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Ontology Engineering

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

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Ontology Engineering

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  1. Ontology Engineering Ron RudnickiLab #1 - August 26, 2013

  2. 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 GM10331601 from the National Institute of General Medical Sciences of the United States National Institutes of Health

  3. 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: http://en.wikipedia.org/wiki/Ontology_editor

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

  5. 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 IE500) 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

  6. 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

  7. 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 = “OEF13_”, 6) Digit Count = 7 and 7) Start = 101 results in the URI of: • http://www.buffalo.edu<course_id>/<email>/<ontology_name>/OEF13_0000101

  8. 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, !)

  9. 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

  10. 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

  11. 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)

  12. 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

  13. 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

  14. 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

  15. 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

  16. Readings • OWL 2 Web Ontology Language Structural Specification and Functional Style Syntax – Sections 3.1 through 3.3 (http://www.w3.org/TR/owl2-syntax/) • Accepted OBO Foundry Principles (http://www.obofoundry.org/wiki/index.php/Category:Accepted)

  17. Websites • NCBO Bioportal (http://bioportal.bioontology.org/) • ChEBI (http://www.ebi.ac.uk/chebi/) • ThomasNet (http://www.thomasnet.com/browse) • Schema.org (http://schema.org/) • NIST Manufacturing Ontologies Portal (http://www.nist.gov/manufacturing-ontologies-portal.cfm) • NASA Sweet Ontologies (http://sweet.jpl.nasa.gov/ontology/)

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