Data Integration in the Life Sciences: 5th International Workshop, DILS 2008, Evry, France, June 25-27, 2008, Proceedings (Lecture Notes in Computer Science)

Title Page Preface Organization Table of Contents Ontologies and Data Integration in Biomedicine: Success Stories and Challenging Issues Introduction Gene Ontology Cancer Biomedical Informatics Grid (caBIG) Semantic Web for Health Care and Life Sciences Challenging Issues References BioWarehouse: Relational Integration of Eleven Bioinformatics Databases and Formats Introduction The BioWarehouse Schema The BioWarehouse Loaders Discussion Data Integration in the Life Sciences: Fun, Findings and Frustrations Introduction Observations Analyzing the Evolution of Life Science Ontologies and Mappings Introduction Evolution and Measurement Framework Framework Models Framework Measures Analysis of Ontology Evolution Overview and Versioning Aspects Influence of Evolution on Ontology Structures Evolution of Annotation and Ontology Mappings Evaluation Scenario Evolution of Instance Source vs. Ontologies Evolution on Annotation Mapping Level Evolution on Ontology Mapping Level Related Work Conclusions References Ontology Design Principles and Normalization Techniques in the Web Introduction Materials and Conventions Analysis of BioPAX Ontology Ontology Compatibility Compatibility of BioPAX Ontologies Methods to Improve Ontology’s Sharing Ontology Design Principles Ontology Engineering Conclusion References Exploiting Ontology Structure and Patterns of Annotation to Mine Significant Associations between Pairs of Controlled Vocabulary Terms Introduction Prior Results on LSLINK Association Mining Support and Confidence for $LSLINK$ Mining Results from Mining Motivation for Aggregation Methodology for Aggregation Simple Solution for Aggregation (1L) Limitations of the Simple Solution Comprehensive Solution for Aggregation (2SS) Related Work Experimental Evaluation Generating User Datasets Examples of Identifying Significant Associations Via Aggregation Impact of on Boosted Rank Conclusion Automatic Methods for Integrating Biomedical Data Sources in a Mediator-Based System Introduction Materials and Methods Materials Methods Results Basic Elements of Our Mediator-Based System Application Discussion Contribution of the Proposed Methods Limitations Perspectives References VisGenome and Ensembl: Usability of Integrated Genome Maps Introduction Related Work VisGenome and Ensembl A User Study Experimental Results Discussion User Study Lessons Learnt Conclusions An Entity Resolution Framework for Deduplicating Proteins Introduction Background Protein Entity Resolution Framework (PERF) Mentions The Framework Schema Virtual Attribute Dependencies (VADs) Framework Deduplication Procedure PERF Implementation and Evaluation Evaluation of Mention Resolution Evaluation of Duplicate Resolution Conclusions and Future Work Semantic Representation and Querying of caBIG Data Services Introduction Background Query Processing Result Merging Experimental Results and Discussion Related Work Conclusion References SisGen: A CORBA–Based Data Management Program for DNA Sequencing Projects Introduction Methods Results Platform Design System Features Practical Applications Discussion Conclusion Bgee: Integrating and Comparing Heterogeneous Transcriptome Data Among Species Introduction Designing Homology Relationships between Anatomical Ontologies by an Ontology Alignment Approach Mapping of the Developmental Ontologies Integrating Heterogeneous Data on Anatomical and Developmental Ontologies Mapping Expression Data to Ontologies Statistical Analyses Database and Web-Interface of Bgee Conclusions References ENFIN - An Integrative Structure for Systems Biology Introduction Data Types and Standards The ENFIN Platform: Integrating Tools and Data The EnCORE Platform Extending the Reach of EnCORE Perspectives References A System for Ontology-Based Annotation of Biomedical Data Introduction System Architecture Example Demonstrating the Processing of a GEO Dataset Integration with NCBO BioPortal Conclusion References Bio2RDF : A Semantic Web Atlas of Post Genomic Knowledge about Human and Mouse Introduction Semantic Web Ranking Materials and Methods Results Discussion Conclusion References OMIE: Ontology Mapping within an Interactive and Extensible Environment Introduction Related Works OMIE Description Functionalities The Mapping Process Results Conclusion Chemical Knowledge for the Semantic Web Introduction Methods Chemical Knowledge Representation Open Babel: Chemical File Conversion to OWL DrugBank DBpedia Integration Results Discussion Conclusion References Combining One-Class Classification Models Based on Diverse Biological Data for Prediction of Protein-Protein Interactions Introduction Analysis of Positive Gold Standard Set Parzen OCC Method Integration of Biological Information mRNA Expression Integration Protein Secondary Structure Integration Combination of Diverse OCC Models Diversity of Classification Models Combination Strategies Conclusions Semi Supervised Spectral Clustering for Regulatory Module Discovery Introduction Background and Related Work Spectral Clustering System and Methods Semi Supervised Spectral Clustering Parameter Selection Discussion Conclusion UniProtKB/Swiss-Prot: New and Future Developments References EBI Proteomics Services Bio-ontologies Tutorial Description Target Audience Author Index Annotation This book constitutes the refereed proceedings of the 5th International Workshop on Data Integration in the Life Sciences, DILS 2008, held in Evry, France in June 2008. The 18 revised full papers presented together with 3 keynote talks and a tutorial paper were carefully reviewed and selected from 54 submissions. The papers adress all current issues in data integration and data management from the life science point of view and are organized in topical sections on Semantic Web for the life sciences, designing and evaluating architectures to integrate biological data, new architectures and experience on using systems, systems using technologies from the Semantic Web for the life sciences, mining integrated biological data, and new features of major resources for biomolecular data