Ontology Engineering Ron Rudnicki Lab #1 - August 26, 2013

Overview of Protégé  A platform for constructing ontology documents, 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 GM from the National Institute of General Medical Sciences of the United States National Institutes of Health 2

Overview of Protégé  Constructs documents in a number of formats of the Web Ontology Language (OWL) and a few other languages as well (OBO, KRSS2 and LaTex)  Widely used, 225,000 registered users  Open-source, extendable, plug-in architecture  Other options are available: 3

Installing Protégé Version 4.3  Three Options  InstallAnywhere platform independent installer program  Recommended  Handles identifying the correct version (1.6) 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  nywhere/Web_Installers/ 4

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 / where the course id is the id of the course in which you’ve enrolled (PHI 598 or IE500) and name is your UB address without the domain name) /< _name  This will now be automatically populated in the Ontology IRI field in the Active Ontology tab 5

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”:  / / /LandVehic le 6

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_18c9b )  Example: Choosing 1) Active Ontology, 2) “/”, 3) Auto Generated ID, 4) Numeric, 5) Prefix = “OEF13_”, 6) Digit Count = 7 and 7) Start = 101 results in the URI of:  / / /OEF13_

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, !) 8

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 9

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 10

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) 11

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 12

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 13

Versioning Ontologies  A World Wide Web Consortium (W3C) Recommendation  Every ontology may have an Ontology IRI (O-IRI)  If an ontology has an O-IRI, then it may also have a version IRI (V-IRI)  The O-IRI and V-IRI may be the same, but if an ontology does not have an O-IRI it must not contain a V-IRI 14

Versioning Ontologies  Uniqueness requirements:  If Ontology1 has an O-IRI but not a V-IRI, then no other ontology can have the same O-IRI but not a V-IRI  If Ontology 1 has both an O-IRI and a V-IRI, then no other ontology can have the same O-IRI and V-IRI  No other combinations of O-IRI and V-IRI are required to be unique  Two different ontologies may have neither an O-IRI nor a V-IRI  An ontology with an O-IRI but no V-IRI may coexist with another ontology having the same O-IRI but a V-IRI 15

Readings 16  OWL 2 Web Ontology Language Structural Specification and Functional Style Syntax – Sections 3.1 through 3.3 (  Accepted OBO Foundry Principles ( epted)

Websites 17  NCBO Bioportal (  ChEBI (  ThomasNet (  Schema.org (  NIST Manufacturing Ontologies Portal (  NASA Sweet Ontologies (