| Vol-698 urn:nbn:de:0074-698-4 Copyright © 2010 for the individual papers by the papers' authors. Copying permitted only for private and academic purposes. This volume is published and copyrighted by its editors.

# SWAT4LS-2010
Semantic Web Applications and Tools for Life Sciences 2010

### Proceedings of the Workshop on Semantic Web Applications and Tools for Life Sciences

### Berlin, Germany, December 10, 2010.

Edited by

### Albert Burger 1,2
M. Scott Marshall 3,4
Paolo Romano 5
Adrian Paschke 6
Andrea Splendiani 7

1 School of Mathematical and Computer Sciences, Heriot-Watt University
2 MRC Human Genetics Unit, Edinburgh, United Kingdom
3 Adaptive Information Disclosure, Informatics Institute, University of Amsterdam, The Netherlands
4 Department of Medical Statistics and Bioinformatics, Leiden University Medical Center, The Netherlands
5 Bioinformatics, National Cancer Research Institute, Genova, Italy
6 Corporate Semantic Web, Free University Berlin, Berlin
7 Rothamsted Research, Harpenden, United Kingdom

## Table of Contents

- Preface

### Papers

1. Analysis of Cancer Omics Data In A Semantic Web Framework
   Matthew E. Holford, James P. McCusker, Kei-Hoi Cheung, Michael Krauthammer
2. Constraint-Guided Workflow Composition Based on the EDAM Ontology
   Anna-Lena Lamprecht, Stefan Naujokat, Bernhard Steffen, Tiziana Margaria
3. Building Conceptual Spaces for Exploring and Linking Biomedical Resources
   R. Berlanga, E. Jimenez-Ruiz, V. Nebot
4. Process Makna - A Semantic Wiki for Scientific Workflows
   Adrian Paschke, Zhili Zhao
5. Argudas: Arguing with Gene Expression Information
   Kenneth McLeod, Gus Ferguson, Albert Burger
6. The CALBC RDF Triple Store: Retrieval over Large Literature Content
   Samuel Croset, Christoph Grabmueller, Chen Li, Silvestras Kavaliauskas, Dietrich Rebholz-Schumann
7. Populous: A Tool for Populating Templates for OWL Ontologies
   Simon Jupp, Matthew Horridge, Luigi Iannone, Julie Klein, Stuart Owen, Joost Schanstra, Robert Stevens, Katy Wolstencroft
8. User Centered and Ontology Based Information Retrieval System for Life Sciences
   Sylvie Ranwez, Vincent Ranwez, Mohameth-Francois Sy, Jacky Montmain, Michel Crampes
9. Ontology-based Queries over Cancer Data
   Alejandra Gonzalez-Beltran, Ben Tagger, Anthony Finkelstein
10. YeastMed: an XML-Based System for Biological Data Integration of Yeast
    Abdelaali Briache, Kamar Marrakchi, Amine Kerzazi, Ismael Navas-Delgado, Jose F. Aldana-Montes, Badr D. Rossi Hassani, Khalid Lairini
11. FreePub: Collecting and Organizing Scientific Material Using Mindmaps
    Theodore Dalamagas, Tryfon Farmakakis, Manolis Maragkakis, Artemis G. Hatzigeorgiou
12. Benchmarking Triple Stores with Biological Data
    Vladimir Mironov, Nirmala Seethappan, Ward Blonde, Erick Antezana, Bjorn Lindi, Martin Kuiper
13. Evaluating Modelling Approaches for Medical Image Annotations
    Jasmin Opitz, Bijan Parsia, Ulrike Sattler

### Demos

14. The AIDA Toolkit - a Tool for Users and Developers
    Adianto Wibisono, Marco Roos, M. Scott Marshall
15. Analysis and Visualisation of RDF Resources in Ondex
    Catherine Canevet, Artem Lysenko, Andrea Splendiani, Matthew Pocock, Christopher Rawlings
16. Use of Semantic Technologies for the Development of a Dynamic Trajectories Generator in a Semantic Chemistry eLearning Platform
    Richard Huber, Kirsten Hantelmann, Alexandru Todor, Sebastian Krebs, Ralf Hesse, Adrian Paschke
17. SPARQL Assist Language-Neutral Query Composer
    Luke McCarthy, Ben Vandervalk, Mark Wilkinson

### Posters

18. Import of ENZYME Data into the ConceptWiki and its Representation as RDF
    Paul Boekschoten, Kees Burger, Barend Mons, Christine Chichester
19. Using Semantic Wikis for Structured Argument in Medical Domain
    Adrian Groza, Radu Balaj
20. First Steps in the Logic-based Assessment of Post-composed Phenotypic Descriptions
    E. Jimenez-Ruiz, B. Cuenca Grau, R. Berlanga, Dietrich Rebholz-Schuhmann
21. Provenance and Evidence in UniProtKB
    Jerven Bolleman, Alain Gateau, Sebastien Gehant, Nicole Redaschi, and the UniProt Consortium
22. Creating a new Ontology: a Modular Approach
    Julia Dmitrieva, Fons J. Verbeek
23. Querying Biomedical Ontologies in Natural Language using Answer Set Programming
    Halit Erdogan, Umut Oztok, Yelda Erdem, Esra Erdem
24. Ontology Usage at ZFIN
    Doug Howe, Christian Pich
25. Rule Responder: A Rule-Based Semantic eScience Service Infrastructure
    Adrian Paschke, Zhili Zhao
26. A Concept Annotation System for Clinical Records
    Ning Kang, Rogier Barendse, Zubair Afzal, Bharat Singh, Martijn J. Schuemie, Erik M. van Mulligen, Jan A. Kors
27. Fundamentals of Semantic Web Technologies in Medical Environments: A Case in Breast Cancer Risk Estimation
    Iker Huerga, Ainhoa Serna, Jon Kepa Gerrikagoitia
28. Linked Environment Data for the Life Sciences
    Maria Ruether, Thomas Bandholz, Antoine Logean
29. Are SNOMED CT Browsers Ready for Institutions? Introducing MySNOM
    Pablo Lopez-Garcia
30. A Semantic Approach for the Requirement-driven Discovery of Web Services in the Life Sciences
    Maria Perez, Rafael Berlanga, Ismael Sanz
31. Ontology and Knowledge Management System on Epilepsy and Epileptic Seizures
    Pedro Almeida, Paulo Gomes, Francisco Sales, Ana Nogueira, Antonio Dourado
32. ChemCloud: Chemical e-Science Information Cloud
    Alexandru Todor, Adrian Paschke, Stephan Heineke
33. semanticsSBML 2.0 - A Collection of Online Services for SBML Models
    Falko Krause, Marvin Schulz, Timo Lubitz, Wolfram Liebermeister
34. A Study on the Relation between Linguistics-oriented and Domain-specific Semantics
    He Tan
35. Scientific Collaborations: Principles of WikiBridge Design
    Eric Leclercq, Marinette Savonnet

7-Feb-2011: submitted by Albert Burger
7-Feb-2011: published on CEUR-WS.org
14-Feb-2011: corrected author names of some papers