Note: Intro -- Title Page -- Preface -- Organization -- Table of Contents -- Keynote Presentations -- Data Integration and Exchange for Scientific Collaboration -- Introduction -- Collaborative Data Sharing Systems -- Conclusions -- References -- Data Integration and Semantic Enrichment of Systems Biology Models and Simulations -- Introduction -- Describing Quantitative Models -- MIRIAM -- SBO -- SBML -- Describing Simulation Protocols -- MIASE -- KiSAO -- SED-ML -- Describing Simulation Results -- TEDDY -- SBRML -- Conclusions -- References -- Graph-Based Modelling and Integration -- Linking Life Sciences Data Using Graph-Based Mapping -- Introduction -- Methods -- Data Import and Export -- Data Integration Methods and Algorithms -- Graph Analysis and Visualisation -- Evaluation Methods -- Results -- Mapping Methods - Enzyme Nomenclature vs. Gene Ontology -- Mapping Methods - KEGG vs. AraCyc -- Visualising Results -- Discussion -- References -- Integration of Full-Coverage Probabilistic Functional Networks with Relevance to Specific Biological Processes -- Introduction -- Network Analysis -- Probabilistic Networks -- Dataset Relevance -- Methods -- Network Integration -- Network Evaluation -- Results -- Functional Prediction -- Clustering -- Discussion -- Network Performance -- Conclusions -- References -- OpenFlyData: The Way to Go for Biological Data Integration -- Introduction -- Building the OpenFlyData Software System -- System Architecture -- Data Management -- Semantic Interoperability -- The OpenFlyData Application -- Conclusion -- References -- Annotation -- On the Reachability of Trustworthy Information from Integrated Exploratory Biological Queries -- Introduction -- Related Work -- Methods -- Data Integration for Exploring Graphical Models -- A Fault Tolerance Model over Arbitrary Query Graphs. , Estimating Tolerance of Biological Queries for High-Quality Data -- Results -- Discussion -- References -- Estimating the Quality of Ontology-Based Annotations by Considering Evolutionary Changes -- Introduction -- Annotation Models -- Annotation Mapping and Quality Models -- Evolution Model -- Measures to Quantify Annotation Evolution and Changes -- Assessment of Annotation Stability -- Evaluation -- Provenance Analysis -- Age and Stability Analysis -- Related Work -- Conclusion and Future Work -- References -- Integration and Mining of Genomic Annotations: Experiences and Perspectives in GFINDer Data Warehousing -- Introduction -- GFINDer System and Data Warehouse -- GFINDer Updater -- GFINDer Data Warehouse Releases -- Discussion -- Conclusions and Future Developments -- References -- Structure Inference -- Site-Wide Wrapper Induction for Life Science Deep Web Databases -- Introduction -- Online Life Science Databases: Observations and Implications -- Wrapper Induction -- Page-Level Wrapper Induction -- Site-Wide Wrapper Induction -- Error-Detection by Mutual Reinforcement -- Results and Evaluation -- Page-Level Wrapper Induction Results -- Site-Wide Wrapper Induction -- Related Work -- Conclusions -- References -- An Adaptive Combination of Matchers: Application to the Mapping of Biological Ontologies for Genome Annotation -- Introduction -- O'Browser Method -- A Semi-automatic System -- Matchers -- AdaptiveWeighting -- Structure-BasedMatcher -- O'Browser Modules -- Application: Mapping of Subtilist to FunCat -- Experimental Settings -- Results -- Discussion and Conclusion -- References -- Slicing through the Scientific Literature -- Introduction -- Example Scenario -- Theoretical Foundations -- Slices -- Aligned Ontology Slices -- Framework -- Implementation -- Example Scenario Revisited -- Related Work -- Conclusion -- References. , Data and Work Flows -- Exploiting Parallelism to Accelerate Keyword Search on Deep-Web Sources -- Introduction -- Background and Problem Definition -- System Design and Implementation -- Parallelism in Query Plans -- System Details -- Exploiting Parallelism -- Implementation and Evaluation Study -- Detailed Analysis -- Related Work -- Conclusions -- References -- A Visual Interface for on-the-fly Biological Database Integration and Workflow Design Using VizBuilder -- Introduction -- A Motivating Application: BioFlow by Example -- VizBuilder System Overview -- Operator Definition Using eXtensible Vizbuilder Markup Language (XVML) -- A Sample VizBuilder Application Design Session -- BioFlow with VizBuilder -- {\tt Process} Panel -- {\tt Read} and {\tt Write} Panels -- Revisiting miRNA Regulation: The Running Example -- Related Research -- Summary and Future Research -- References -- EpiC: A Resource for Integrating Information and Analyses to Enable Selection of Epitopes for Antibody Based Experiments -- Introduction -- Rationale for Project -- Why Go for Distributed Data Collection -- Methods -- Distributed Annotation System and Webservices -- Protein Affinity Reagent Ontology -- From Webpage to Application -- Results: Exploring the Epitopes -- Discussion -- References -- Data Integration for Systems Biology -- Design and Architecture of Web Services for Simulation of Biochemical Systems -- Introduction -- Design of COPASI Modeling and Simulation Web Services (CopasiWS) -- CopasiWS Design Issues -- Design of CopasiWS Interface -- CopasiWS WSDL Development -- CopasiWS Architecture -- Resource Layer -- Logic Layer -- Services Interaction Layer -- Prototype Implementation, Testing and Example Usage -- Web Portal User Interface (CopasiWeb) -- Example Usage -- Conclusion and Further Work -- References. , An Integration and Analysis Pipeline for Systems Biology in Crop Plant Metabolism -- Introduction -- Methods -- Model Storage and Reconstruction -- Model Analysis and Simulation -- Model Visualisation -- Case Study -- Conclusion -- References -- Towards Enhanced Retrieval of Biological Models through Annotation-Based Ranking -- Introduction -- State of the Art -- Model Annotations -- Model Repositories -- A Database Schema for Annotated Black-Box Storage of Biological Models -- Determining Similarities between Biological Models -- Similarity Criteria for Biochemical Models -- Sample Search and Ranking -- Conclusions -- References -- Author Index.