Data Integration in the Life Sciences: Third International Workshop, DILS 2006, Hinxton, UK, July 20-22, 2006. Proceedings

Victor M. Markowitz (auth.), Ulf Leser, Felix Naumann, Barbara Eckman (eds.)3540365931, 9783540365938

Data management and data integration are fundamental problems in the life sciences. Advances in molecular biology and molecular medicine are almost u- versallyunderpinned by enormouse?orts in data management,data integration, automatic data quality assurance, and computational data analysis. Many hot topics in the life sciences, such as systems biology, personalized medicine, and pharmacogenomics, critically depend on integrating data sets and applications producedby di?erent experimentalmethods, in di?erent researchgroups,andat di?erent levels of granularity. Despite more than a decade of intensive research in these areas, there remain many unsolved problems. In some respects, these problems are becoming more severe, both due to continuous increases in data volumes and the growing diversity in types of data that need to be managed. And the next big challenge is already upon us: the need to integrate the di?- ent “omics” data sets with the vast amounts of clinical data, collected daily in thousands of hospitals and physicians’ o?ces all over the world. DILS 2006 is the third in an annual workshop series that aims at fostering discussion, exchange, and innovation in research and development in the areas of data integration and data management for the life science. DILS 2004 in Leipzig and DILS 2005 in San Diego each attracted around 100 researchersfrom all over the world. This year the number of submitted papers again increased. The Program Committee selected 23 papers out of 50 strong full submissions.

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Table of contents :
Front Matter….Pages –
An Application Driven Perspective on Biological Data Integration….Pages 1-1
Towards a National Healthcare Information Infrastructure….Pages 2-2
Data Access and Integration in the ISPIDER Proteomics Grid….Pages 3-18
A Cell-Cycle Knowledge Integration Framework….Pages 19-34
Link Discovery in Graphs Derived from Biological Databases….Pages 35-49
Towards an Automated Analysis of Biomedical Abstracts….Pages 50-65
Improving Text Mining with Controlled Natural Language: A Case Study for Protein Interactions….Pages 66-81
SNP-Converter: An Ontology-Based Solution to Reconcile Heterogeneous SNP Descriptions for Pharmacogenomic Studies….Pages 82-93
SABIO-RK: Integration and Curation of Reaction Kinetics Data….Pages 94-103
SIBIOS Ontology: A Robust Package for the Integration and Pipelining of Bioinformatics Services….Pages 104-113
Data Structures for Genome Annotation, Alternative Splicing, and Validation….Pages 114-123
BioFuice: Mapping-Based Data Integration in Bioinformatics….Pages 124-135
A Method for Similarity-Based Grouping of Biological Data….Pages 136-151
On Querying OBO Ontologies Using a DAG Pattern Query Language….Pages 152-167
Using Term Lists and Inverted Files to Improve Search Speed for Metabolic Pathway Databases….Pages 168-184
Arevir: A Secure Platform for Designing Personalized Antiretroviral Therapies Against HIV….Pages 185-194
The Distributed Annotation System for Integration of Biological Data….Pages 195-203
An Information Management System for Collaboration Within Distributed Working Environment….Pages 204-215
Ontology Analysis on Complexity and Evolution Based on Conceptual Model….Pages 216-223
Distributed Execution of Workflows in the INB….Pages 224-231
Knowledge Networks of Biological and Medical Data: An Exhaustive and Flexible Solution to Model Life Science Domains….Pages 232-239
On Characterising and Identifying Mismatches in Scientific Workflows….Pages 240-247
Collection-Oriented Scientific Workflows for Integrating and Analyzing Biological Data….Pages 248-263
Towards a Model of Provenance and User Views in Scientific Workflows….Pages 264-279
An Extensible Light-Weight XML-Based Monitoring System for Sequence Databases….Pages 280-296
Back Matter….Pages –