Data Integration in the Life Sciences

The explosion in the number and size of life science data resources, and the rapid growth in the variety and volume of laboratory data has been fueled by world-wide research activity and the emergence of new technologies. The m- eling, management and analysis of this data often requires a comprehensive - tegration of heterogeneous and typically semistructured data, distributed across many possibly data sources. Recent interoperability standards such as XML and WSDL solve some (easy) problems, but data and process integration often - main time-consuming and error-pone manual tasks. The di?culty of these tasks is compounded by the high degree of semantic heterogeneity across data sources, varying data quality, and other domain-speci?c application requirements. DILS 2005 was the 2nd International Workshop on Data Integration in the Life Sciences, following a successful ?rst DILS workshop, March 2004 in Leipzig, Germany. For a specialized workshop, the DILS 2005 call for papers created a largeinterest(over50abstractsandeventually42papersubmissions;anincrease ofover20%overDILS2004),outofwhichtheinternationalProgramCommittee selected 15 full papers, as well as 5 short papers, and 8 posters/demonstrations, which are all included in this volume. They cover a wide spectrum of theoretical and practical issues including scienti?c/clinical work?ows, ontologies, tools and systems, and integration techniques. DILS 2005 also featured keynotes by Dr. PeterBuneman,ProfessorattheSchoolofInformatics,UniversityofEdinburgh, and Dr. Shankar Subramaniam, Professor at the Department of Bioengineering andChemistry,UCSanDiego.Theprogramalsoincluded6invitedpresentations and reports on ongoing research activities in academia and industry and a panel organized by the AMIA Geomics Working Group.

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Keynotes.- Challenges in Biological Data Integration in the Post-genome Sequence Era.- Curated Databases.- User Applications.- A User-Centric Framework for Accessing Biological Sources and Tools.- BioLog: A Browser Based Collaboration and Resource Navigation Assistant for BioMedical Researchers.- Learning Layouts of Biological Datasets Semi-automatically.- Ontologies.- Factors Affecting Ontology Development in Ecology.- Querying Ontologies in Relational Database Systems.- Scientific Names Are Ambiguous as Identifiers for Biological Taxa: Their Context and Definition Are Required for Accurate Data Integration.- The Multiple Roles of Ontologies in the BioMediator Data Integration System.- Data Integration IIV.- Integrating Heterogeneous Microarray Data Sources Using Correlation Signatures.- Knowledge-Based Integrative Framework for Hypothesis Formation in Biochemical Networks.- Semantic Correspondence in Federated Life Science Data Integration Systems.- Assigning Unique Keys to Chemical Compounds for Data Integration: Some Interesting Counter Examples.- Integrating and Warehousing Liver Gene Expression Data and Related Biomedical Resources in GEDAW.- Information Integration and Knowledge Acquisition from Semantically Heterogeneous Biological Data Sources.- Cluster Based Integration of Heterogeneous Biological Databases Using the AutoMed Toolkit.- Hybrid Integration of Molecular-Biological Annotation Data.- Setup and Annotation of Metabolomic Experiments by Integrating Biological and Mass Spectrometric Metadata.- Performance-Oriented Privacy-Preserving Data Integration.- Potpourri.- Building a Generic Platform for Medical Screening Applications Based on Domain Specific Modeling and Process Orientation.- Automatic Generation of Data Types for Classification of Deep WebSources.- BioNavigation: Selecting Optimum Paths Through Biological Resources to Evaluate Ontological Navigational Queries.- Posters and Demonstrations.- Support for BioIndexing in BLASTgres.- An Environment to Define and Execute In-Silico Workflows Using Web Services.- Web Service Mining for Biological Pathway Discovery.- SemanticBio: Building Conceptual Scientific Workflows over Web Services.- PLATCOM: Current Status and Plan for the Next Stages.- SOAP API for Integrating Biological Interaction Databases.- Collaborative Curation of Data from Bio-medical Texts and Abstracts and Its integration.- Towards an Ontology Based Visual Query System.- Invited Briefings.- Data Integration in the Biomedical Informatics Research Network (BIRN).- Data Integration and Workflow Solutions for Ecology.- Eco-Informatics for Decision Makers Advancing a Research Agenda.- An Architecture and Application for Integrating Curation Data at the Residue Level for Proteins.- The Biozon System for Complex Analysis of Heterogeneous Interrelated Biological Data and Discovery of Emergent Structures.