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| Preface | |
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| Introduction to Ontologies | |
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| Hierarchies and Relationships | |
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| Traditional Record Structures | |
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| The eXtensible Markup Language | |
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| Hierarchical Organization | |
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| Creating and Updating XML | |
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| The Meaning of a Hierarchy | |
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| Relationships | |
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| Namespaces | |
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| Exercises | |
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| XML Semantics | |
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| The Meaning of Meaning | |
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| Infosets | |
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| XML Schema | |
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| XML Data | |
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| Exercises | |
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| Rules and Inference | |
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| Introduction to Rule-Based Systems | |
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| Forward- and Backward-Chaining Rule Engines | |
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| Theorem Provers and Other Reasoners | |
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| Performance of Automated Reasoners | |
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| The Semantic Web and Bioinformatics Applications | |
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| The Semantic Web in Bioinformatics | |
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| The Resource Description Framework | |
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| XML Topic Maps | |
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| The Web Ontology Language | |
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| Exercises | |
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| Survey of Ontologies in Bioinformatics | |
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| Bio-Ontologies | |
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| Unified Medical Language System | |
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| The Gene Ontology | |
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| Ontologies of Bioinformatics Ontologies | |
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| Ontology Languages in Bioinformatics | |
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| Macromolecular Sequence Databases | |
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| Nucleotide Sequence Databases | |
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| Protein Sequence Databases | |
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| Structural Databases | |
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| Nucleotide Structure Databases | |
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| Protein Structure Databases | |
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| Transcription Factor Databases | |
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| Species-Specific Databases | |
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| Specialized Protein Databases | |
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| Gene Expression Databases | |
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| Transcriptomics Databases | |
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| Proteomics Databases | |
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| Pathway Databases | |
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| Single Nucleotide Polymorphisms | |
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| Building and Using Ontologies | |
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| Information Retrieval | |
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| The Search Process | |
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| Vector Space Retrieval | |
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| Using Ontologies for Formulating Queries | |
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| Organizing by Citation | |
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| Vector Space Retrieval of Knowledge Representations | |
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| Retrieval of Knowledge Representations | |
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| Sequence Similarity Searching Tools | |
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| Basic Concepts | |
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| Dynamic Programming Algorithm | |
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| Fasta | |
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| Blast | |
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| The BLAST Algorithm | |
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| BLAST Search Types | |
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| Scores and Values | |
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| Blast Variants | |
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| Exercises | |
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| Query Languages | |
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| XML Navigation Using XPath | |
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| Querying XML Using XQuery | |
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| Semantic Web Queries | |
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| Exercises | |
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| The Transformation Process | |
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| Experimental and Statistical Methods as Transformations | |
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| Presentation of Information | |
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| Changing the Point of View | |
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| Transformation Techniques | |
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| Automating Transformations | |
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| Transforming with Traditional Programming Languages | |
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| Text Transformations | |
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| Line-Oriented Transformation | |
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| Multidimensional Arrays | |
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| Perl Procedures | |
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| Pattern Matching | |
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| Perl Data Structures | |
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| Transforming XML | |
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| Using Perl Modules and Objects | |
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| Processing XML Elements | |
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| The Document Object Model | |
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| Producing XML | |
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| Transforming XML to XML | |
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| Exercises | |
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| The XML Transformation Language | |
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| Transformation as Digestion | |
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| Programming in XSLT | |
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| Navigation and Computation | |
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| Conditionals | |
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| Precise Formatting | |
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| Multiple Source Documents | |
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| Procedural Programming | |
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| Exercises | |
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| Building Bioinformatics Ontologies | |
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| Purpose of Ontology Development | |
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| Selecting an Ontology Language | |
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| Ontology Development Tools | |
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| Acquiring Domain Knowledge | |
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| Reusing Existing Ontologies | |
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| Designing the Concept Hierarchy | |
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| Uniform Hierarchy | |
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| Classes vs. Instances | |
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| Ontological Commitment | |
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| Strict Taxonomies | |
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| Designing the Properties | |
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| Classes vs. Property Values | |
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| Domain and Range Constraints | |
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| Cardinality Constraints | |
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| Validating and Modifying the Ontology | |
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| Exercises | |
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| Reasoning with Uncertainty | |
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| Inductive vs. Deductive Reasoning | |
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| Sources and Semantics of Uncertainty | |
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| Extensional Approaches to Uncertainty | |
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| Intensional Approaches to Uncertainty | |
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| Bayesian Networks | |
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| The Bayesian Network Formalism | |
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| Stochastic Inference | |
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| Constructing Bayesian Networks | |
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| BN Requirements | |
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| Machine Learning | |
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| Building BNs from Components | |
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| Ontologies as BNs | |
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| BN Design Patterns | |
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| Validating and Revising BNs | |
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| Exercises | |
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| Combining Information | |
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| Combining Discrete Information | |
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| Combining Continuous Information | |
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| Information Combination as a BN Design Pattern | |
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| Measuring Probability | |
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| Dempster-Shafer Theory | |
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| The Bayesian Web | |
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| Introduction | |
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| Requirements for Bayesian Network Interoperability | |
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| Extending the Semantic Web | |
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| Ontologies for Bayesian Networks | |
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| Answers to Selected Exercises | |
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| References | |
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| Index | |