SWAT4LS 2014
Semantic Web Applications and Tools for Life Sciences

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