| Vol-1320 urn:nbn:de:0074-1320-6 Copyright © 2014 for the individual papers by the papers' authors. Copying permitted for private and academic purposes. This volume is published and copyrighted by its editors.

# SWAT4LS 2014
Semantic Web Applications and Tools for Life Sciences

### Proceedings of the 7th International Workshop on Semantic Web Applications and Tools for Life Sciences

### Berlin, Germany, December 9-11, 2014.

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
*** IRCCS AOU San Martino - IST National Cancer Research Institute, Genova, Italy
**** MAASTRO Clinic, Maastricht, The Netherlands
***** Novartis NIBR, Switzerland

## Table of Contents

- Preface

### Full Papers

- SAFE: Policy Aware SPARQL Query Federation Over RDF Data Cubes
  Yasar Khan, Muhammad Saleem, Aftab Iqbal, Muntazir Mehdi, Aidan Hogan, Axel-Cyrille Ngonga Ngomo, Stefan Decker, Ratnesh Sahay
- Scoring Semantic Annotations Returned by The NCBO Annotator
  Soumia Melzi, Clement Jonquet
- Analysis and Visualization of Disease Courses in a Semantic Enabled Cancer Registry
  Angel Esteban-Gil, Jesualdo Tomas Fernandez-Breis, Martin Boeker
- A SPARQL Endpoint Profiler for an Efficient Question Answering System
  Yasunori Yamamoto
- Building a Semantic Web-based Metadata Repository for Facilitating Detailed Clinical Modeling in Cancer Genome Studies
  Guoqian Jiang, Deepak Sharma, Harold Solbrig, Cui Tao, Chunhua Weng, Christopher Chute
- An Intelligent Ontology Alignment Tool Dealing with Complicated Mismatches
  Efthymios Chondrogiannis, Vassiliki Andronikou, Efstathios Karanastasis, Theodora Varvarigou
- Leveraging Post-marketing Drug Safety Research through Semantic Technologies: The PharmacoVigilance Signal Detectors Ontology
  Vassilis Koutkias, Marie-Christine Jaulent
- DebugIT: Ontology-mediated Layered Data Integration for Real-time Antibiotics Resistance Surveillance
  Daniel Schober, Remy Choquet, Kristof Depraetere, Frank Enders, Philipp Daumke, Marie-Christine Jaulent, Douglas Teodoro, Emilie Pasche, Christian Lovis, Martin Boeker

### Position Papers

- GSO: A Semantic Web Ontology to Capture 3D Genome Structure
  Jim Zheng, Jingcheng Du, Jijun Tang, Cui Tao
- SEBI: An Architecture for Biomedical Image Discovery, Interoperability and Reusability Based on Semantic Enrichment
  Syed Ahmad Chan Bukhari, Michael Krauthammer, Christopher Baker

### Short Papers

- A Work Domain Ontology for Modeling Emergency Department Workflow
  Cui Tao, Nnaemeka Okafor, Amit Mehta, Charles L. Maddow, David Robinson, Brent King, Jiajie Zhang, Amy Franklin
- Automatic Summarization for Terminology Recommendation: The Case of the NCBO Ontology Recommender
  Pablo López-García, Stefan Schulz, Roman Kern
- Publishing Diachronic Life Science Linked Data
  Katerina Gkirtzou, Thanasis Vergoulis, Artemis Hatzigeorgiou, Timos Sellis, Theodore Dalamagas
- A Semantic Web Platform for Automating the Interpretation of Finite Element Bio-simulations
  Andre Freitas, Kartik Asooja, Joao Jares, Stefan Decker, Ratnesh Sahay

### Posters

- Representing NCBO Annotator Results in Standard RDF with the Annotation Ontology
  Soumia Melzi, Clement Jonquet
- Bring Your Own Data Workshops: A Mechanism to Aid Data Owners to Comply with Linked Data Best Practices
  Marco Roos, Alasdair J G Gray, Andra Waagmeester, Mark Thompson, Rajaram Kaliyaperumal, Eelke van der Horst, Barend Mons, Mark Wilkinson
- Genome Annotation using Nanopublications: An Approach to Interoperability of Genetic Data
  Rajaram Kaliyaperumal, Peter Bram 'T Hoen, Mark Thompson, Eelke van der Horst, Marco Roos
- Prototype Implementation of SPARQL Builder for Life-science Databases by Intelligent Schema Analysis on RDF datasets
  Norio Kobayashi, Kai Lenz, Hongyan Wu, Kouji Kozaki, Atsuko Yamaguchi
- How Can Semantic Annotations Support the Identification of Network Similarities?
  Christian Rosenke, Dagmar Waltemath
- Effects of Two-way Data Binding on Better User Experience and Easier Development of Clinical Information Systems
  Nihad Omerbegovic, Nedim Omerbegovic, Abdulhamit Subasi
- Aber-OWL: A Framework for Ontology-based Data Access in Biology
  Robert Hoehndorf, Luke Slater, Paul N. Schofield, Georgios Gkoutos

### Demos

- Querying Life Science Ontologies with SemFacet
  Bernardo Cuenca Grau, Evgeny Kharlamov, Sarunas Marciuska, Dmitriy Zheleznyakov, Yujiao Zhou
- Annotopia: An Open Source Universal Annotation Server for Biomedical Research
  Paolo Ciccarese, Tim Clark
- OCMiner: Text Processing, Annotation and Relation Extraction for the Life Sciences
  Timo Böhme, Matthias Irmer, Anett Püschel, Claudia Bobach, Ulf Laube, Lutz Weber
- Graphity: Generic Processor for Declarative Linked Data Applications
  Martynas Jusevičius
- Using eXframe to Build Semantic Web Genomics Repositories
  Emily Merrill, Shannan Ho Sui, Stéphane Corlosquet, Tim Clark, Sudeshna Das
- MaSyMoS: Finding Hidden Treasures in Model Repositories
  Ron Henkel, Dagmar Waltemath
- D3SPARQL: JavaScript Library for Visualization of SPARQL Results
  Toshiaki Katayama
- The NewProt Self-Service Portal for Protein Engineering
  Andreas Schwarte, Hanka Venselaar, Peter Haase, Gert Vriend
- The CombineArchiveWeb Application - A Web-based Tool to Handle Files Associated with Modelling Results
  Martin Scharm, Florian Wendland, Martin Peters, Markus Wolfien, Tom Theile, Dagmar Waltemath

2014-12-24: submitted by Adrian Paschke, metadata incl. bibliographic data published under Creative Commons CC0
2014-12-24: published on CEUR-WS.org |valid HTML5|