Alasdair J G Gray

Connecting the dots in the World's data

Basic OWL Lab Session

In this OWL lab you will get started using Protégé to create and edit an ontology.

Remember to regularly save your work as you go through by clicking ‘File -> Save’

Starting Protégé

Local Installation

If you have installed your own copy of Protégé then you should start this up in the usual way for your platform.

MACS Lab/VM Installation

To open Protégé on the MACS Linux machines or VM follow these steps:

  1. Click on the ‘Applications’ menu in the top left
  2. Choose protege from within the Programming menu
  3. Click ‘Not Now’ from the plugins popup menu once Protégé has started

Opening Shell Ontology

I have created a shell ontology which contains basic metadata that all ontologies should provide as a minimum. We are going to use this as a starting point for the Lab.

  1. Select ‘File -> Open from URL…’
  2. Enter the URL for the ontology https://alasdairgray.github.io/ns/ontology-start.owl
  3. Save the ontology to your local disk
    1. ‘File -> Save’
    2. Select ‘Turtle Syntax’
    3. Give the ontology a suitable filename
    4. Choose where to save the file and click ‘Save’

Your ontology should look something like the following screenshot.

shell-ontology

Updating the Ontology Metadata

To edit a metadata element, click on the circle icon and type in the new value. Do this for the following elements:

  • dcterms:creator where the value is Alasdair Gray; put your own name in
  • dcterms:description replace with your own description text
  • dcterms:title replace with your own ontology title

To remove a metadata element, click on the x in a circle next to the element. Do this for the creator element that has a URL.

Creating our first Classes

We will now create some classes to represent people and courses within a university.

  1. Click on the ‘Entities’ tab

  2. Click on owl:Thing; all classes must be defined below this most general class

  3. Click on the icon containing two yellow balls with a + sign create-subclass

  4. Type in the name of the class that we are creating Course Note: for the ease of discussion we will use labels as names. In real-world scenarios it is considered best practice to use opaque identifiers.

  5. Now create a sibling class to Course called Person ; you can do this same way as for the Course class or use the add sibling class option.

  6. Now let’s declare Course and Person to be disjoint since no individual could be both an instance of both of them.

    1. In one of the classes, click on the + icon next to the text Disjoint With
    2. In the popup window, browse through the class hierarchy and choose the class that you are declaring to be disjoint with

Running the Reasoner

We will now run the reasoner to ensure that our ontology is consistent. It is good practice to regularly check your ontology for consistency.

  1. Click on the ‘Reasoner’ menu item
  2. Select ‘HermiT’
  3. Click on the ‘Reasoner’ menu item
  4. Select ‘Start reasoner’

Creating some Individuals

We will now create some individuals for our ontology.

  1. Click on the ‘Individuals’ tab within the ‘Entities’ tab
  2. Click on the purple diamond icon create-individual
  3. Create an individual called alice by typing ‘alice’ into the popup and clicking OK
  4. Declare alice to be of type Person by clicking on the + icon next to Types and then choosing Person from the ‘Class hierarchy’
  5. Create the individual f20bd to be of type Course

Deliberate Inconsistency

We are now going to create a deliberate inconsistency so that we understand when the reasoner is informing us of a problem.

  1. Select alice from the individuals that you created
  2. Click on the + icon next to Types and state that alice is of type Course
  3. Synchronise the reasoner by going to the ‘Reasoner’ menu and selecting ‘Synchronize reasoner’

You should now see the following screenshot

reasoner-error

Click on the ‘Explain’ button to get an indication of what axioms in the ontology have led to the inconsistency. The explanation shown in the following screenshot states that Course and Person are disjoint and that alice has been declared to be of type both of them.

reasoner-explanation

Click OK and then fix the ontology by removing the declaration that alice is of type Course.

Note that Protégé has highlighted in red the two axioms that led to the contradiction.

Once you have performed your fix, synchronise the reasoner.

Creating Multiple Children Classes

We are now going to create multiple children to be subclasses of Person. These classes will be for staff and students and their sub classes. We will not declare them to be disjoint since it is permissible for staff members to be students.

  1. Click on the ‘Classes’ tab within the ‘Entities’ tab

  2. Choose the Person class

  3. Click on the ‘Tools’ menu and select ‘Create class hierarchy…’

  4. Within the resulting popup enter the class names; each on their own line with indentation to capture the desired hierarchy.

    Staff
	Academic
	Administrative
Student
	Undergraduate
	Postgraduate

    Note: you can use the prefix and suffix options at the bottom of the popup to give all your classes the same start or end.

  5. Uncheck the checkbox for making siblings disjoint since a student could be a staff member

  6. Click ‘Finish’

You should now see the classes in the class hierarchy

class-hierarchy

Bad habits come easily

Unfortunately, Protégé does not encourage best practice. In this case, I mean that we have not defined any of our classes by annotating them with labels and descriptions; the class identifiers we have been using do not count as labels and should not be relied upon to define the entity.

  1. Select the Staff class
  2. Click on the + icon next to ‘Annotations’
  3. Select rdfs:label and enter the text Staff member in the box at the side
  4. Select en from the ‘Lang’ dropdown item and click OK
  5. Click on the + icon again
  6. Select rdfs:comment and enter the text A person who works at the university.
  7. Again select en from the ‘Lang’ dropdown and click OK.

annotated-class

Now annotate all the other classes.

Creating Object Properties

Now that we have some classes, we want to be able to relate them. We will create relationships between academics, courses, and students.

In line with good practice, we will assume that you are annotating the properties with labels and descriptions. The instructions here will focus on the creation of the object properties.

We will create multiple object properties at the same time. Again, you can have a hierarchy of properties, although this is not as common.

  1. Click on the ‘Object properties’ tab

  2. Select the owl:topObjectProperty property

  3. Click on the ‘Tools’ menu item and select ‘Create object property hierarchy…’

  4. Enter the following properties into the popup window

    teaches
taughtBy
studies
hasStudent

    Note that I have not been consistent in the way I’m calling my properties. This is to show you different styles. Instead of taughtBy it would be better to use hasTeacher.

  5. Do not make the properties disjoint

object-property-hierarchy

Now provide labels and definitions for each of the properties.

Defining Characteristics of our Object Properties

We will only define domain, range, and inverse property definitions for the properties that we created since non of the other characteristics hold for these properties.

  1. Click on the studies property
  2. Click on the + icon next to ‘Inverse Of’
  3. In the list of properties, select hasStudent and click OK
  4. If you click on hasStudent you will see that it now has studies as an inverse property
  5. Go back to studies and click on the + icon next to Domains
  6. Select Student from the class hierarchy
  7. Now click on the + icon next to Ranges and select Course from the class hierarchy

Now repeat this for the other properties. Courses should be taught by an academic.

Defining Data Properties

This is done in the same way as for Object Properties.

Create a data property hasName that gives the name of a Person, i.e. its domain is Person.

Create a data property courseTitle that gives the title of a Course.

Exploiting the Reasoner

We are now going to declare the :alice :studies :f21bd.

  1. Create the individual :f21bd but do not declare it to be of any type.
  2. Select :alice and click on the + icon next to ‘Object property assertions’
  3. Enter studies and f21bd into the respective boxes and click OK

Now synchronise the reasoner and see what it has inferred for :alice and :f21bd. They should both have types highlighted in yellow.

About Me

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I'm an Associate Professor in Computer Science at Heriot-Watt University. My research focuses on linking datasets. Read more

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