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

✍ Scribed by Sarah Cohen-Boulakia Christine Froidevaux,Amos Bairoch

• Publisher: Springer
• Year: 2008
• Tongue: English
• Leaves: 221
• Category: Library

✦ Synopsis

Book by

✦ Table of Contents

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