Data Integration in the Life Sciences

Third International Workshop, DILS 2006, Hinxton, UK, July 20-22, 2006. Proceedings

  • Ulf Leser
  • Felix Naumann
  • Barbara Eckman
Conference proceedings DILS 2006

DOI: 10.1007/11799511

Part of the Lecture Notes in Computer Science book series (LNCS, volume 4075)

Table of contents (25 papers)

  1. Front Matter
  2. Keynotes

  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

About these proceedings

Introduction

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.

Keywords

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

Editors and affiliations

  • Ulf Leser
    • 1
  • Felix Naumann
    • 2
  • Barbara Eckman
    • 3
  1. 1.Humboldt-Universität zu Berlin 
  2. 2.Humboldt-Universität zu BerlinBerlinGermany
  3. 3.IBM Application and Integration MiddlewareWest ChesterUSA

Bibliographic information

  • Copyright Information Springer-Verlag Berlin Heidelberg 2006
  • Publisher Name Springer, Berlin, Heidelberg
  • eBook Packages Computer Science
  • Print ISBN 978-3-540-36593-8
  • Online ISBN 978-3-540-36595-2
  • Series Print ISSN 0302-9743
  • Series Online ISSN 1611-3349