| Hybrid Reasoning with Rules and Ontologies | p. 1 |
| Introduction | p. 1 |
| Overview of Approaches | p. 2 |
| RDF and RDF Schema | p. 2 |
| The Web Ontology Language OWL | p. 5 |
| Rule Languages for Integration | p. 7 |
| Rule Interchange Format RIF | p. 9 |
| Approaches to Integration | p. 9 |
| Hybrid Rules and Ontologies in REWERSE | p. 12 |
| Extensions of Expressive Non-monotonic Logic Programs by DL-Programs and HEX-Programs | p. 14 |
| DL-Programs | p. 14 |
| HEX-Programs | p. 19 |
| Extensions of Well-Founded Semantics by Hybrid Well-Founded Semantics | p. 26 |
| Variants and Extensions of the Basic Formalisms | p. 34 |
| Probabilistic DL-Programs | p. 35 |
| Fuzzy DL-Programs | p. 37 |
| CQ-Programs | p. 40 |
| Conclusion | p. 41 |
| Four Lessons in Versatility or How Query Languages Adapt to the Web | p. 50 |
| Introduction | p. 50 |
| Versatile Data | p. 54 |
| Extensible Markup Language (XML) | p. 54 |
| Resource Description Framework (RDF) | p. 56 |
| Versatile Queries | p. 58 |
| XML Queries-Examples and Patterns | p. 61 |
| RDF Queries-Examples and Patterns | p. 68 |
| Rules-Separation of Concern and Reasoning | p. 79 |
| State of the Art: The SPARQL Query Language and Its Extensions | p. 82 |
| Versatile Semantics | p. 96 |
| Simulation as Foundation for a Semantics of Versatile Queries | p. 96 |
| Rules with Negation and Versatile Queries: Local Stratification | p. 100 |
| Rules with Negation and Versatile Queries: Well-Founded Semantics | p. 104 |
| A Relational Semantics for Versatile Queries | p. 107 |
| Versatile Evaluation | p. 125 |
| Evaluating Queries: Structure Scaling with CIQCAG | p. 126 |
| Evaluating Rules: Subsumption under Rich Unification | p. 142 |
| Conclusion | p. 152 |
| Evolution and Reactivity in the Semantic Web | p. 161 |
| Introduction | p. 161 |
| Starting Point and Related Work | p. 164 |
| Conceptualization of ECA Rules and Their Components: A General Framework for ECA Rules | p. 167 |
| The Rule Level | p. 168 |
| The Event Component | p. 170 |
| The Condition Component | p. 171 |
| The Action Component | p. 172 |
| Languages and Language Borders | p. 173 |
| Languages Types, Service Types, and Tasks | p. 175 |
| Architecture and Processing: Cooperation between Resources | p. 178 |
| The RDF Level: Language Elements and Their Instances as Resources | p. 179 |
| MARS Implementation | p. 180 |
| r3 Implementation | p. 183 |
| X Change-A Concrete Web-Based ECA Rule Language | p. 184 |
| Representing, Querying, and Constructing Web Data | p. 185 |
| Event-Condition-Action (ECA) Rules | p. 187 |
| Events | p. 187 |
| Conditions | p. 190 |
| Actions | p. 191 |
| Applications | p. 192 |
| Conclusions and Outlook | p. 194 |
| Rule-Based Policy Representations and Reasoning | p. 201 |
| Introduction | p. 201 |
| A Review of the State-of-the-Art in Policy Languages | p. 202 |
| Related Work | p. 203 |
| Background | p. 203 |
| Presentation of the Considered Policy Languages | p. 205 |
| Presentation of the Considered Criteria | p. 206 |
| Comparison | p. 209 |
| Discussion | p. 215 |
| A Framework for Semantic Web Policies | p. 216 |
| Policies as Semantic Markup in Protune | p. 217 |
| Negotiations | p. 217 |
| Protune's Policy Language and Framework | p. 219 |
| Explanations: Protune-X | p. 221 |
| The Engine | p. 225 |
| Demo: Policy-Driven Protection and Personalization of Web Content | p. 227 |
| Experimental Evaluation | p. 227 |
| Discussion and Conclusions | p. 229 |
| Component Models for Semantic Web Languages | p. 233 |
| Introduction | p. 233 |
| Background | p. 235 |
| Composition Systems and Component Models | p. 235 |
| Web Query Language Xcerpt | p. 237 |
| Description Logics and OWL | p. 239 |
| State of the Art: Semantic Web Components and Invasive Software Component Models | p. 240 |
| Query Modularization | p. 240 |
| Ontology Modularization | p. 241 |
| Invasive Component Models in Software Engineering | p. 243 |
| Use-Cases: Components on the Web | p. 249 |
| Modular Xcerpt | p. 250 |
| Role Models as Ontology Components | p. 253 |
| Universal Component Models | p. 255 |
| Universal Grammar-Based Modularization (U-GBM) | p. 256 |
| Universal Invasive Software Composition (U-ISC) | p. 259 |
| Universal Syntactic Abstractions with Embedded ISC | p. 263 |
| Example Application: Modular Xcerpt | p. 268 |
| Conclusions | p. 271 |
| Controlled English for Reasoning on the Semantic Web | p. 276 |
| Why Use Controlled Natural Languages for the Semantic Web? | p. 276 |
| Controlled Natural Languages: State of the Art | p. 278 |
| Attempto Controlled English (ACE) | p. 279 |
| Overview of Attempto Controlled English | p. 279 |
| From Attempto Controlled English to First-Order Logic | p. 283 |
| Attempto Parsing Engine (APE) | p. 286 |
| Fitting ACE into the Semantic Web | p. 287 |
| OWL and SWRL | p. 287 |
| AceRules: Rules in ACE | p. 290 |
| The Protune Policy Language | p. 292 |
| Other Web Languages | p. 295 |
| ACE Tools for the Semantic Web | p. 295 |
| Attempto Reasoner RACE | p. 295 |
| ACE View Ontology and Rule Editor | p. 297 |
| AceWiki: ACE in a Semantic Wiki | p. 300 |
| Protune | p. 304 |
| Conclusions | p. 305 |
| Semantic Search with GoPubMed | p. 309 |
| Biomedical Literature Search | p. 309 |
| Limits of Classical Search | p. 310 |
| Biomedical Search Engines | p. 311 |
| The Ontology-Based Search Paradigm | p. 321 |
| Answering Biomedical Questions | p. 322 |
| Characterization of Question Types | p. 324 |
| Using Background Knowledge to Answer Questions | p. 326 |
| Revealing Trends in the Literature | p. 330 |
| Important Topic: Apotosis | p. 333 |
| Important Topic: Endosome | p. 334 |
| Important Place: Dresden | p. 334 |
| Important Journal: Which Are the 10 Most Frequently Used GO Terms in Nature, Cell and Science? | p. 335 |
| 20 Journals for the Molecular Biologist | p. 336 |
| Conclusion | p. 338 |
| Information Integration in Bioinformatics with Ontologies and Standards | p. 343 |
| Introduction | p. 343 |
| Resources | p. 345 |
| Data Sources | p. 345 |
| Ontologies | p. 346 |
| Standards | p. 348 |
| Integrating the Resources | p. 352 |
| Integration Model | p. 352 |
| Integration of Data Sources | p. 354 |
| Data Sources and Ontologies | p. 355 |
| Ontology Alignment | p. 356 |
| Integrating Standards | p. 365 |
| Connection between Standards and Other Resources | p. 367 |
| Conclusion | p. 369 |
| Author Index | p. 377 |
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