Data Integration in the Life Sciences

1. Front Matter

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2. Changing the Model in Pharma and Healthcare – Can We Afford to Wait Any Longer?

   • Erich Alfred Gombocz

   Pages 1-22

3. Ibidas: Querying Flexible Data Structures to Explore Heterogeneous Bioinformatics Data

   • Marc Hulsman, Jan J. Bot, Arjen P. de Vries, Marcel J. T. Reinders

   Pages 23-37

4. From Questions to Effective Answers: On the Utility of Knowledge-Driven Querying Systems for Life Sciences Data

   • Amir H. Asiaee, Prashant Doshi, Todd Minning, Satya Sahoo, Priti Parikh, Amit Sheth et al.

   Pages 38-45

5. OmixAnalyzer – A Web-Based System for Management and Analysis of High-Throughput Omics Data Sets

   • Thomas Stoltmann, Karin Zimmermann, André Koschmieder, Ulf Leser

   Pages 46-53

6. The RDF Pipeline Framework: Automating Distributed, Dependency-Driven Data Pipelines

   • David Booth

   Pages 54-68

7. Towards Interoperable BioNLP Semantic Web Services Using the SADI Framework

   • Ahmad C. Bukhari, Artjom Klein, Christopher J. O. Baker

   Pages 69-80

8. Optimizing Similarity Computations for Ontology Matching - Experiences from GOMMA

   • Michael Hartung, Lars Kolb, Anika Groß, Erhard Rahm

   Pages 81-89

9. Semi-automatic Adaptation of Mappings between Life Science Ontologies

   • Anika Groß, Julio Cesar Dos Reis, Michael Hartung, Cédric Pruski, Erhard Rahm

   Pages 90-104

10. Next Generation Cancer Data Discovery, Access, and Integration Using Prizms and Nanopublications

    • Jamie P. McCusker, Timothy Lebo, Michael Krauthammer, Deborah L. McGuinness

    Pages 105-112

11. Putting It All Together: The Design of a Pipeline for Genome-Wide Functional Annotation of Fungi in the Modern Era of “-Omics” Data and Systems Biology

    • Greg Butler

    Pages 113-127

12. Mining Anti-coagulant Drug-Drug Interactions from Electronic Health Records Using Linked Data

    • Jyotishman Pathak, Richard C. Kiefer, Christopher G. Chute

    Pages 128-140

13. Back Matter

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This book constitutes the refereed proceedings of the 9th International Conference on Data Integration in the Life Sciences, DILS 2013, held in Montreal, QC, Canada, in July 2013. The 10 revised papers included in this volume were carefully reviewed and selected from 23 submissions. The papers cover a range of important topics such as algorithms for ontology matching, interoperable frameworks for text mining using semantic web services, pipelines for genome-wide functional annotation, automation of pipelines providing data discovery and access to distributed resources, knowledge-driven querying-answer systems, prizms, nanopublications, electronic health records and linked data.

• actionable knowledge
• big data
• ontology alignment
• parallel hardware
• semantic Web services

• Department of Computer Science and Applied Statistics, University of New Brunswick, Saint John, Canada

  Christopher J. O. Baker

• Department of Computer Science, Concordia University, Montreal, Canada

  Greg Butler

• Ontario Cancer Institute, University of Toronto, Toronto, Canada

  Igor Jurisica

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