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# Semantic Web Applications and Tools for Life Sciences
SWAT4LS 2008

### Proceedings of the Workshop on Semantic Web Applications and Tools for Life Sciences (SWAT4LS)
Edinburgh, United Kingdom, November 28, 2008.

Edited by

### Albert Burger 1), 2)
Adrian Paschke 3), 4)
Paolo Romano 5)
Andrea Splendiani 6), 7)

1) School of Mathematical and Computer Sciences, Heriot-Watt University
2) MRC Human Genetics Unit, Edinburgh, United Kingdom
3) Corporate Semantic Web, Free University Berlin, Berlin
4) Biotechnology Centre, TU Dresden, Dresden, Germany
5) Bioinformatics, National Cancer Research Institute, Genova, Italy
6) Medical Informatics Department, University of Rennes 1, Rennes, France
7) Rothamsted Research, Harpenden, United Kingdom

## Table of Contents

### Preface

### Oral Communications

1. GoWeb: A Semantic Search Engine for the Life Science Web
   Heiko Dietze and Michael Schroeder
2. PathExplorer: Service Mining for Biological Pathways on the Web
   George Zheng, Athman Bouguettaya
3. Knowledge Representation for Web Navigation
   Simon Jupp, Robert Stevens, Sean Bechhofer, Yeliz Yesilada and Patty Kostkova.
4. Structuring the Life Science Resourceome for Semantic Systems Biology: Lessons from the BioGateway Project
   Erick Antezana, Ward Blondé, Mikel Egaña, Alistair Rutherford, Robert Stevens, Bernard De Baets, Vladimir Mironov and Martin Kuiper
5. Semantic Data Integration for Francisella tularensis novicida Proteomic and Genomic Data
   Nadia Anwar, Ela Hunt, Walter Kolch and Andrew Pitt
6. Close Integration of ML and NLP Tools in BioAlvis for Semantic Search in Bacteriology
   Robert Bossy, Alain Kotoujansky, Sophie Aubin and Claire Nedellec
7. KASBi: Knowledge-Based Analysis in Systems Biology
   Maria del Mar Roldan-Garcia, Ismael Navas-Delgado, Amine Kerzazi, Othmane Chniber, Joaquin Molina, Jose F Aldana Montes
8. Use of Shared Lexical Resources for Efficient Ontological Engineering
   Antonio Jimeno, Ernesto Jimenez-Ruiz, Rafael Berlanga, Dietrich Rebholz-Schuhmann

### Highlight Posters

1. Supporting Process Development in Bio-jETI by Model Checking and Synthesis
   Anna-Lena Lamprecht, Tiziana Margaria, Bernhard Steffen
2. Structuring Mined Knowledge for the Support of Hypothesis Generation in Molecular Biology
   Marco Roos, M. Scott Marshall, Andrew Gibson, Pieter Adriaans
3. Knowledge Management Using Wikipedia
   Dongeun Sun, Seongbin Parki, Hyosook Jung
4. Knowledge Translation: Computing the Query Potential of Bio-ontologies
   Wee Tiong Ang, Rajaraman Kanagasabai, Christopher Baker

### Posters

1. BioGateway: Integrated RDF for Life Science Queries
   Erick Antezana, Ward Blondà, Mikel Egaña, Alistair Rutherford, Robert Stevens, Bernard De Baets, Vladimir Mironov, Martin Kuiper
2. The Generation Challenge Programme Model Driven Architecture: Scientific Domain Model and Ontology
   Genevieve Mae Aquino, Jeffrey Detras, Rosemary Shrestha, Martin Senger, Kevin Manansala, Elizabeth Arnaud, Reinhard Simon, Jayashree Balaiji, Thomas Hazekamp, Guy Davenport, Graham McLaren, Theo van Hintum, Richard Bruskiewich
3. The Cell Cycle Ontology: An Application Ontology Supporting the Life Sciences
   Erick Antezana, Mikel Egaña, Ward Blondé, Robert Stevens, Bernard De Baets, Vladimir Mironov, Martin Kuiper
4. The ChEBI Ontology: An Ontology for Chemistry within a Biological Context
   Janna Hastings, Kirill Degtyarenko, Paula de Matos, Marcus Ennis, Christoph Steinbeck
5. LifeDB: An Autonomous System for Semantic Integration of Life Science Data on Hidden Web
   Anupam Bhattacharjee, Aminul Islam, Mohammad Amin, Shahriyar Hossain, Shazzad Hosain, Hasan Jamil
6. The DC-THERA Directory: A Knowledge Management System to Support Collaboration on Dendritic Cell and Immunology Research
   Michaela Guendel, Ciro Scognamiglio, Marco Brandizi, Andrea Splendiani
7. Goal-Oriented Task Composition for Bioinformatics
   Karen Sutherland, Albert Burger
8. An Integrated Ontological Knowledge Base About Orthologous Genes and Proteins
   Jose Antonio Minarro Gimenez, Marisa Madrid, Jesualdo Tomas Fernandez-Breis
9. Penta and Hexa Statements are Suitable for Representing Omics Knowledge on the Semantic Web
   Norio Kobayashi, Tetsuro Toyoda
10. LifeSKIM: Application for Large Scale Biomedical Semantic Annotations
    Vassil Momtchev, Georgi Georgiev, Deyan Peychev
11. A Secure Data Repository Integrating Huge Volumes of Digital Contents as a Semantic Web
    Norio Kobayashi, Yuko Makita, Eli Kaminuma, Shuji Kawaguchi, Yuko Yoshida, Yoshiki Mochizuki, Akihiro Matsushima, Manabu Ishii, Ryo Umetsu, Satomi Asano, Naohiko Heida, Tetsuya Sakurai, Takashi Kuromori, Kazuo Shinozaki, Tetsuro Toyoda
12. Bio-informatics Reactivity Features Through the Semantic Web
    Tiago Franco, Jose Julio Alferes, Ludwig Krippahl, Ricardo Amador
13. A User-Centred Evaluation Framework for the SeaLife Semantic Web Browsers
    Gayo Diallo, Gemma Madle, Gawesh Jawaheer, Patty Kostkova, Dimitra Alexopoulou, Robert Stevens, Simon Jupp, Khaled Khelif

05-Feb-2009: submitted by Paolo Romano
05-Feb-2009: published on CEUR-WS.org