| Vol-1114 urn:nbn:de:0074-1114-0 Copyright © 2013 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 2013
Semantic Web Applications and Tools for Life Sciences

### Proceedings of the 6th International Workshop on Semantic Web Applications and Tools for Life Sciences

### Edinburgh, UK, December 10, 2013.

Edited by

### Adrian Paschke *
Albert Burger **
Paolo Romano ***
M. Scott Marshall ****
Andrea Splendiani *****

* Freie Universitaet Berlin, Department of Mathematics and Computer Science, AG Corporate Semantic Web, 14195 Berlin, Germany
** School of Mathematical and Computer Sciences, Heriot-Watt University, and Human Genetics Unit, Medical Research Council, Edinburgh, Scotland, United Kingdom
*** Bioinformatics, IRCCS AOU San Martino - IST National Cancer Research Institute, Genova, Italy
**** MAASTRO Clinic,The Netherlands
***** intelliLeaf, UK and DERI, IE

## Table of Contents

- Preface

### Full Papers

- Refining Health Outcomes of Interest using Formal Concept Analysis and Semantic Query Expansion
  Olivier Curé, Henri Maurer, Nigam Shah, Paea Lependu
- Computable Declarative Representation of Clinical Assessment Scales in EHRs
  Mercedes Arguello Casteleiro, Nicolas Matentzoglu, Bijan Parsia, Sebastian Brandt
- Using Semantic Web Techologies for the Generation of Domain Templates to Support Clinical Study Meta-Data
  Guoqian Jiang, Julie Evans, Cory Endle, Harold Solbrig, Christopher Chute
- Identifying Latent Semantics in High-Dimensional Web Data
  Ajit Kumar, Sanjeev Maskara, Jau-Min Wong, I-Jen Chiang
- Organic Synthesis as Artificial Intelligence Planning
  Arman Masoumi, Mikhail Soutchanski, Andrea Marrella
- Using Linked Data for Better Navigation in Summaries of Product Characteristics
  Jakub Kozák, Martin Necaský, Jan Dedek, Jakub Klímek, Jaroslav Pokorný
- Nanopublications for Exposing Experimental Data in the Life-sciences: A Huntington's Disease Case Study
  Eleni Mina, Mark Thompson, Rajaram Kaliyaperumal, Jun Zhao, Kristina Hettne, Erik Schultes, Marco Roos
- A Formal Model for Weakly-structured Scientific Workflows
  Zhili Zhao, Adrian Paschke
- A Pattern-driven Approach to Biomedical Ontology Engineering
  Jennifer Warrender, Phillip Lord
- An Ontology for Drug-drug Interactions
  Maria Herrero-Zazo, Janna Hastings, Isabel Segura-Bedmar, Samuel Croset, Paloma Martinez, Christoph Steinbeck
- Estimating Coordination in Medical Terminologies
  Cornelia Hedeler, Bijan Parsia, Sebastian Brandt
- Ontology-based Temporal Analysis for Medical Device Adverse Event - A Use Case Study on Late Stent Thrombosis
  Kimberly Clark, Deepak Sharma, Rui Qin, Christopher Chute, Cui Tao
- Computing Identity Co-Reference Across Drug Discovery Datasets
  Christian Y. A. Brenninkmeijer, Ian Dunlop, Carole Goble, Alasdair J. G. Gray, Steve Pettifer, Robert Stevens

### Position Papers

- On the Annotation of Drug Databases with the Anatomical Therapeutic Chemical Classification System
  Olivier Curé

### Posters and Demos

- Linked Data Services for Scientists Exemplified Using Drosophila Melanogaster Datasets
  Martijn van Iersel, Nadia Anwar, Liz Reynolds
- Patient History Navigation with the Use of Common Data Elements
  A. Anil Sinaci, Gokce B. Laleci Erturkmen, Suat Gonul, H. Alper Cinar, Atakan Kaya
- A Web Prototype for Detecting Chemical Compounds and Drugs
  Daniel Sánchez-Cisneros, Sara Lana-Serrano, Isabel Segura Bedmar, Leonardo Campillos Llanos, Paloma Martínez Fernández
- OpenPHACTS Explorer 2: Bringing the Web to the Semantic Web
  Ian Dunlop, Rishi Ramgolam, Steve Pettifer, Alasdair Gray, James Eales, Carole Goble, Jan Velterop
- Demonstration of the SALUS Semantic Interoperability Framework for Case Series Characterization Studies
  Mustafa Yuksel, Suat Gonul, Gokce Banu Laleci Erturkmen, Ali Anil Sinaci, Kristof Depraetere, Jos De Roo, Tomas Bergvall
- OntoMaven API4KB - A Maven-based API for Knowledge Bases
  Adrian Paschke
- Interactive Platform for Semantic Gene Expression Analysis of Alzheimer's Disease
  Toshiaki Katayama, Masataka Kikuchi, Soichi Ogishima
- Towards Learning Based Strategy for Improving the Recall of the ServOMap Matching System
  Gayo Diallo, Amal Kammoun
- Applying the Semantic Web to Computational Chemistry
  Neil Ostlund, Mirek Sopek
- DisGeNET RDF: A Gene-Disease Association Linked Open Data Resource
  Núria Queralt-Rosinach, Laura I. Furlong
- Assessing and Improving SKOS Mapping Quality
  Hong Sun, Jos De Roo, Giovanni Mels, Kristof Depraetere, Marc Twagirumukiza, Boris De Vloed, Dirk Colaert
- A Semantic-enabled Framework for Drug Recommendations
  Charalampos Doulaverakis, George Nikolaidis, Athanasios Kleontas, Ioannis Kompatsiaris
- PosMed: A Biomedical Entity Prioritisation Tool Based on Statistical Inference over Literature and the Semantic Web
  Norio Kobayashi, Yuko Makita, Manabu Ishii, Akihiro Matsushima, Yoshiki Mochizuki, Koji Doi, Koro Nishikata, David Gifford, Terue Takatsuki, Hiroshi Masuya, Tetsuro Toyoda
- Semantic Rule Processing for Real-time Data Integration
  Pedro Lopes, José Luis Oliveira
- Exploring Nanopublishing with COEUS
  Pedro Lopes, Pedro Sernadela, José Luis Oliveira
- Weighting Indirect Relations to Elucidate the Direct Association of SNP-Disease by Use of SPARQL Queries
  Remzi Çelebi, Özgür Gümüs, Yedim Aysin Son
- Workflows and Services for Concept Profile Generation
  Eelke van der Horst, Marco Roos, Kristina Hettne
- Social-aware and Context-aware Multi-sensor Fall Detection Platform
  Femke De Backere, Femke Ongenae, Floris Van den Abeele, Jeroen Hoebeke, Stijn Verstichel, Ann Ackaert, Filip De Turck

2014-01-07: submitted by Adrian Paschke
2014-01-07: published on CEUR-WS.org |valid HTML5|