ONTOLOGY ENGINEERING

Lab #1 - August 25, 2014

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Lab Syllabus

Lab 1 – 8/25: Introduction and Overview of Protégé

Lab 2 – 9/8: Building an ontology with RDF, RDF-S and OWL

Lab 3 – 9/15: Describing Domains with Axioms I

Lab 4 – 9/22: Describing Domain with Axioms II Lab 5 – 9/29: Lab Assignment 1 Due, RDF,

RDF-S and OWL Summary Lab 6 – 10/6: SPARQL Select Queries

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Lab Syllabus

Lab 7 – 10/13: Manipulating SPARQL Result Sets Lab 8 – 10/20: SPARQL Functions and Operators Lab 9 – 10/27: SPARQL Describe, Ask, and

Construct Queries Lab 10 – 11/3: Lab Assignment 2 Due, SPARQL

Summary Lab 11 – 11/10: Ontology Mapping Languages I Lab 12 – 11/17: Ontology Mapping Languages II Final Exam – Date to be determined

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Semantic Web Stack

Content of Labs

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Overview of Protégé

A platform for constructing ontologies in the Web Ontology Language, or OWL , that is, machine processable versions of ontologies

Developed at the Stanford Center for Biomedical Informatics Research at the Stanford University School of Medicine in collaboration with The University of Manchester

Development was supported by grant GM10331601 from the National Institute of General Medical Sciences of the United States National Institutes of Health

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Overview of Protégé

Constructs documents in a number of formats other than OWL such as OBO, KRSS2 and LaTex

Widely used, 225,000 registered users Open-source, extendable, plug-in

architecture Documentation available at:

http://protegewiki.stanford.edu/wiki/Main_Page

Other options are available: http://en.wikipedia.org/wiki/Ontology_editor

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Installing Protégé

Installing the Version 5 Beta Download the .zip from http://protegewiki.stanford.edu/wiki/Install_Protege5 Make certain you have version 7 of the Java Virtual Machine on your

computer Extract the files to a location of your choosing and run the .bat file

Installing the Version 4.3 Release - Three Options InstallAnywhere platform independent installer program

Recommended Handles identifying the correct version of the Java VM Provides an .exe file that launches Protégé

Zip file Must identify the correct version of the Java VM For users not needing an .exe file

Application Bundle File For OS X users

http://protege.stanford.edu/download/protege/4.3/installanywhere/Web_Installers/

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Setting Up Protégé

Menu item: File/Preferences New Ontologies Tab

Automatically constructs the base of the Internationalized Resource Identifier (IRI) of the ontologies created in Protégé.

Change Default Base URI to http://www.buffalo.edu/<course_id>/<email_name> where the course id is the id of the course in which you’ve enrolled (PHI 598 or CSE 510) and email name is your UB email address without the domain name)

This will now be automatically populated in the Ontology IRI field in the Active Ontology tab

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Setting Up Protégé

Menu Item: File/Preferences New Entities Tab

Builds the identifier for the elements of the ontology (Classes, Properties and Individuals)

Entity URI has an initial three components Start with: either the Active Ontology URI or a Specified URI Followed by: either #, /, or : End with: User supplied name or Auto Generated ID

Example: Choosing 1) Active Ontology URI, 2) “/”, and 3) User supplied name results in the following for a class with a supplied name of “LandVehicle”:

http://www.buffalo.edu/<course_id>/<email>/<ontology_name>/LandVehicle

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Setting Up Protégé

Menu Item: File/Preferences New Entities Tab

Choosing the End with: option of Auto Generated ID results in needing to make some additional choices

Entity Label: used to store a human-readable name The Same as label renderer option will result in using the rdfs:label annotation

property The Custom label option allows you to choose among other options of

annotation properties (including ones you create) and the language in which they’ll be stored

Auto Generated ID: creates the rule for generating the ID Numeric can include a Prefix, Suffix, Digit Count, Start Number, and End

Number Globally Unique generates a GUID (e.g.

f5f7f6d6_cc18_486c_8b6a_18c9b3205285)

Example: Choosing 1) Active Ontology, 2) “/”, 3) Auto Generated ID, 4) Numeric, 5) Prefix = “OEF14_”, 6) Digit Count = 7 and 7) Start = 101 results in the URI of: http://www.buffalo.edu<course_id>/<email>/<ontology_name>/

OEF14_0000101

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Setting Up Protégé

Menu Item: File/Preferences Renderer Tab

Entity Rendering: Four choices are available (also available under the View menu)

Render by name (rdf:id) – this will be the URI that you’ve created for the entity Render by qualified name – this will be the full name of the entity including all

three pieces of the URI Render by annotation property (e.g. rdfs:label, skos:prefLabel) – this will be the

entity label (most likely the rdfs:label property) Render by prefixed annotation property – this will be and annotation property of

your choosing If your annotation property stores a value with an associated language (e.g.

“en”) then it will not render unless that language is specified in the configure window.

If you specify a language in the configure window, then only those annotation property instances that have that language associate will render

Enter the required language code(s) and a value of “!” to solve the problem (e.g. en, en-US, !)

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Navigating Protégé

The color coding of window frames and the entities they contain is helpful for orientation Purple – ontologies Harvest Gold – classes Blue – object properties Green – datatype properties Red - Individuals

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Navigating Protégé

Frame Views Have headers that are updated with the selection in the

hierarchy changes Broken into subsections Entries with a + button can be edited

Three standard operations: annotate, delete and edit Hovering help

Shows where a statement was asserted Context menu is made visible by right clicking on a

highlighted statement and has three main options Switch: makes the ontology that contains the assertion the active

ontology Pull: moves the assertion into the current active ontology Move: moves the assertion into a specified ontology

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Navigating Protégé

Hierarchy Views Selection of an item in a hierarchy updates other

views Arrow keys

Up and Down arrow keys ascend or descend a branch Right and Left arrow keys open or close a branch

Drag and Drop is supported Push Buttons perform three standard operations

Add a child entity Add a sibling entity Delete an entity

Hovering Help displays the qualified name (no context menu is available)

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Navigating Protégé

Frames can be split horizontally, vertically, floated or deleted

Tabs can be added or removed using the Window/Tab menu item.

Views can be added using the Window/View menu item Can be added as an additional tab within a view or as

a distinct view to the left, right, top, or bottom of existing views.

A tab can be returned to its original state by selecting the Window/Reset selected tab to default state menu item

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Navigating Protégé

Opening Ontologies – 4 options New Open Open from URL Open recent

Importing Ontologies – 4 options Import an ontology contained in a specific file Import an ontology contained in a document located on

the web Import an ontology that is already loaded in the

workspace Import an ontology that is contained in one of the

ontology libraries

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Assignment

Read Sections 1 – 3.2 of the Highway Functional Classification Concepts, Criteria and Procedures 2013 Edition (available at: http://www.fhwa.dot.gov/planning/processes/statewide/related/highway_functional_classifications/fcauab.pdf)

Represent the Federal Functional Classification Decision Tree (p. 18) as a taxonomy in Protégé.

Represent the travel characteristics in Table 2.1 (p. 11) as a taxonomy in Protégé.