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

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Ulf Leser, Felix Naumann, Barbara Eckman
Springer Science & Business Media, Jul 6, 2006 - Computers - 298 pages
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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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Contents

An Application Driven Perspective on Biological Data Integration
1
Towards a National Healthcare Information Infrastructure
2
Data Access and Integration in the ISPIDER Proteomics Grid
3
A CellCycle Knowledge Integration Framework
19
Link Discovery in Graphs Derived from Biological Databases
35
Towards an Automated Analysis of Biomedical Abstracts
50
A Case Study for Protein Interactions
66
An OntologyBased Solution to Reconcile Heterogeneous SNP Descriptions for Pharmacogenomic Studies
82
Using Term Lists and Inverted Files to Improve Search Speed for Metabolic Pathway Databases
168
A Secure Platform for Designing Personalized Antiretroviral Therapies Against HIV
185
The Distributed Annotation System for Integration of Biological Data
195
An Information Management System for Collaboration Within Distributed Working Environment
204
Ontology Analysis on Complexity and Evolution Based on Conceptual Model
216
Distributed Execution of Workflows in the INB
224
An Exhaustive and Flexible Solution to Model Life Science Domains
232
On Characterising and Identifying Mismatches in Scientific Workflows
240

Integration and Curation of Reaction Kinetics Data
94
A Robust Package for the Integration and Pipelining of Bioinformatics Services
104
Data Structures for Genome Annotation Alternative Splicing and Validation
114
MappingBased Data Integration in Bioinformatics
124
A Method for SimilarityBased Grouping of Biological Data
136
On Querying OBO Ontologies Using a DAG Pattern Query Language
152
CollectionOriented Scientific Workflows for Integrating and Analyzing Biological Data
248
Towards a Model of Provenance and User Views in Scientific Workflows
264
An Extensible LightWeight XMLBased Monitoring System for Sequence Databases
280
Author Index
297
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