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