DeutschesFachbuch.de : The Semantic Web Semantics for Data and Services on the Web Von Vipul Kashyap, Christoph Bussler, Matthew Moran

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Contents
Part IPreliminaries 1
1 Introduction 3
1.1 Motivation: Why Semantic Web?4
1.2 A Framework for Semantic Web 5
1.3 Use Case : Translational Medicine Clinical Vignette 7
1.4 Scope and Organization 9
2 Use Case and Functional Requirements 11
2.1 Detailed Clinical Use Case 12
2.2 Stakeholders and Information Needs 13
2.3 Conceptual Architecture 15
2.4 Functional Requirements 17
2.5 Research Issues 18
2.6 Summary 19
Part IIInformation Aspects of the Semantic Web 21
3 Semantic Web Content 23
3.1 Nature of Web Content 23
3.2 Nature of Semantic Web Content 24
3.3 Metadata 25
3.3.1 Metadata Usage in Various Applications 26
3.3.2 Metadata: A Tool for Describing and Modeling Information 27
3.4 Ontologies : Vocabularies and Reference Terms for Metadata 30
3.5 Summary 33
4 Metadata Frameworks 35
4.1 Examples of Metadata Frameworks 35
4.1.1 XML-Based Metadata Framework 36
4.1.2 RDF-Based Metadata Framework 36
4.1.3 OWL-Based Metadata Framework 37
4.1.4 WSMO-Based Metadata Framework 37
4.2 Two Perspectives: Data Models and Model-Theoretic Semantics 38
4.2.1 Data Models 38
4.2.2 Multiple Syntaxes for RDF: A Short Note 47
4.2.3 Model-Theoretic Semantics 48
4.3 Query Languages 51
4.3.1 Query Languages for XML Data 51
4.3.2 Query Languages for RDF Data 62
4.3.3 Extending Query Languages with Reasoning and Entailment 73
4.4 Clinical Scenario Revisited 74
4.4.1 Semantic Web Specifications: LIMS and EMR Data 74
4.4.2 Linking data from Multiple Data Sources 76
4.4.3 Advantages and Disadvantages of using Semantic Web Specifications 78
4.5 Summary 78
5 Ontologies and Schemas 79
5.1 What is an Ontology?79
5.2 Ontology Representation Languages 84
5.2.1 XML Schema 84
5.2.2 RDF Schema 92
5.2.3 Web Ontology Language 100
5.2.4 The Web Service Modeling Ontology (WSMO)112
5.2.5 Comparison of Ontology Representation Languages 118
5.3 Integration of Ontology and Rule Languages 122
5.3.1 Motivation and Requirements 122
5.3.2 Overview of Languages and Approaches 123
5.3.3 Semantic Web Rules Language 124
5.4 Clinical Scenario Revisited 126
5.4.1 A Domain Ontology for Translational Medicine 126
5.4.2 Integration of Ontologies and Rules for Clinical Decision Support 130
5.4.3 Advanatages and Disadvantages of using Semantic Web Specifications 135
5.5 Summary 135
6 Ontology Authoring and Management 137
6.1 Ontology Building Tools 137
6.1.1 Ontology Editors: Brief Descriptions 138
6.1.2 Ontology Editors : A Comparative Evaluation 143
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Index
Aabstract processes 244, 245
Abstract service discovery 280
Abstract State Machine (ASM) 272
activities 245
Adaptive IE 166
Adaptive Information Extraction 168
Aero-DAML 167, 168
Aero-SWARM 8 167
AI Planning 281
Aktive-Doc 168
ALCQHIR 156
AL-log 187
Amaya 164
Amilcare 165, 166
analog telephone 196
Anchor-PROMPT 181
annotation frameworks, tools and environments 163
Annotation Process 191
annotation process 162
Annotation Storage 163
Annotea 163
Annozilla 164
Apollo 138
Application-to-Application (A 2 A) Protocols 211
Application-to-Application Communication 241
Armadillo 166, 168
Artemis 179
artifacts 245
assumptions 271
asynchronous communication 195
asynchronous connection 196
ATP 147
autonomous systems 234
BBasic Formal Ontology (BFO) 300
behavior of communication 198
best profile covering 277
BFO 84
BioPAX 18
BioPax 32, 299
BPEL 222
BPEL 4 WS 244
BPMN 222
Business Process Modeling Notation (BPMN) 245
Business-to-Business (B 2 B) Protocols 210
Business-to-Business Communication 240
BUSTER 186, 187, 188
CC++ 139
CAFETIERE 166, 168
Capability 271
CARIN 123, 187
Carnot 183
CEL 154
Chimaera 151
Choreography 238
choreography 246, 272
Ciao Prolog 147
CIM/DMTF 298
Classes 96
CLASSIC 149, 187
Classification 80
Classification of Schema-matching Approaches 173
Clinical Use Case 12
clinical workflow 311
COBra 141
COBWEB 149
Coding Systems 80
COHSE 164
COIN 186, 187
collaboration 245
COMA 180
combination of business logic 243
Combination of matchers 173
combination of several specialized ontologies 185
Combination ofMAtching algorithms (COMA) 180
Common Information Model (CIM) 82
communication 195
communication channel 196
communication partners 195
communication protocols 195
community of agents 79
Comparison of Ontology Representation Languages 118
compensating actions 245
compensation 237
Complex types 87
component invocation 235
composed components 235
composed objects 235
composing object). 235
composition 233, 243
composition implementation 239
Composition in context of communication 234
Composition in context of complex business logic 234
Computational Aspects of the Semantic Web 7
conditional branching 235
conjunction 120
connecting objects 245
connection 196
containment principle 234
Content Models 90
Context 118
CORBA 215
CREAM 163, 164
Cupid 179
Cyc 299
Cyc Ontology 32
DDAML 260
DAML+OIL 303
DAML-ONT 303
DAML-S 260, 303
DARPA Agent Markup Language (DAML) 303
data flow 236
data formats 195
Data mediation 274, 340
data mediation 284
Data Model 35
Data Models and Semantics 38
data sources 236
Datalog 187
declarative compositions 235
deep Web 23
Defined Mappings 189
Definition of Composition 235
Définition of Terms 188
Description Logics 116
description logics 100, 187
description logics (DL) 178
description logics (DL) EL 154
Description Logics Program (DLP) 124
Descriptive Ontology for Linguistic and Cognitive Engineering (DOLCE) 177
DIG Description Logics Interface 297
DIP 303
Direct 3 D 165
Discovery 276
disjunction 120
Distributed Management Task Force 82
distributed transactions 237
DLEL+155
DL reasoners 147
DLS 170
Document and Annotation consistency 163
document classification and composition 29
document vectors 29
DOLCE 84
domain ontology 186
Domain Specific Metadata 28
domain specific ontology 185
DWQ 183, 187, 188, 189, 191
Dynamic Composition 239
dynamic composition 233
EEDI 210
effects 271
Electronic Health Record (EHR) 15
Elementary matchers 173
Enterprise Application Integration (EAI) 211, 241
Entity-Relationship Models 81
exactly-once transmission 210
exceptions 245
executable processes 244
explicit composition 234
Expose 191
Expressive XML Query Languages 53
Extended Entity-Relationship (EER) 140
extensible Markup Language (XML)35, 293
Extensible Stylesheet language (XSL)36
extensible Stylesheet Transformation Language (XSLT) 294
external behavior 238
externally visible behavior 238
FFaCT++ 155
Finite State Machines 253
First-Order Logic 116
First-Order Logic Ontology for Web Services (FLOWS) 261, 302
F-Logic 187 flow objects 245
FLOWS-Core 263 formats and protocols 197
foundation ontology 84
Frame Representation Systems (FRSs) 141
Framework for Semantic Web 5 fuzzy-DL 155
GGalen Medical Knowledge Base (GALEN) 155
GALEN methodology 146
GATE 167
Gene Ontology 18, 32, 298
Gene Ontology (GO) 155
general concept inclusions (GCI) 154
general ontology 186
Generic Knowledge Base (GKB) Editor 141
GENIA biomedical corpus 166
GGMediators 274
global ontology 184
global processes 245
GO 141
Goal 270
Goal discovery 280
Goal refinement 280
goal-based orchestration 283
GRAIL 187
Graphic Query Interfaces 53
HHaystack 168
Hierarchical Task Planning (HTN) 282
Higher Order Theories 83
HIPP A A 210
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