Theory and Applications of Ontology: Computer Applications

Preface

Contents

Contributors

Introduction

1 The Interplay Between Ontology as Categorial Analysis and Ontology as Technology

1.1 Introduction

1.2 Ontology_c

1.3 Ontology_t

1.3.1 Ontology_t Definitions

1.3.2 Ontology_t and Epistemology

1.3.3 Ontology_t as Theory with Philosophical Stances

1.4 Interplay Between Ontologyc and Ontologyt

1.4.1 Developing Formalized Ontologies

1.4.2 Ontology, Science, and Levels of Reality

1.4.3 Example: An Ontology of Biology

1.5 Looking Toward the Future

1.5.1 Better Ordering Relations for Ontologies

1.5.2 Elaboration of the Distinctions Among Ontology Levels

1.5.3 Ontology Modularity, Mapping, and Formalization of Context

1.5.4 Representation vs. Reasoning

1.5.5 Final Words

1.6 Acknowledgments and Disclaimers

References

2 Ontological Architectures

2.1 Introduction

2.2 Ontological and Ontology Architecture: Overview

2.2.1 Truth and Belief: Ontology, Epistemology, Contextual Semantics, Language, and Applications

2.2.2 The Big Picture

2.2.3 The Ontology Spectrum

2.2.4 The Ontology Maturity Model

2.3 Ontological Architecture: Upper, Mid-level, Domain Ontologies

2.3.1 What Is an Upper Ontology?

2.3.1.1 Upper Ontology Definition

2.3.1.2 Upper Ontology vs. Mid-Level Ontology

2.3.1.3 Upper Ontology vs. Domain Ontology

2.3.2 Why Do We Care About Upper Ontology?

2.3.2.1 How Upper Ontologies May Help

2.3.2.2 A Software Engineer Analogy

2.3.3 What Foundational Ontologies Provide: Ontological Choices

2.3.3.1 Descriptive vs. Revisionary

2.3.3.2 Multiplicative vs. Reductionist

2.3.3.3 Universals, Particulars, Sets, Possible Worlds

2.3.3.4 Endurants and Perdurants

2.3.4 Upper Ontology Initiatives and Candidates

2.4 Structuring the Ontological and Meta-Ontological Space

2.4.1 Knowledge Representation Languages and Meta-Ontologies

2.4.2 The Lattice of Theories

2.4.3 Modularity and Context in the Ontological Space

2.4.4 Microtheories, Little Theories, Ontology Versioning

2.4.5 Information Flow Framework Meta-Ontology

2.5 What the Future Holds: A Vision

References

3 Organization and Management of Large Categorical Systems

3.1 Introduction

3.2 Terminological Systems in Medicine

3.2.1 Compositionality

3.2.2 Navigation

3.3 Complex Systems and Modularization in General

3.4 Abstract Framework for Modules

3.4.1 Overview

3.4.2 Formal Preliminaries

3.4.3 Defining Modules

3.4.4 Example Module Types

3.4.4.1 Basic Modules

3.4.4.2 Modules in Distributed First Order Logic

3.5 Characteristics of Module Notions

3.5.1 Informal Characteristics

3.5.2 Formal Characteristics

3.5.2.1 Characteristics Primarily Based on Either Interfaces, Modules or Systems

3.5.2.2 Characteristics with Respect to the Interplay of Modules and Systems

3.5.3 Discussion of Characteristics

3.6 Analytic Overview of Logical Approaches

3.6.1 Conservativity and Disjoint Languages

3.6.2 Partition-Based Reasoning

3.6.3 Semantic Encapsulation

3.6.4 Package-based Description Logics

3.6.5 Distributed Logics

3.6.6 Summarizing Overview

3.7 Concluding Remarks

3.7.1 Further Related Areas

3.7.2 Conclusions

References

4 The Information Flow Approach to Ontology-Based Semantic Alignment

4.1 Introduction

4.2 Ontology-Based Semantic Integration: Basic Concepts and Definitions

4.2.1 Semantic Matching

4.2.2 Integration Theory

4.2.3 Semantic Alignment

4.3 Semantic Alignment Through Meaning Coordination

4.4 Semantic Alignment Hypotheses

4.5 Applications and Explorations

4.6 Conclusions

References

5 Ontological Evaluation and Validation

5.1 Introduction

5.2 Current Approaches in Ontology Evaluation and Validation

5.2.1 Evolution-Based

5.2.2 Logical (Rule-Based)

5.2.3 Metric-Based (Feature-Based)

5.3 OntoQA: Metric-Based Ontology Quality Analysis

5.3.1 Schema Metrics

5.3.1.1 Relationship Richness

5.3.1.2 Inheritance Richness

5.3.1.3 Attribute Richness

5.3.2 Knowledgebase Metrics

5.3.2.1 Class Richness

5.3.2.2 Class Connectivity

5.3.2.3 Class Importance

5.3.2.4 Cohesion

5.3.2.5 Relationship Richness

5.3.3 OntoQA Results

5.4 Conclusion

References

6 Tools for Ontology Engineering and Management

6.1 Introduction

6.2 Classification of Ontology Tools

6.2.1 Specialized Ontology Engineering Tools

6.2.1.1 Ontology Engineering Tools

6.2.1.2 Ontologies Combination Tools

6.2.1.3 Ontology Management Tools

6.2.2 Integrated Ontology Engineering Environments

6.3 Selecting the Appropriate Ontology Engineering And Management Tool

6.4 Conclusion

References

7 Ontological Tools: Requirements, Design Issues and Perspectives

7.1 Introduction

7.2 The Engineering of Ontologies

7.2.1 The HCOME Methodology

7.2.1.1 Specification Phase

7.2.1.2 Conceptualization Phase

7.2.1.3 Exploitation Phase

7.2.2 The DILIGENT Methodology

7.3 Next-Generation Ontology Engineering Tools

7.4 Supporting Ontology Engineering

7.4.1 Integrated O.E Environments

7.4.2 Self-Standing O.E Tools

7.5 Conclusion

References

8 Using the Unified Foundational Ontology (UFO) as a Foundation for General Conceptual Modeling Languages

8.1 Introduction

8.2 The Unified Foundational Ontology (UFO)

8.2.1 The Core Categories: Object--Object Universal, Moment--Moment Universal

8.2.2 Qualities, Qualia and Modes

8.2.3 Relations, Relators and Qua Individuals

8.2.4 Object Universals

8.3 A Framework for Language Evaluation and (Re)Design

8.4 Evaluating and Redesigning the UML 2.0 Metamodel

8.5 Reinforcing the Isomorphism Between UFO and UML

8.6 Final Considerations

References

9 Lightweight Ontologies

9.1 Introduction

9.2 Lightweight Ontologies

9.2.1 Lightweight Ontologies and the Semantic Spectrum

9.2.2 Folksonomies and Lightweight Ontologies

9.2.3 Thesauri and Lightweight Ontologies

9.2.4 Formal Classification and Lightweight Ontologies

9.3 Ontologies and the Semantic Web

9.4 Ontologies and Information Integration

9.5 Ontologies and Knowledge Management

9.5.1 Limitations of Current Technology

9.5.2 Applying Ontologies in Knowledge Management

9.5.3 Semantic Knowledge Management Tools

9.5.3.1 Squirrel Semantic Search Engine

9.6 Ontologies and Service-Oriented Environments

9.6.1 Web Service Modeling Ontology (WSMO)

9.6.2 Web Service Modeling Language (WSML)

9.6.3 Web Service Modeling Execution Environment (WSMX)

9.7 Ontologies and Computer Science

9.8 Conclusion

References

10 WordNet

10.1 Introduction

10.2 Design and Contents

10.3 Coverage

10.4 Relations

10.5 Nouns in WordNet

10.5.1 Hyponymy

10.5.2 Types vs. Instances

10.5.3 Meronymy

10.6 Verbs

10.7 Adjectives

10.8 Where do Relations Come from?

10.9 WordNet as a Thesaurus

10.10 Semantic Distance and Lexical Gaps

10.11 WordNet as an Ontology

10.12 WordNet and Formal Ontology

10.13 Wordnets in Other Languages

10.14 The EuroWordNet Model

10.15 Global WordNets

10.16 WordNet as a Tool for Natural Language Processing

10.17 Conclusions

References

11 Controlled English to Logic Translation

11.1 Introduction

11.2 WordNet Mappings

11.3 Simple Parsing and Interpretation

11.3.1 Word Sense Disambiguation

11.4 Issues in Translation

11.4.1 Case Roles and Word Order

11.4.2 Statives

11.4.3 Attributes

11.4.4 Counting

11.4.5 Copula Expressions

11.4.6 Prepositions

11.4.7 Quantification

11.4.8 Possessives

11.4.9 Anaphor

11.4.10 Conjunction and Disjunction

11.4.11 Negation

11.5 CELT Components

References

12 Cyc

12.1 Introduction

12.1.1 The Form of the Language

12.1.2 Vocabulary

12.1.3 OpenCyc and ResearchCyc

12.2 Upper Ontology

12.2.1 Higher Order Classes

12.3 Contexts

12.3.1 Dimensions of Context Space

12.3.2 Vocabulary/Theory/Data Contexts

12.3.3 Spindles

12.3.4 Problem Solving Contexts

12.3.5 Hypothetical Contexts

12.3.6 Fictional Contexts

12.3.7 UniversalVocabularyMt

12.4 Functions

12.4.1 Prototypes

12.4.2 Skolemization

12.5 Reasoning

12.5.1 Forward and Backward Chaining

12.5.2 Don't Care Variables

12.5.3 Rule Macro Predicates

12.5.4 Monotonic vs. Default Reasoning

12.5.5 Exceptions to Rules

12.6 Events

12.7 Conceptual Works

12.8 Open/Closed World Assumption

12.9 Geopolitical Entities

12.10 Temporal Reasoning

12.11 Natural Language Support

12.12 Cyc and the Semantic Web

12.13 Summary

References

13 Ontological Foundations of DOLCE

13.1 Introduction

13.2 A Bit of History

13.3 Ontological vs. Conceptual Level

13.4 Properties

13.5 Basic Categories

13.6 Parthood

13.7 Time

13.8 Temporary Parthood

13.9 Concepts

13.10 Qualities and Locations

13.11 Objects and Events

References

14 General Formal Ontology (GFO): A Foundational Ontology for Conceptual Modelling

14.1 Introduction

14.2 Basic Assumptions and Logical Methods

14.2.1 Philosophical Assumptions

14.2.2 Concepts, Symbols, and Universals

14.2.3 The Axiomatic Method

14.2.4 Representation of Ontologies

14.2.5 Types of Realism

14.2.6 Levels of Reality

14.3 Meta-Ontological Architecture of GFO

14.4 The Basic Categories of Individuals of GFO

14.4.1 Space-Time

14.4.2 Principal Distinctions

14.4.3 Material Structures Material Structure

14.4.4 Processual Complexes, Processes, and Occurrents

14.4.4.1 Processual Complexes

14.4.4.2 Processes

14.4.4.3 Occurrents

14.4.4.4 Basic Classification of Processes

14.4.5 Attributives

14.4.5.1 Properties

14.4.5.2 Relations and Roles

14.4.5.3 Functions

14.4.6 Facts, Propositions, and Situations

14.5 Basic Relations of GFO

14.5.1 Existential Dependency

14.5.2 Set and Set-Theoretical Relations

14.5.3 Instantiation and Categories

14.5.4 Property Relations and Relators

14.5.5 Property Bearer Parthood Relation

14.5.6 Boundaries, Coincidence, and Adjacence

14.5.7 Relations of Concrete Individuals to Space and Time

14.5.8 Participation

14.5.9 Association

14.5.10 Ontical Connectedness and Causality

14.6 Object-Process Integration

14.6.1 Processual Unification and Cognition

14.6.2 Completed Categories and Integrated Individuals

14.6.3 Comparison to Other 4D-Ontologies

14.7 Principles of Ontology Development and Ontological Modelling

14.7.1 Domains and Conceptualizations

14.7.2 Steps of Ontology Development

14.7.3 Ontological Modelling

References

15 Ontologies in Biology

15.1 Introduction

15.2 Ontologies in Biomedicine

15.2.1 The Open Biomedical Ontologies

15.2.2 The Gene Ontology

15.2.3 Ontology Representation

15.2.4 Ontology Curation

15.2.5 Annotation

15.3 Criticism and Extension of the Gene Ontology

15.4 Biomedical Ontology Integration Through the Application of Ontological Design Principles

15.4.1 The OBO Relationship Ontology

15.4.2 BioTop and the Simple Bio Upper Ontology

15.4.3 GFO-Bio

15.4.4 Defaults and Exceptions for Ontology Interoperability

15.5 Applications

15.5.1 Annotation and Retrieval of Data

15.5.2 Statistical Analysis of Experiments

15.5.3 Automatic Annotation and Community-Developed Ontologies

15.5.3.1 Automatic Annotation

15.5.3.2 Community Development

15.5.4 Reasoning for Experimental Hypothesis Testing

15.6 Summary and Conclusions

References

16 The Ontology of Medical Terminological Systems: Towards the Next Generation of Medical Ontologies

16.1 Introduction

16.2 Terminological Systems and Ontologies

16.3 Domains and Graduated Conceptualizations

16.4 Analyses of Terminological Systems

16.5 Medical Terminological Systems

16.5.1 ICD

16.5.2 SNOMED-CT

16.5.3 UMLS

16.5.4 LOINC

16.5.5 GALEN

16.5.6 MeSH

16.6 Conclusions and Future Research

References

17 Ontologies of Language and Language Processing

17.1 Introduction

17.2 Lexical Databases and Ontology

17.3 Grammatical Motivation and Linguistic Ontology

17.4 Discussion

References

18 Business Ontologies

18.1 Introduction

18.1.1 Domain-Level Ontologies

18.1.2 Application-Level Ontologies

18.2 Socio-Instrumental Pragmatism

18.2.1 Restructuring the Taxonomy

18.2.1.1 Actors

18.2.1.2 Objects

18.2.1.3 Actions

18.2.1.4 Agents

18.2.2 The Resulting Meta-model

18.3 Enterprise Ontology

18.3.1 World Ontology Specification Language

18.3.2 The Axioms of Enterprise Ontology

18.3.2.1 The Operation Axiom

18.3.2.2 The Transaction Axiom

18.3.2.3 The Composition Axiom

18.3.2.4 The Distinction Axiom

18.4 Conclusion

References

19 Ontologies for E-government

19.1 Motivation

19.2 State of the Art in E-Government Ontologies

19.3 Ontologies to Formalize a Shared Understanding of Meaning

19.3.1 Starting with Terms

19.3.2 Transforming Terms and Facts to Concepts and Properties

19.3.3 Negotiating Reuse

19.4 Ontologies for Modelling Semantically Enriched Processes

19.5 Ontologies for Modelling Business Rules

19.5.1 Business Rules Classification

19.5.2 Semi-Formal Rule Respresentation

19.5.3 Formalization

19.5.3.1 Property Restriction

19.5.3.2 Semantic Web Rule Language

19.6 Ontologies for Modelling Agile E-Government Processes A process is considered agile when its execution model is created flexible at runtime, based on the results of triggered rules instead of static pre-defined models.

19.7 Conclusion

References

20 An Ontology-Driven Approach and a Context Management Framework for Ubiquitous Computing Applications

20.1 Introduction

20.2 Ontology Based Modeling of Context Aware Ubiquitous Computing Systems

20.3 An Ontology-Driven Meta-Model for Ubiquitous Computing Systems

20.3.1 Underlying Concepts

20.3.2 Focused Ontology

20.3.3 Core vs. Application Ontology

20.4 Context Management Framework

20.4.1 Context Management Process

20.4.2 Rules

20.4.2.1 Rules for Artifact State Assessment

20.4.2.2 Rules for the Local Decision-Making Process

20.4.2.3 Rules for the Global Decision-Making Process

20.4.3 Implementation

20.4.4 Engineering Applications

20.5 Prototype Application Example

20.5.1 Scenario

20.5.2 Components

20.5.3 Implementation

20.5.4 Semantic-Based Service Discovery

20.6 Conclusions

References

21 Category Theory as a Mathematics for Formalizing Ontologies

21.1 Introduction

21.2 Categories

21.3 Limits, Colimits, and Concepts as Theories

21.4 Structural Mappings

21.5 Categories of Categories, Functors, and Natural Transformations

21.6 Universal Arrows and Adjunctions

References

22 Issues of Logic, Algebra and Topology in Ontology

22.1 Introduction

22.2 Ingredients of Logic

22.2.1 Interpretations and Ontology

22.2.2 Theories and Models

22.3 Geometric Logic

22.3.1 Rules of Inference

22.3.2 Soundness

22.3.3 Beyond Rules of Inference

22.3.4 Geometric Ontology

22.4 Topology

22.5 Algebra

22.5.1 Lists and Finite Sets

22.5.2 Free Algebras

22.6 Categories

22.6.1 Sheaves

References

23 The Institutional Approach

23.1 Introduction

23.1.1 Ontologies

23.1.2 Semantic Integration

23.1.3 Architecture

23.2 Contexts

23.2.1 General Theory

23.2.2 Special Theory

23.3 Indexed Contexts

23.3.1 General Theory

23.3.2 Special Theory

23.4 Diagrams

23.4.1 General Theory

23.4.2 Special Theory

23.5 Coalescence

23.6 Fusion

23.6.1 General Theory

23.6.2 Special Theory

23.7 Formalism

References

24 Ontology Engineering, Universal Algebra, and Category Theory

24.1 Introduction

24.2 Representing Ontologies

24.3 Presenting Ontologies

24.4 Views Versus Sub-Ontologies

24.5 Interoperations

24.6 Solving View Updates

24.7 Interoperations with Instances

24.8 Nulls and Partial Functions

24.9 Universal Nulls

24.10 Conclusion

References