasAncestor ∋ Adam
• OWL-Full?
• Cardinality restrictions
– Pertain to the number of relationships an individual
must participate in
– Relies on counting distinct individuals
• OWL does not make the Unique Name Assumption
• … but Racer does!
– Potentially, individuals will be inferred to be the same
Restrictions: Exercise
• Man and Woman Classes
– hasSex ∋ “Male”, hasSex ∋ “Female” respectively
• Spouse class
– Has at least one spouse
• Parent class
– Is parent of at least one person
• Father class
– Is father of at least one person
• Husband class
– Has wife at least one woman
• Similarly for Mother and Wife classes
• Try out the English Prose Tooltip Generator
– Move the mouse over one of the classes you have given
restrictions to in the class hierarchy
Primitive and Defined Classes
• Primitive classes (aka partial classes)
– Have necessary conditions only
• If an individual is a member of the class it must
satisfy these conditions
• NOT if an individual satisfies these conditions then it
is a member of the class
– Necessary conditions are conjunctive
• Defined classes (aka complete classes)
– Also have necessary and sufficient conditions
• These allow class membership to be inferred
– Multiple sets of necessary and sufficient
conditions are permitted (disjunctive)
Creating Defined Classes 1
Right-click
the class to
be defined
Select
“Convert to
defined
class”
Necessary
conditions
moved to
Necessary
and Sufficient
slot
Creating Defined Classes 2
Right click
• You can also click and
drag necessary
conditions to the
necessary and
sufficient slot
• Create multiple
necessary and
sufficient conditions
by right-clicking the
“NECESSARY &
SUFFICIENT” slot
header
Create new necessary
and sufficient block
Defined classes: Exercise
• Decide which classes created so far
can be converted to defined classes
• Convert them
Creating Individuals
• Forms tab
– Allows you to edit the form widgets used to
enter the individuals’ data
• Individuals tab
– Used to enter the data
– Select the class on to create an individual of
from the hierarchy on the left hand pane
– Press the create individual icon (purple
diamond with a plus sign) from the centre pane
– Enter the individual’s data on the right hand
pane
Creating individuals
Click here
Enter details
Select class
Individuals: Exercise
• Experiment with the Person entry form
• Create some instances of Person
– Try creating instances that will test the
inference engine: e.g.
• Domain and range
• Functional properties
• Create an instance of OWL: Thing
– Useful to check what happens to it when using
reasoner
Overview
• Obtaining, installing & community
• Creating and loading ontologies
• Creating classes, properties,
restrictions & individuals
• Using the reasoner
• Diagramming
Three uses for the reasoner
• Checking the consistency of the ontology
• Classifying the taxonomy
– Uses defined classes to determine new class
hierarchy
• Logically consistent with ontology
• Classifying individuals
– Deciding which classes individuals belong to
• ONE enhancement request…
–WHY?
Reasoner prerequisites
• OWL-DL or OWL-Lite sublanguage
• Racer needs to be in a writable directory
• Port numbers configured correctly
– Watch out for clashes with other software (unlikely)
– Racer can be configured to use different ports on the command
line
• -p <TCP port>
• -http <HTTP port>
– This is the one Protégé needs to know about
• The reasoner does not have to be on the same machine
– Can connect to one over the web
• The reasoner needs to be running!
– Double-click racer.exe to start Racer
Determining OWL sublanguage
OWL menu
Determine/Convert
OWL Sublanguage…
OWL Full cannot be
used with the
reasoner (decidability
not guaranteed), but
is more expressive
Checking reasoner port number 1
OWL menu
Preferences…
Checking reasoner port number 2
Address:port where Protégé
expects to find the reasoner
Address:port where Racer
expects to talk to Protege
Checking consistency
Check consistency…
also under OWL menu
Click here
Checking consistency: result
Husband and Wife are
inconsistent in this
ontology when Spouse
is disjoint from Woman
If no inconsistent
concepts are found, then
your ontology is OK
Checking the consistency of one class
Right-click
the class
Select Check
concept
consistency…
from the menu
Protégé built-in ontology checks
Click here (bug icon)
• Run ontology
tests… is also an
option in the OWL
menu
• See Test settings…
under OWL menu
to choose the tests
to run
• Does not require
reasoner
Classifying the
taxonomy
Click here
(also available
under OWL menu)
Inferred
hierarchy
(changes
in blue)
Asserted
hierarchy
Summary
of results
Inferred
conditions
tab
Classifying individuals
Membership
of each class
viewable next
to each class
as (asserted /
inferred)
Click here
(also under
OWL menu)
Inferred class
members tab
Finding members of a single class
Right-click
the class
Select
“Compute
individuals
belonging
to class…”
Results
returned in
pop-up
window
Reasoner: Exercise
• Try the following
–
–
–
–
Check consistency
Check consistency of a single class
Classify taxonomy
Run ontology tests
• Remember this doesn’t require the reasoner
– Classify individuals
– Find members of a class
• Are the results as you expect?
– What changes would you make to your
ontology?
Overview
• Obtaining, installing & community
• Creating and loading ontologies
• Creating classes, properties,
restrictions & individuals
• Using the reasoner
• Diagramming
Diagramming
• Protégé has plug-ins
– Diagramming tools are instances of this
– Details of plug-ins stored in .pprj file
– You tell Protégé which plug-ins to use by configuring
your project
• OWLViz and Ontoviz are diagramming plug-ins
– Require graphviz (from graphviz.org)
– If a project using either is loaded into Protégé without
graphviz installed, then you get error messages
• These can be ignored…
• … but be aware when passing .pprj and .owl files on to
others
Adding tabs for diagramming 1
Project > Configure …
Adding tabs for diagramming 2
Tab Widgets tab
Click the check boxes
for OWLViz and Ontoviz
OWLViz tab
• Lets you view and interact with the asserted and
inferred class hierarchies
Export to
Show or hide
image
classes
Click on
a class…
Diagram
asserted
or inferred
model
…Disjoint
classes
shown
with ¬
Ontoviz tab
• Diagram classes and relationships
• Select classes
• Click the add
classes icon
• Choose diagram
components
• Click the “Op”
icon for options
– Including save
image to file
• Saved in
project working
directory
• Click the draw
icon
Ontoviz tab diagram components
• sub: sub-classes
– Includes anonymous classes
• Which aren’t shown very nicely (font limitations?)
•
•
•
•
sup: super-classes
slx: no idea!
isx: no idea!
slt: give a table of the class’s properties
– Limited number of rows by default
• Can be changed in the options
• sle: draw relationships between classes
• ins: show instances
– Asserted instances only
• sys: system classes?
Diagramming individuals with Ontoviz
• Select the class you
want individuals
diagrammed
• Click the I+ icon to get
the instance browser
(right)
• Select the instances
• Click add
• Then select
diagramming options
as for classes
Diagramming individuals: result
Query view
Right-click an instance
Select “Show in
Query View”
Result of query view
• Allows you to
explore
relationships
between
individuals
Diagramming: Exercise
• Create an inferred class hierarchy diagram
using OWLViz and save it to a file
• Create a diagram of some of the classes in
your ontology and relationships between
them
• Create a diagram of individuals in your
ontology
• Have a go with query view
Summary
Ground covered
•
•
•
•
Installing Protégé and associated software
Running Protégé and Racer
Creating a new ontology
Creating classes, properties, restrictions and
instances
– What each of these mean!
• Using the reasoner
– Check consistency, classify taxonomy & individuals
• Diagramming tools
• Should suffice for Grampian & Odra ontologies
Other things to look at
• Version control
– See under Project menu
• Dublin Core metadata
– Contains various annotation properties
• e.g. creator, etc.
– Widely used
• See metadata tab and new project creation wizard
– Should we have an ‘evidence’ metadatum in the CAVES
project?
• Importing ontologies
– Searching for ontologies
• Swoogle: http://swoogle.umbc.edu/index.php
• Publishing ontologies and defining namespaces
• Protégé OWL Pizza Tutorial
– On the CD
Final exercise/homework
• Choose some of the following classes of people to define
–
–
–
–
–
–
–
–
–
–
–
YAPPIE: Young Affluent Parent
OINK: One Income No Kids
DINKY: Dual Income No Kids Yet
DUMP: Destitute Unemployed Mature Person
SITCOM: Single Income, Two Kids, Outrageous Mortgage
SINK: Single, Independent, No Kids
KIPPERS: Kids in Parents’ Pockets Eroding Retirement Savings
SILKY: Single Income Loads of Kids
WOOPIE: Well Off Older Person
SKIPPIE: School Kid with Income and Purchasing Power
TIREDS: Thirtysomething Radical Educated Dropout
• You may need to add supporting classes to your ontology…