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Ontology Engineering Ron Rudnicki Lab #1 - August 26, 2013
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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 2
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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 3
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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/installa nywhere/Web_Installers/ 4
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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/ / 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) http://www.buffalo.edu/ /<email_name This will now be automatically populated in the Ontology IRI field in the Active Ontology tab 5
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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/ / / /LandVehic le 6
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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 = “OEF13_”, 6) Digit Count = 7 and 7) Start = 101 results in the URI of: http://www.buffalo.edu / / /OEF13_0000101 7
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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, !) 8
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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 9
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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 10
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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) 11
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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 12
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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 13
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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
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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
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Readings 16 OWL 2 Web Ontology Language Structural Specification and Functional Style Syntax – Sections 3.1 through 3.3 (http://www.w3.org/TR/owl2-syntax/)http://www.w3.org/TR/owl2-syntax/ Accepted OBO Foundry Principles (http://www.obofoundry.org/wiki/index.php/Category:Acc epted)
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Websites 17 NCBO Bioportal (http://bioportal.bioontology.org/)http://bioportal.bioontology.org/ ChEBI (http://www.ebi.ac.uk/chebi/)http://www.ebi.ac.uk/chebi/ ThomasNet (http://www.thomasnet.com/browse)http://www.thomasnet.com/browse Schema.org (http://schema.org/)http://schema.org/ NIST Manufacturing Ontologies Portal (http://www.nist.gov/manufacturing-ontologies-portal.cfm)http://www.nist.gov/manufacturing-ontologies-portal.cfm NASA Sweet Ontologies (http://sweet.jpl.nasa.gov/ontology/)http://sweet.jpl.nasa.gov/ontology/
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