SWAT4LS 2016
Semantic Web Applications and Tools for Life Sciences

Table of Contents

• Preface
  
  

Long Papers

• Studying the Cohesion Evolution of Genes Related to Chronic Lymphocytic Leukemia Using Semantic Similarity in Gene Ontology and Self-Organizing Maps
  Efstratios Kontopoulos, Theodoros Moysiadis, Maria Tsagiopoulou, Sándor Darányi, Peter Wittek, Nikos Papakonstantinou, Stavroula Ntoufa, Georgios Meditskos, Yiannis Kompatsiaris, Kostas Stamatopoulos
• Capturing the Relationship between Evolving Biomedical Concepts via Background Knowledge
  Cédric Pruski, Julio Cesar Dos Reis, Marcos Da Silveira
• Understanding the Behaviour of Complex Biomolecular Networks by Combining Logical and Semantic Modeling
  Ali Ayadi, Cecilia Zanni-Merk, Franćois de Bertrand de Beuvron
• Making Linked Data SPARQL with the InterMine Biological Data Warehouse
  Maxime Déraspe, Gail Binkley, Daniela Butano, Matthew Chadwick, J. Michael Cherry, Justin Clark-Casey, Sergio Contrino, Jacques Corbeil, Josh Heimbach, Kalpana Karra, Rachel Lyne, Julie Sullivan, Yo Yehudi, Gos Micklem, Michel Dumontier
• Ontology Learning with Deep Learning: a Case Study on Patient Safety Using PubMed
  Mercedes Arguello Casteleiro, Maria Jesus Fernandez-Prieto, George Demetriou, Nava Maroto, Warren Read, Diego Maseda Fernandez, Jose Julio Des Diz, Goran Nenadic, John Keane, Robert Stevens
• SWISH for Prototyping Clinical Guideline Interactions Theory
  Veruska Zamborlini, Jan Wielemaker, Marcos Da Silveira, Cédric Pruski, Annette Ten Teije, Frank Van Harmelen
• Scaling Out Federated Queries for Life Sciences Data in Production
  Dieter De Witte, Laurens De Vocht, Filip Pattyn, Hans Constandt, Erik Mannens, Ruben Verborgh
• Registries of Domain-Relevant Semantic Reference Models Help Bootstrap Interoperability in Domains with Fragmented Data Resources
  Marco Roos, Mark Wilkinson, Rajaram Kaliyaperumal, Mark Thompson, Claudio Carta, Ronald Cornet, Luiz Olavo Bonino Da Silva Santos
• MuEVo, a Breast Cancer Consumer Health Vocabulary Built Out of Web Forums
  Solène Eholié, Mike Donald Tapi Nzali, Sandra Bringay, Clement Jonquet
• Case Report Form based on semantic Web technologies
  Angel Esteban-Gil, Jesualdo Tomás Fernández-Breis
• SCRY: Extending SPARQL with Custom Data Processing Methods for the Life Sciences
  Bas Stringer, Albert Meroño-Peñuela, Sanne Abeln, Frank Van Harmelen, Jaap Heringa
• Discovering Information from an Integrated Graph Database
  Erik van Mulligen, Wytze Vlietstra, Rein Vos, Jan Kors
• Progressive Data Integration and Semantic Enrichment Based on LinkedScales and Trails
  Matheus Silva Mota, Fagner Pantoja, Julio Cesar Dos Reis, André Santanchè

Short Papers

• Ontology-Driven Context Interpretation and Conflict Resolution in Dialogue-Based Home Care Assistance
  Georgios Meditskos, Efstratios Kontopoulos, Stefanos Vrochidis, Yiannis Kompatsiaris
• Web Service APIs for Scribe Registrars, Nexus Diristries, PORTAL Registries and DOORS Directories in the NPD System
  Adam Craig, Seung-Ho Bae, Teja Veeramacheneni, Koby Taswell , Carl Taswell
• An RDF Based Semantic Approach to Model Temporal Relations in Health Records
  Oya Beyan, Stefan Decker
• Towards the Creation of the Cardiovascular Magnetic Resonance Quality Assessment Ontology (CMR-QA)
  Ernesto Jimenez-Ruiz, Valentina Carapella, Elena Lukaschuk, Nay Aung, Kenneth Fung, Jose Paiva, Mihir Sanghvi, Stefan Neubauer, Steffen Petersen, Ian Horrocks, Stefan Piechnik
• Slim-o-matic: a Semi-Automated Way to Generate Gene Ontology Slims
  Melanie Courtot, Alex Mitchell, Maxim Scheremetjew, Janet Piñero, Laura I. Furlong, Robert D. Finn , Helen Parkinson
• Easy-to-use Semantic Search of Pharmacological Data
  Angel Esteban-Gil, Jesualdo Tomás Fernández-Breis

Posters

• Ontology-based Reflective Iot Middleware-Enabled Agriculture Decision Support System
  Tommaso Di Noia, Marina Mongiello, Francesco Nocera, Eugenio Di Sciascio
• The Organisation of Bring Your Own Data (BYOD) Workshops to Make Life Science Data Linkable at the Source
  Mascha Jansen, Claudio Carta, Marco Roos, Luiz Olavo Bonino Da Silva Santos
• Semantics and Interoperability in a Reporting System for Infectious Disease Control
  Olga Streibel, Göran Kirchner
• Drug Discovery and Big Linked Data
  Ronald Siebes, Victor de Boer, Bryn Williams-Jones, Stian Soiland-Reyes
• A Poster about a New Graph-based Taxonomy RESTful Data Service
  Leyla Jael García Castro, Leonardo Gonzales, Maria Martin
• AgroLD Indexing Tools with Ontological Annotations
  Stella Zevio, Nordine El Hassouni, Manuel Ruiz, Pierre Larmande
• Ontologies Guidelines and Evaluation of Ontologies Mapping Tools and Algorithms
  Ian Harrow, Martin Romacker, Andrea Splendiani, Stefan Negru, Peter Woollard, Scott Markel, Yasmin Alam-Faruque, Martin Koch, Erfan Younesi, James Malone, Ernesto Jimenez-Ruiz
• Umaka-Yummy Data: A Place to Facilitate Communication between Data Providers and Consumers
  Yasunori Yamamoto, Atsuko Yamaguchi, Andrea Splendiani
• HL7 FHIR and Schema.org
  Harold Solbrig, Eric Prud'Hommeaux, Guoqian Jiang
• Finding Drugs with Common Downstream Effects, Using Direction Information in Biological Pathways
  Ryan Miller, Jonathan Melius, Nuno Nunes, Egon Willighagen, Peter Woollard, Chris Evelo
• Updates from the EMBL-EBI RDF platform
  Thomas Liener, Tony Burdett, Simon Jupp
• Answering Scientific Questions with linked European Nanosafety Data
  Egon Willighagen, Micha Rautenberg, Denis Gebele, Linda Rieswijk, Friederike Ehrhart, Jiakang Chang, Georgios Drakakis, Penny Nymark, Pekka Kohonen, Gareth Owen, Haralambos Sarimveis, Christoph Helma, Nina Jeliazkova
• Semantic Web Technologies for a Knowledge Base of Biomedical Facts Extracted from Scientific Literature
  Valentin Grouès, Maria Biryukov, Christophe Trefois, Venkata Satagopam
• SPARQL Query Construction with Monitoring Service for Endpoints
  Atsuko Yamaguchi, Yasunori Yamamoto, Kouji Kozaki, Kai Lenz, Hiroshi Masuya, Norio Kobayashi
• Semantic Linking and Integration of Researchers and Research Organizations in DISQOVER
  Filip Pattyn, Steven Vandeschaeve, Stijn Vermaere, Paulo Van Huffel, Kenny Knecht, Hans Constandt
• FLOPO - An Ontology for the Integration of Trait Data from Digitized Floras and Plant Image Collections
  Claus Weiland, Robert Hoehndorf, George Gosline, Quentin Groom, Thomas Hamann, Marco Schmidt
• Linking Wikidata to the Rest of the Semantic Web
  Andra Waagmeester, Egon Willighagen, Núria Queralt Rosinach, Elvira Mitraka, Sebastian Burgstaller-Muehlbacher, Tim E Putman, Julia Turner, Lynn M Schriml, Paul Pavlidis, Andrew I Su, Benjamin M Good