1. ONTOLOGY ENGINEERING Lab #1 - August 25, 2014

2. Lab Syllabus 2  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

3. Lab Syllabus 3  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

4. Semantic Web Stack 4 Content of Labs

5. Overview of Protégé 5  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

6. Overview of Protégé 6  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

7. Installing Protégé 7  Installing the Version 5 Beta  Download the.zip from http://protegewiki.stanford.edu/wiki/Install_Protege5http://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_Installe rs/ http://protege.stanford.edu/download/protege/4.3/installanywhere/Web_Installe rs/

8. Setting Up Protégé 8  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/ / 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) http://www.buffalo.edu/ /<email_name This will now be automatically populated in the Ontology IRI field in the Active Ontology tab

9. Setting Up Protégé 9  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/ / / /LandVehicle

10. Setting Up Protégé 10  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 / / /OEF14_0 000101

11. Setting Up Protégé 11  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, !)

12. Navigating Protégé 12  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

13. Navigating Protégé 13  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

14. Navigating Protégé 14  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)

15. Navigating Protégé 15  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

16. Navigating Protégé 16  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

17. Assignment 17  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/state wide/related/highway_functional_classifications/fc auab.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.