BASIC CONCEPTS Ontologies and Applications of Ontologies in Biomedicine What Is an Ontology? Ontologies and Bio-Ontologies Ontologies for Data Organization, Integration, and Searching Computer Reasoning with Ontologies Typical Applications of Bio-Ontologies Mathematical Logic and Inference Representation and Logic Propositional Logic First-Order Logic Sets Description Logic Probability Theory and Statistics for Bio-Ontologies Probability Theory Bayes'' Theorem Introduction to Graphs Bayesian Networks Ontology Languages OBO RDF and RDFS OWL and the Semantic Web BIO-ONTOLOGIES The Gene Ontology A Tool for the Unification of Biology Three Subontologies Relations in GO GO Annotations GO Slims Upper-Level Ontologies Basic Formal Ontology The Big Divide: Continuants and Occurrents Universals and Particulars Relation Ontology Revisiting Gene Ontology Revisiting GO Annotations A Selective Survey of Bio-Ontologies OBO Foundry The National Center for Biomedical Ontology Bio-Ontologies What Makes a Good Ontology? GRAPH ALGORITHMS FOR BIO-ONTOLOGIES Overrepresentation Analysis Definitions Term-for-Term Multiple Testing Problem Term-for-Term Analysis: An Extended Example Inferred Annotations Lead to Statistical Dependencies in Ontology DAGs Parent-Child Algorithms Parent-Child Analysis: An Extended Example Topology-Based Algorithms Topology-elim: An Extended Example Other Approaches Summary Model-Based Approaches to GO Analysis A Probabilistic Generative Model for GO Enrichment Analysis A Bayesian Network Model MGSA: An Extended Example Summary Semantic Similarity Information Content in Ontologies Semantic Similarity of Genes and Other Items Annotated by Ontology Terms Statistical Significance of Semantic Similarity Scores Frequency-Aware Bayesian Network Searches in Attribute Ontologies Modeling Queries Probabilistic Inference for the Items Parameter-Augmented Network The Frequency-Aware Network Benchmark INFERENCE IN ONTOLOGIES Inference in the Gene Ontology Inference over GO Edges Cross-Products and Logical Definitions RDFS Semantics and Inference Definitions Interpretations RDF Entailment RDFS Entailment Entailment Rules Summary Inference in OWL Ontologies The Semantics of Equality The Semantics of Properties The Semantics of Classes The Semantics of the Schema Vocabulary Conclusions Algorithmic Foundations of Computational Inference The Tableau Algorithm Developer Libraries SPARQL SPARQL Queries Combining RDF Graphs Conclusions Appendix A: An Overview of R Appendix B: Information Content and Entropy Appendix C: W3C Standards: XML, URIs, and RDF Appendix D: W3C Standards: OWL Bibliography Index Exercises and Further Reading appear at the end of each chapter. lt;/P> BIO-ONTOLOGIES The Gene Ontology A Tool for the Unification of Biology Three Subontologies Relations in GO GO Annotations GO Slims Upper-Level Ontologies Basic Formal Ontology The Big Divide: Continuants and Occurrents Universals and Particulars Relation Ontology Revisiting Gene Ontology Revisiting GO Annotations A Selective Survey of Bio-Ontologies OBO Foundry The National Center for Biomedical Ontology Bio-Ontologies What Makes a Good Ontology? GRAPH ALGORITHMS FOR BIO-ONTOLOGIES Overrepresentation Analysis Definitions Term-for-Term Multiple Testing Problem Term-for-Term Analysis: An Extended Example Inferred Annotations Lead to Statistical Dependencies in Ontology DAGs Parent-Child Algorithms Parent-Child Analysis: An Extended Example Topology-Based Algorithms Topology-elim: An Extended Example Other Approaches Summary Model-Based Approaches to GO Analysis A Probabilistic Generative Model for GO Enrichment Analysis A Bayesian Network Model MGSA: An Extended Example Summary Semantic Similarity Information Content in Ontologies Semantic Similarity of Genes and Other Items Annotated by Ontology Terms Statistical Significance of Semantic Similarity Scores Frequency-Aware Bayesian Network Searches in Attribute Ontologies Modeling Queries Probabilistic Inference for the Items Parameter-Augmented Network The Frequency-Aware Network Benchmark INFERENCE IN ONTOLOGIES Inference in the Gene Ontology Inference over GO Edges Cross-Products and Logical Definitions RDFS Semantics and Inference Definitions Interpretations RDF Entailment RDFS Entailment Entailment Rules Summary Inference in OWL Ontologies The Semantics of Equality The Semantics of Properties The Semantics of Classes The Semantics of the Schema Vocabulary Conclusions Algorithmic Foundations of Computational Inference The Tableau Algorithm Developer Libraries SPARQL SPARQL Queries Combining RDF Graphs Conclusions Appendix A: An Overview of R Appendix B: Information Content and Entropy Appendix C: W3C Standards: XML, URIs, and RDF Appendix D: W3C Standards: OWL Bibliography Index Exercises and Further Reading appear at the end of each chapter. Term Multiple Testing Problem Term-for-Term Analysis: An Extended Example Inferred Annotations Lead to Statistical Dependencies in Ontology DAGs Parent-Child Algorithms Parent-Child Analysis: An Extended Example Topology-Based Algorithms Topology-elim: An Extended Example Other Approaches Summary Model-Based Approaches to GO Analysis A Probabilistic Generative Model for GO Enrichment Analysis A Bayesian Network Model MGSA: An Extended Example Summary Semantic Similarity Information Content in Ontologies Semantic Similarity of Genes and Other Items Annotated by Ontology Terms Statistical Significance of Semantic Similarity Scores Frequency-Aware Bayesian Network Searches in Attribute Ontologies Modeling Queries Probabilistic Inference for the Items Parameter-Augmented Network The Frequency-Aware Network Benchmark INFERENCE IN ONTOLOGIES Inference in the Gene Ontology Inference over GO Edges Cross-Products and Logical Definitions RDFS Semantics and Inference Definitions Interpretations RDF Entailment RDFS Entailment Entailment Rules Summary Inference in OWL Ontologies The Semantics of Equality The Semantics of Properties The Semantics of Classes The Semantics of the Schema Vocabulary Conclusions Algorithmic Foundations of Computational Inference The Tableau Algorithm Developer Libraries SPARQL SPARQL Queries Combining RDF Graphs Conclusions Appendix A: An Overview of R Appendix B: Information Content and Entropy Appendix C: W3C Standards: XML, URIs, and RDF Appendix D: W3C Standards: OWL Bibliography Index Exercises and Further Reading appear at the end of each chapter. re Bayesian Network Searches in Attribute Ontologies Modeling Queries Probabilistic Inference for the Items Parameter-Augmented Network The Frequency-Aware Network Benchmark INFERENCE IN ONTOLOGIES Inference in the Gene Ontology Inference over GO Edges Cross-Products and Logical Definitions RDFS Semantics and Inference Definitions Interpretations RDF Entailment RDFS Entailment Entailment Rules Summary Inference in OWL Ontologies The Semantics of Equality The Semantics of Properties The Semantics of Classes The Semantics of the Schema Vocabulary Conclusions Algorithmic Foundations of Computational Inference The Tableau Algorithm Developer Libraries SPARQL SPARQL Queries Combining RDF Graphs Conclusions Appendix A: An Overview of R Appendix B: Information Content and Entropy Appendix C: W3C Standards: XML, URIs, and RDF Appendix D: W3C Standards: OWL Bibliography Index Exercises and Further Reading appear at the end of each chapter. mp;lt;/P> Algorithmic Foundations of Computational Inference The Tableau Algorithm Developer Libraries SPARQL SPARQL Queries Combining RDF Graphs Conclusions Appendix A: An Overview of R Appendix B: Information Content and Entropy Appendix C: W3C Standards: XML, URIs, and RDF Appendix D: W3C Standards: OWL Bibliography Index Exercises and Further Reading appear at the end of each chapter.