Data Integration in the Life Sciences

1. Front Matter

   PDF

2. Keynotes

   1. An Application Driven Perspective on Biological Data Integration

      • Victor M. Markowitz

      Pages 1-1

   2. Towards a National Healthcare Information Infrastructure

      • Sarah Knoop

      Pages 2-2

3. Data Integration

   1. Data Access and Integration in the ISPIDER Proteomics Grid

      • Lucas Zamboulis, Hao Fan, Khalid Belhajjame, Jennifer Siepen, Andrew Jones, Nigel Martin et al.

      Pages 3-18

   2. A Cell-Cycle Knowledge Integration Framework

      • Erick Antezana, Elena Tsiporkova, Vladimir Mironov, Martin Kuiper

      Pages 19-34

   3. Link Discovery in Graphs Derived from Biological Databases

      • Petteri Sevon, Lauri Eronen, Petteri Hintsanen, Kimmo Kulovesi, Hannu Toivonen

      Pages 35-49

4. Text Mining

   1. Towards an Automated Analysis of Biomedical Abstracts

      • Barbara Gawronska, Björn Erlendsson, Björn Olsson

      Pages 50-65

   2. Improving Text Mining with Controlled Natural Language: A Case Study for Protein Interactions

      • Tobias Kuhn, Loïc Royer, Norbert E. Fuchs, Michael Schröder

      Pages 66-81

   3. SNP-Converter: An Ontology-Based Solution to Reconcile Heterogeneous SNP Descriptions for Pharmacogenomic Studies

      • Adrien Coulet, Malika Smaïl-Tabbone, Pascale Benlian, Amedeo Napoli, Marie-Dominique Devignes

      Pages 82-93

5. Systems I

   1. SABIO-RK: Integration and Curation of Reaction Kinetics Data

      • Ulrike Wittig, Martin Golebiewski, Renate Kania, Olga Krebs, Saqib Mir, Andreas Weidemann et al.

      Pages 94-103

   2. SIBIOS Ontology: A Robust Package for the Integration and Pipelining of Bioinformatics Services

      • Malika Mahoui, Zina Ben Miled, Sriram Srinivasan, Mindi Dippold, Bing Yang, Li Nianhua

      Pages 104-113

   3. Data Structures for Genome Annotation, Alternative Splicing, and Validation

      • Sven Mielordt, Ivo Grosse, Jürgen Kleffe

      Pages 114-123

   4. BioFuice: Mapping-Based Data Integration in Bioinformatics

      • Toralf Kirsten, Erhard Rahm

      Pages 124-135

6. Potpourri

   1. A Method for Similarity-Based Grouping of Biological Data

      • Vaida Jakonienė, David Rundqvist, Patrick Lambrix

      Pages 136-151

   2. On Querying OBO Ontologies Using a DAG Pattern Query Language

      • Amarnath Gupta, Simone Santini

      Pages 152-167

   3. Using Term Lists and Inverted Files to Improve Search Speed for Metabolic Pathway Databases

      • Greeshma Neglur, Robert L. Grossman, Natalia Maltsev, Clement Yu

      Pages 168-184

7. Systems II

   1. Arevir: A Secure Platform for Designing Personalized Antiretroviral Therapies Against HIV

      • Kirsten Roomp, Niko Beerenwinkel, Tobias Sing, Eugen Schülter, Joachim Büch, Saleta Sierra-Aragon et al.

      Pages 185-194

   2. The Distributed Annotation System for Integration of Biological Data

      • Andreas Prlić, Ewan Birney, Tony Cox, Thomas A. Down, Rob Finn, Stefan Gräf et al.

      Pages 195-203

   3. An Information Management System for Collaboration Within Distributed Working Environment

      • Maria Samsonova, Andrei Pisarev, Konstantin Kozlov, Ekaterina Poustelnikova, Arthur Tkachenko

      Pages 204-215

8. Short Papers

   1. Ontology Analysis on Complexity and Evolution Based on Conceptual Model

      • Zhe Yang, Dalu Zhang, Chuan Ye

      Pages 216-223

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.

• Annotation
• DOM
• Web services
• XML
• bioinformatics
• biomedical data analysis
• clustering
• data analysis
• data mining
• data transformation ontologies
• databases
• genome
• indexing
• interoperability
• life sciences

• Humboldt-Universität zu Berlin,  

  Ulf Leser

• Humboldt-Universität zu Berlin, Berlin, Germany

  Felix Naumann

• IBM Application and Integration Middleware, West Chester, USA

  Barbara Eckman

Policies and ethics