| Vol-952 urn:nbn:de:0074-952-0 Copyright © 2012 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 2012
Semantic Web Applications and Tools for Life Sciences 2012

### Proceedings of the 5th International Workshop on Semantic Web Applications and Tools for Life Sciences

### Paris, France, November 28-30, 2012.

Edited by

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

1 Corporate Semantic Web,Freie Universitaet Berlin, Germany
2 School of Mathematical and Computer Sciences, Heriot-Watt University, and Human Genetics Unit, Medical Research Council, Edinburgh, Scotland, United Kingdom
3 Bioinformatics, IRCCS AOU San Martino - IST National Cancer Research Institute, Genova, Italy
4 MAASTRO Clinic,The Netherlands
5 intelliLeaf, UK and DERI, IE

## Table of Contents

- Preface

### Keynotes

- Semantic Technology Goes Mainstream
  Mark Musen
- Formal Ontologies for the Semantic Web
  Christine Golbreich
- The World is Flat, but the Earth is Round
  Michael Gibson
- Joining Private and Public Forces to Boost Innovation in Healthcare: The Innovative Medicines Initiative and Knowledge Management
  Ann Marie Martin

### Full Papers

- Catching Inconsistencies with the Semantic Web: A Biocuration Case Study
  Jerven Bolleman, Sebastien Gehant, Nicole Redaschi
- Improved Dataset Coverage and Interoperability with Bio2RDF Release 2
  Alison Callahan, Jose Cruz-Toledo, Peter Ansell, Dana Klassen, Giovanni Tumarello, Michel Dumontier
- OWL Model of Clinical Trial Eligibility Criteria Compatible with Partially-known Information
  Olivier Dameron, Paolo Besana, Oussama Zekri, Annabel Bourdé, Anita Burgun, Marc Cuggia
- Effective Method for Large Scale Ontology Matching
  Gayo Diallo, Mouhamadou Ba
- Annotating Evidence Based Clinical Guidelines - A Lightweight Ontology
  Rinke Hoekstra, Anita De Waard, Richard Vdovjak
- Building Standardized Semantic Web RESTful Services to Support ICD-11 Revision
  Guoqian Jiang, Harold Solbrig, Christopher Chute
- Semantic Web Atlas: Putting Gene Expression Data into Biological Context
  Simon Jupp, Helen Parkinson, James Malone
- Using CDISC ODM and the RDF Data Cube for the Semantic Enrichment of Longitudinal Clinical Trial Data
  Hugo Leroux, Laurent Lefort
- Ontology-Based Classification of Chemicals: a Logic Programming Approach
  Despoina Magka
- Ecotoxicology Data Federation with SADI Semantic Web Services
  Alexandre Riazanov, Matthew Hindle, E. Scott Goudreau, Chris Martyniuk, Christopher Baker

### Position Papers

- Semantic-sensitive Extraction of EHR data to Support Adverse Drug Event Reporting
  Gunnar Declerck, Sajjad Hussain, Yves Parès, Christel Daniel, Marie-Christine Jaulent, Mustafa Yuksel, Ali Anil Sinaci, Gokce Banu Laleci Erturkmen
- Towards Computational Evaluation of Evidence for Scientific Assertions with Nanopublications
  Andrew P Gibson, Jesse C. J. van Dam, Erik A Schultes, Marco Roos, Barend Mons
- Best Practices for Workflow Design: How to Prevent Workflow Decay
  Kristina Hettne, Katherine Wolstencroft, Khalid Belhajjame, Carole Goble, Eleni Mina, Harish Dharuri, David De Roure, Lourdes Verdes-Montenegro, Julian Garrido, Marco Roos
- EHR4CR: A Semantic Web Based Interoperability Approach for Reusing Electronic Healthcare Records in Protocol Feasibility Studies
  Sajjad Hussain, David Ouagne, Eric Sadou, Thierry Dart, Marie-Christine Jaulent, Boris De Vloed, Dirk Colaert, Christel Daniel
- Flexible Integration and Visualisation of Drosophila Melanogaster Datasets
  Martijn P. van Iersel, Julian A. T. Dow, Nadia Anwar
- Delivering 'Cool URIs' That Do Not Change
  Nick Juty, Nicolas Le Novère, Henning Hermjakob, Camille Laibe
- Placing Landmarks in the Knowledge Space: A Web Tool for Crowd-sourcing Landmark Publications to Benchmark Text-mining Predictions
  Mark Thompson, Herman van Haagen, Erik Schultes
- Building Linked Open Data of Life Science Dictionary
  Yasunori Yamamoto, Shoko Kawamoto

### Posters and Demos

- Ontologies Put More Meaning into Meaningful Use
  Tomasz Adamusiak, Naoki Shimoyama, Alexandra Fuiks, Mary Shimoyama
- Conceptual Exploration of Documents and Digital Libraries in the Biomedical Domain
  Leyla Jael García Castro, Alexander Garcia, John Gómez
- Using Semantic Web Technology to Accelerate Plant Breeding
  Pierre-Yves Chibon, Benoît Carrères, Helena de Weerd, Richard Visser, Richard Finkers
- Profiling of Semantically Annotated Proteins
  Jens Hollunder, Vladimir Mironov, Erick Antezana, Robert Hoehndorf, Martin Kuiper
- Cross-lingual Access to Biomedical Terminologies and Ontologies
  Julien Grosjean, Lina F. Soualmia, Tayeb Merabti, Nicolas Griffon, Badisse Dahamna, Stéfan J. Darmoni
- Semi-automatic Generation of Semantic Web Services for Relational Biological Databases
  Wollbrett Julien, Pierre Larmande, Manuel Ruiz
- Semantic Integration of the Genome Annotations
  Toshiaki Katayama, Shinobu Okamoto, Shuichi Kawashima, Hiroshi Mori, Takamoto Fujisawa
- Extracting Medical Information Using Linked Data
  Jakub Kozák, Martin Necaský, Jaroslav Pokorný
- Visual Presentation of Mappings Between Biomedical Ontologies
  Simon Kocbek, Jean-Luc Perret, Jin-Dong Kim
- Towards Reconstructing the Provenance of Clinical Guidelines
  Sara Magliacane, Paul Groth
- DisGeNET: from MySQL to Nanopublication, Modelling Gene-Disease Associations for the Semantic Web
  Núria Queralt-Rosinach, Laura Inés Furlong
- SemScape: Visualizating Semantic Web Data Landscapes with Cytoscape 3.0
  Andrea Splendiani, Andra Waagmeester, Carina Haupt, Helena Deus
- YummyData: Measuring the "Sparkliness" of Biomedical Sparql Endpoints
  Andrea Splendiani, Johan Nystromm-Persson, Michel Dumontier, Yasunori Yamamoto
- Using Nanopublications to Incentivize the Semantic Exposure of Life Science Information
  Mark Thompson, Erik Schultes
- Potential of Linked Open Data in Health Information Representation on the Semantic Web
  Binyam Tilahun

03-Jan-2013: submitted by Adrian Paschke
04-Jan-2013: published on CEUR-WS.org