Part I Preliminaries ............................................ 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 II Information 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
6.2. Ontology Bootstrapping Approaches ..................... 148
6.3. Ontology Merge and Integration Tools .................. 150
6.3.1. Ontology Merge and Integration Tools:
A Brief Description ............................ 151
6.3.2. Evaluation of Ontology Merge and Integration
Tools .......................................... 152
6.4. Ontology Engines and Reasoners ........................ 154
6.5. Clinical Scenario Revisited ........................... 157
6.6. Summary ............................................... 158
7. Applications of Metadata and Ontologies .................... 161
7.1. Tools and Techniques for Metadata Annotation .......... 161
7.1.1. Requirements for Metadata Annotation ........... 162
7.1.2. Tools and Technologies for Metadata
Annotation ..................................... 163
7.1.3. Comparative Evaluation ......................... 168
7.2. Techniques for Schema/Ontology Mapping ................ 173
7.2.1. A Classification of Schema-matching
Approaches ..................................... 173
7.2.2. Schema-matching Techniques: Overview ........... 179
7.3. Ontology Driven Information Integration ............... 183
7.3.1. The Role of Ontologies in Information
Integration .................................... 183
7.3.2. Ontology Representations Used in Information
Integration .................................... 187
7.3.3. The Role of Mapping in Information
Integration .................................... 188
7.3.4. The Role of Ontology Engineering in
Information Integration ........................ 190
7.4. Summary ............................................... 192
Part III Process Aspects of the Semantic Web .................. 193
8. Communication .............................................. 195
8.1. Communication Concepts ................................ 195
8.1.1. Fundamental Types .............................. 196
8.1.2. Formats and Protocols (FAP) .................... 197
8.1.3. Separation of Interface and Logic .............. 198
8.1.4. Communicating Parties .......................... 199
8.1.5. Mediation ...................................... 201
8.1.6. Non-functional Aspects ......................... 202
8.2. Communication Paradigms ............................... 203
8.2.1. Client/Server (C/S) ............................ 204
8.2.2. Queueing ....................................... 204
8.2.3. Peer-to-Peer (P2P) ............................. 205
8.2.4. Blackboard ..................................... 205
8.2.5. Web Services ................................... 206
8.2.6. Representational State Transfer (REST) ......... 207
8.2.7. Agents ......................................... 207
8.2.8. Tuple Spaces ................................... 208
8.2.9. Co-location .................................... 208
8.2.10.Summary ........................................ 209
8.3. Long-Running Communication ............................ 209
8.3.1. Business-to-Business (B2B) Protocols ........... 210
8.3.2. Application-to-Application (A2A) Protocols ..... 211
8.4. Web Services .......................................... 211
8.5. Clinical Use Case ..................................... 212
8.6. Summary ............................................... 214
9. State of the Art in Web Services ........................... 215
9.1. History ............................................... 215
9.2. Traditional Web Services .............................. 216
9.2.1. WSDL ........................................... 217
9.2.2. SOAP ........................................... 218
9.2.3. UDDI ........................................... 219
9.2.4. Summary ........................................ 219
9.3. Emerging Web Service Specifications (WS*-Stack) ....... 220
9.3.1. Standards ...................................... 220
9.3.2. Web Service Standards .......................... 221
9.3.3. Semantic-Web-Service-Related Standards ......... 222
9.4. Service-oriented Architecture (SOA) ................... 223
9.4.1. Service Paradigm ............................... 223
9.4.2. SOA and Web Services ........................... 224
9.4.3. Open Issues and Technical Challenges ........... 224
9.5. Semantics and Web Services ............................ 226
9.5.1. Semantics, What Semantics? ..................... 227
9.5.2. Data Semantics ................................. 228
9.5.3. Process Semantics .............................. 229
9.5.4. Selection Semantics ............................ 229
9.5.5. Other Types of Semantics ....................... 230
9.6. Clinical Use Case ..................................... 231
9.7. Summary ............................................... 232
10.Web Service Composition .................................... 233
10.1.Composition ........................................... 233
10.1.1.Motivation ..................................... 233
10.1.2.Definition of Composition ...................... 235
10.1.3.Web Services and Composition ................... 237
10.1.4.Choreography and Orchestration ................. 238
10.2.Dynamic Composition ................................... 239
10.3.Business-to-Business Communication .................... 240
10.4.Application-to-Application Communication .............. 241
10.5.Complex Business Logic ................................ 242
10.6.Standards and Technologies ............................ 243
10.6.1.Web Services Business Process Execution
Language (WS-BPEL) ............................. 244
10.6.2.Business Process Modeling Notation (BPMN) ...... 245
10.6.3.Web Service Choreography Description Language
(WS-CDL) ....................................... 245
10.6.4.Java Business Integration (JBI) ................ 246
10.7.Clinical Use Case ..................................... 247
10.8.Summary ............................................... 247
11.Semantic Web Services ...................................... 249
11.1.Semantics of Web Services ............................. 249
11.1.1.Why Semantic Web Services? ..................... 249
11.1.2.Interface vs.Implementation .................... 251
11.1.3.Modeling of State .............................. 251
11.2.Alternatives for Capturing Semantics of Web
Services .............................................. 253
11.2.1.Finite State Machines .......................... 253
11.2.2.Statechart Diagrams ............................ 254
11.2.3.Petri Nets ..................................... 254
11.2.4.Process Algebras .................................... 256
11.3.Semantic Web Service Approaches ....................... 259
11.3.1.OWL-S .......................................... 259
11.3.2.SWSF ........................................... 261
11.3.3.WSDL-S ......................................... 266
11.3.4.SAWSDL ......................................... 268
11.3.5.WSMO, WSML and WSMX ............................ 269
11.4.Reasoning with Web Service Semantics .................. 276
11.4.1.Discovery ...................................... 276
11.4.2.Semantic Web Service Composition ............... 281
11.4.3.Mediation ...................................... 283
11.5.Clinical Use Case ..................................... 285
11.6.Summary ............................................... 286
Part IV Standards ............................................. 287
12.Semantic Web Standards ..................................... 289
12.1.Relevant Standards Organization ....................... 289
12.1.1.International Organization for Standardization
(ISO) .......................................... 289
12.1.2.International Elecrtotechnical Commission
(IEC) .......................................... 290
12.1.3.Organization for the Advancement of
Structured Information Standards (OASIS) ....... 290
12.1.4.World Wide Web Consortium (W3C) ................ 290
12.1.5.International Engineering Task Force (IETF) .... 291
12.1.6.National Institute of Standards and
Technology (NIST) .............................. 291
12.1.7.The Object Modeling Group (OMG) ................ 291
12.1.8.Semantic Web Services Initiative (SWSI) ........ 292
12.1.9.United States National Library of Medicine
(NLM) .......................................... 292
12.2.Semantic Web Content Standardization Efforts .......... 293
12.2.1.Standard Generalized Markup Language (SGML) .... 293
12.2.2.extensible Markup Language (XML) ............... 293
12.2.3.extensible Stylesheet Transformation Language
(XSLT) ......................................... 294
12.2.4.XPath .......................................... 294
12.2.5.XQuery ......................................... 294
12.2.6.XML Schema ..................................... 294
12.2.7.Resource Description Framework (RDF) ........... 295
12.2.8.SPARQL ......................................... 295
12.2.9.RDF Schema ..................................... 295
12.2.10.Web Ontology Language (OWL) ................... 296
12.2.11.Rule-ML ....................................... 296
12.2.12.Semantic Web Rules Language (SWRL) ............ 296
12.2.13.Ontology Definition Metamodel (ODM) ........... 296
12.2.14.Unified Modeling Language (UML) ............... 297
12.2.15.Knowledge Interchange Format (KIF) ............ 297
12.2.16.Open Knowledge Base Connectivity Protocol
(OKBC) ........................................ 297
12.2.17.DIG Description Logics Interface .............. 297
12.2.18.OWL API ....................................... 298
12.2.19.Standardized Vocabularies and Ontologies ...... 298
12.3.Semantic Web Services Standardization Efforts ......... 300
12.3.1.ISO-18629 Process Specification Language
(PSL) .......................................... 301
12.3.2.W3C Semantic Annotations for the Web Services
Description Language (SAWSDL) .................. 302
12.3.3.OWL-S .......................................... 303
12.3.4.Web Services Modeling Ontology (WSMO) .......... 303
12.3.5.Semantic Web Services Framework (SWSF) ......... 304
12.3.6.WSDL-S ......................................... 304
12.3.7.OASIS Semantic Execution Environment (SEE) ..... 304
12.3.8.OASIS Service-Oriented Architecture Reference
Model (SOA RM) ................................. 305
12.3.9.Semantic Web Services Architecture (SWSA) ...... 306
12.3.10.Semantic Web Services Interest Group
(SWS-IG) ....................................... 307
12.4.Summary ............................................... 307
Part V Putting it All Together and Perspective ................ 309
13.A Solution Approach to the Clinical Use Case ............... 311
13.1.Service Discovery, Composition and Choreography ....... 312
13.1.1.Specification of Clinical Workflow using
WSMO ........................................... 313
13.1.2.Data Structures in Data Flow ................... 316
13.1.3.Data Mediation ................................. 319
13.1.4.Goal Definition ................................ 328
13.1.5.Discovery ...................................... 331
13.1.6.Orchestration/Service Composition .............. 333
13.1.7.Process and Protocol Mediation ................. 339
13.2.Data and Knowledge Integration ........................ 342
13.2.1.Data Integration Services: WSMO/WSML
Specification .................................. 343
13.2.2.Semantic Data Integration Architecture ......... 344
13.2.3.A Domain Ontology for Translational Medicine ... 346
13.2.4.Use of RDF to represent Genomic and Clinical
Data ........................................... 351
13.2.5.The Integration Process ........................ 353
13.3.Decision Support ...................................... 356
13.3.1.Decision Support Services: WSMO/WSML
Specification .................................. 357
13.3.2.Architecture ................................... 358
13.3.3.Business Object Model Design ................... 359
13.3.4.Rule Base Design ............................... 360
13.3.5.Definitions vs.Actions: Ontology Design ........ 360
13.4.Knowledge Maintenance and Provenance .................. 365
14.Outlook: The Good, the Bad and the Ugly? ................... 369
14.1.The Good - Progress and Impact ........................ 369
14.2.The Bad - Major Obstacles to Overcome ................. 371
14.3.The Ugly - Possible Prohibitors ....................... 372
Part VI References and Index .................................. 375
References .................................................... 377
Index ......................................................... 405
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