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CSCE 790 - Ontology Development Lecture 1 - Overview CSCE 790C June 3, 2013 Parmenides

CSCE 790 - Ontology Development Lecture 1 - Overview CSCE 790C June 3, 2013 Parmenides

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CSCE 790 - Ontology DevelopmentLecture 1 - Overview

CSCE 790C June 3, 2013

ParmenidesOutline- CSCE 790C 2013 -Slide - 2 - ProtegePragmaticsAssignments, Papers, and Projects instead of examsOntologiesmedical ontologies, UML, Snowmed, Gene ontologyWordnet, Framenet, Verbnet, SUMOTools: protg, reasoners pellet, fact++, Ontology Languages: RDF, OWL, OWL-lite, OWL 2.0Reasoning about ontologies: consistencyReasoning with OntologiesSemi-automatic constructionSchedule ?- CSCE 790C 2013 -Slide - 3 - ProtegeOntology who owns the term?- CSCE 790C 2013 -Slide - 4 - ProtegeOntology is the philosophical study of the nature of being, becoming, existence, or reality, as well as the basic categories of being and their relations.Traditionally listed as a part of the major branch of philosophy known as metaphysics, (Parmenides)ontology deals with questions concerning what entities exist or can be said to exist, and how such entities can be grouped, related within a hierarchy, and subdivided according to similarities and differences.ontology versus ontology information sciencehttp://en.wikipedia.org/wiki/OntologyOntological Engineering TOC- CSCE 510 2013 -Slide - 5 - ProtegeContents 1 Theoretical Foundations of Ontologies ..............................................1 1.1 From Ontology Towards Ontological Engineering .............................................. 3 1.2 What is an Ontology? .................................................................................. 6 1.3 Which are the Main Components of an Ontology? ............................................... 9 1.3.1 Modeling heavyweight ontologies using frames and first order logic ..... I1 1.3.2 Modeling heavyweight ontologies using description logics ...................... 17 1.3.3 Modeling ontologies with software engineering techniques .................... 21 1.3.4 Modeling ontologies with database technology ....................................... 23 1.3.5 Conclusions ............................................................................................. 25 1.4 Types of Ontologies ........................................................................................... 25 1.4.1 Categorization of ontologies1.4.1.1 Types of ontologies based on the richness of their internal structure ....... 28 1.4.1.2 Types of ontologies based on the subject of the conceptualization ... 29 1.4.2 Ontologies and ontology library systems ..................................................... 34 1.5 Ontological Commitments ................................................................................. 36 1.6 Principles for the Design of Ontologies ............................................................... 38 1.7 Bibliographical Notes and Further Reading

Chap 2 The Most Outstanding Ontologies- CSCE 510 2013 -Slide - 6 - Protege2.1 Knowledge Representation Ontologies ....................................................... 47 2.1.1 The Frame Ontology and the OKBC Ontology2.1.2 RDF and RDF Schema knowledge representation ontologies ................. 52 2.1.3 OIL knowledge representation ontology ................................................. 56 2.1.4 DAML+OIL knowledge representation ontology .................................... 61 2.1.5 OWL knowledge representation ontology ............................................... 65 2.2 Top-level Ontologies ................................................................................... 71 2.2.1 Top-level ontologies of universals and particulars .................................. 72 2.2.2 Sowa's top-level ontology ....................................................................... 75 2.2.3 Cyc's upper ontology ............................................................................... 76 2.2.4 The Standard Upper Ontology (SUO) ..................................................... 77 2.3 Linguistic Ontologies ..................................................................................... 79 2.3.1 WordNet .................................................................................................. 79 2.3.2 EuroWordNet ........................................................................................... 80 2.3.3 The Generalized Upper Model2.3.4 The Mikrokosmos ontology ..................................................................... 83 2.3.5 SENSUS .................................................................................................. 84 2.4 Domain Ontologies ......................................................................................... 85 2.4.1 E-commerce ontologies ........................................................................... 86 2.4.2 Medical ontologies ................................................................................... 92 2.4.3 Engineering ontologies ............................................................................ 96 2.4.4 Enterprise ontologies ............................................................................... 98 2.4.5 Chemistry ontologies ............................................................................. 100 2.4.6 Knowledge management ontologies ...................................................... 102 2.5 Bibliographical Notes and Further Reading

3 Methodologies and Methods for Building Ontologies- CSCE 510 2013 -Slide - 7 - Protege3.1 Ontology Development Process3.2 Ontology Methodology Evolution ................................................................ III3.3 Ontology Development Methods and Methodologies .................................. 113 3.3.1 The Cyc method ..................................................................................... 113 3.3.2 Uschold and King's method .................................................................. 115 3.3.3 Gruninger and Fox's methodology ........................................................ 119 3.3.4 The KACTUS approach ......................................................................... 124 3.3.5 METHONTOLOGY .............................................................................. 125 3.3.5.1 Ontology crossed life cycles ........................................................... 126 3.3.5.2 Conceptual modeling in METHONTOLOGY ................................ 130 3.3.6 SENSUS-based method ......................................................................... 142 3.3.7 On-To-Knowledge ................................................................................. 146 3.3.8 Comparing ontology development methods and methodologies ........... 148 3.3.8.1 Comparison framework3.3.8.2 Conclusions ..................................................................................... 153

- CSCE 510 2013 -Slide - 8 - Protege3.4 Method for Re-engineering Ontologies ........................................................ 154 3.5 Ontology Learning Methods ......................................................................... 157 3.5.1 Maedche and colleagues' method .......................................................... 160 3.5.2 Aussenac-Gilles and colleagues' method .............................................. 161 3.6 Ontology Merging Methods and Methodologies .......................................... 163 3.6.1 ONIONS ................................................................................................ 164 3.6.2 FCA-Merge ............................................................................................ 166 3.6.3 PROMPT ............................................................................................... 171 3.7 Co4: a Protocol for Cooperative Construction of Ontologies ....................... 175 3.8 Methods for Evaluating Ontologies .............................................................. 178 3.8.1 Ontology evaluation terminology3.8.2 Taxonomy evaluation ............................................................................ 180 3.8.3 OntoClean .............................................................................................. 185 3.9 Conclusions .................................................................................................. 195 3.10 Bibliographical Notes and Further Reading

Asuncin Gmez-Prez;Mariano Fernandez-Lopez;Oscar Corcho. Ontological Engineering: with examples from the areas of Knowledge Management, e-Commerce and the Semantic Web. First Edition (p. xi). Kindle Edition.

Chap 4 Languages for Building Ontologies- CSCE 510 2013 -Slide - 9 - Protege4.1 Ontology Language Evolution ...................................................................... 200 4.2 The Selection of an Ontology Language ...................................................... 202 4.2.1 Knowledge representation ..................................................................... 203 4.2.2 Reasoning mechanisms .......................................................................... 204 4.3 Traditional Ontology Languages .................................................................. 204 4.3.1 Ontolingua and KIF4.3.1.1 Knowledge representation .............................................................. 206 4.3.1.2 Reasoning mechanisms ................................................................... 216 4.3.2 LOOM ...................................................................................................216 4.3.2.1 Knowledge representation .............................................................. 216 4.3.2.2 Reasoning mechanisms ................................................................... 222 4.3.3 OKBC .................................................................................................... 222 4.3.3.1 Knowledge representation .............................................................. 223 4.3.3.2 Reasoning mechanisms ................................................................... 226 4.3.4 OCML .................................................................................................... 226 4.3.4.1 Knowledge representation .............................................................. 227 4.3.4.2 Reasoning mechanisms ................................................................... 230 4.3.5 FLogic- CSCE 510 2013 -Slide - 10 - Protege4.3.5.1 Knowledge representation .............................................................. 232 4.3.5.2 Reasoning mechanisms ................................................................... 235 4.4 Ontology Markup Languages .................................................................... 236 4.4.1 SHOE ..................................................................................................... 241 4.4.1.1 Knowledge representation .............................................................. 241 4.4.1.2 Reasoning mechanisms ................................................................... 245 4.4.2 XOL ....................................................................................................... 246 4.4.2.1 Knowledge representation .............................................................. 247 4.4.2.2 Reasoning mechanisms ................................................................... 250 4.4.3 RDF(S): RDF and RDF Schema ............................................................ 250 4.4.3.1 Knowledge representation .............................................................. 251 4.4.3.2 Reasoning mechanisms

- CSCE 510 2013 -Slide - 11 - Protege4.4.4 OIL ........................................................................................................ 258 4.4.4.1 Knowledge representation .............................................................. 259 4.4.4.2 Reasoning mechanisms ................................................................... 263 4.4.5 DAML+OIL ........................................................................................... 264 4.4.5.1 Knowledge representation .............................................................. 265 4.4.5.2 Reasoning mechanisms ................................................................... 273 4.4.6 OWL ...................................................................................................... 274 4.4.6.1 Knowledge representation .............................................................. 275 4.4.6.2 Reasoning mechanisms ................................................................... 284 4.5 Conclusion .................................................................................................... 285 4.5.1 Knowledge representation ..................................................................... 286 4.5.2 Using ontology languages in ontology-base applications ....................290 4.6 Bibliographical Notes and Further Reading

Asuncin Gmez-Prez;Mariano Fernandez-Lopez;Oscar Corcho. Ontological Engineering: with examples from the areas of Knowledge Management, e-Commerce and the Semantic Web. First Edition (p. xii). Kindle Edition. Chap 5 Ontology Tools - CSCE 510 2013 -Slide - 12 - Protege5.1 Ontology Tools Evolution ............................................................................ 296 5.2 Ontology Development Tools and Tool Suites ............................................. 299 5.2.1 Language-dependent ontology development tools ................................ 299 5.2.1.1 The Ontolingua Server .................................................................... 300 5.2.1.2 OntoSaurus ..................................................................................... 304 5.2.1.3 WebOnto ......................................................................................... 307 5.2.1.4 OilEd5.2.2 Extensible language-independent ontology development tools and tool suites .................................................................................................... 313 5.2.2.1 Protege-2000 ................................................................................... 313 5.2.2.2 WebODE ......................................................................................... 319 5.2.2.3 OntoEdit .......................................................................................... 328 5.2.2.4 KAON ............................................................................................. 332 5.2.3 Some other ontology tools ..................................................................... 336 5.3 Ontology Merge Tools .................................................................................. 338 5.3.1 The PROMPT plug-in ............................................................................ 338 5.3.2 Some other ontology merge tools .......................................................... 342 5.4 Ontology-based Annotation Tools ................................................................ 344 5.4.1 COHSE5.4.2 MnM ...................................................................................................... 348 5.4.3 OntoMat-Annotizer and OntoAnnotate ................................................. 350 5.4.4 SHOE Knowledge Annotator ................................................................ 351 5.4.5 UBOT AeroDAML ................................................................................ 353 5.5 Conclusions .................................................................................................. 354 5.6 Bibliographical Notes and Further Reading

Other Texts- CSCE 790C 2013 -Slide - 13 - ProtegeCopyright 2005 Univ. of Manchester14OntologiesSoftware agentsProblem-solving methodsDomain-independent applicationsDatabasesDeclarestructureKnowledgebasesProvidedomaindescriptionThe SemanticWebAn Ontology should be just the BeginningWhat is an ontology?- CSCE 790C 2013 -Slide - 15 - ProtegeAristotle and colleagues: Ontology = metaphysicsEngineering: ontologies (count noun)Investigating reality, representing itPutting an engineering artifact to useWhat then, is this engineering artifact?Copyright 2005 Univ. of Manchester16PizzaMargheritaPizzaVegetarianPizzaSpicy BeefPizzaPizzaToppingVegetabletoppingTomatotoppingMozzarellatoppingCheesetoppingPizza_baseDeepdish baseRegularbaseA simple ontology: PizzasProtege- CSCE 790C 2013 -Slide - 17 - Protege

Protg Views- CSCE 790C 2013 -Slide - 18 - ProtegeData PropertiesAnnotation propertiesIndividiualsOwlVizDL QueryOntoGrafSPARQL QueryOntology DifferencesActive ontologyEntriesClassesObject Properties

- CSCE 790C Summer 201319 Protege

Definitions- CSCE 790C 2013 -Slide - 20 - ProtegeMost quoted: An ontology is a specification of a conceptualization Tom Gruber, 1993A formal specification of a shared conceptualization" Borst, 1997An ontology is a formal, explicit specification of a shared conceptualization" Studer et al., 1998

conceptualization?shared?Ontologies and meaning- CSCE 790C 2013 -Slide - 21 - ProtegeResoning Levels- CSCE 790C 2013 -Slide - 22 - ProtegeLogical level (no structure, no constrained meaning1):Exists-x(Apple(x) ^ Red(x))Epistemological level (structure, no constrained meaning):Exists-x : apple Red(x) (many-sorted logics)Exists-x : red Apple(x)Apple(a) and hasColor (a; red) (description logics2)Red(a) and hasShape(a; apple)Ontological level (structure, constrained meaning):Some structuring choices are excluded because of ontological constraintsApple carries an identiy condition (and is a sortal), Red does not (is a quality [`value'] of the quality [`attribute'] hasColor that a thing has)Description logics- CSCE 790C 2013 -Slide - 23 - ProtegeIan Horrocks - Univ Manchester OxfordAssertions (Abox)mother(sam, mary)mother(mary, ann)doctor (anne)marriedby(bob, mary, Rev. Oaks)Terminology Axioms (Tbox)parentOf ancestorOfbrotherOf parentOf uncleOfRole Restrictions/Role ConstructorsparentOf = childOf-1 (inverse relation)subsetModels of Interpretation- CSCE 790C 2013 -Slide - 24 - ProtegeQuality of an Ontology- CSCE 790C 2013 -Slide - 25 - Protege

Meeka Guarino, 2002)Quality of the ontology- CSCE 790C 2013 -Slide - 26 - ProtegeBad ontologies are those whose general terms lack the relation to corresponding universals in reality, and thereby also to corresponding instances." ) need for groundingGood ontologies are reality representations, and the fact that such representations are possible is shown by the fact that, as is documented in our scientific textbooks, very many of them have already been achieved, though of course always only at some specific level of granularity and to some specific degree of precision, detail and completeness."(Smith, 2004)Examples of published ontologies- CSCE 790C 2013 -Slide - 27 - Protegelist on handoutUpper ontologies- CSCE 790C 2013 -Slide - 28 - Protege

Ontology libraries - CSCE 790C 2013 -Slide - 29 - ProtegeThe following are libraries of human-selected ontologies.COLORE[39] is an open repository of first-order ontologies in Common Logic with formal links between ontologies in the repository.DAML Ontology Library[40] maintains a legacy of ontologies in DAML.Ontology Design Patterns portal[41] is a wiki repository of reusable components and practices for ontology design, and also maintains a list of exemplary ontologies. Started within the NeOn EU project.Protg Ontology Library[42] contains a set of OWL, Frame-based and other format ontologies.SchemaWeb[43] is a directory of RDF schemata expressed in RDFS, OWL and DAML+OIL.

http://en.wikipedia.org/wiki/Ontology_%28information_science%29Protg -- CSCE 790C 2013 -Slide - 30 - Protegedownload protg from http://protege.stanford.edu/Protg 4.3 versus Web Protg build 103getting started with protg-owlProtg-OWL tutorial. http://www.co-ode.org/resources/tutorials/