SWAT4LS 2015
Semantic Web Applications and Tools for Life Sciences

Table of Contents

SWAT4LS 2015 Papers

• 2015 SWAT4LS International Conference Editorial 1
  James Malone, Robert Stevens, Kerstin Forsberg, Andrea Splendiani
• Finding Novel Associations Across Domains Using Linked Data: a Case Study on Genetic Variants Disrupting Transcription Start Sites 2-12
  Mary Doe, Peter Müstermann Eelke van der Horst, Rajaram Kaliyaperumal, Zuotian Tatum, Mark Thompson, Erik Schultes, Eleni Mina, Ivo Fokkema, Johan den Dunnen, Marco Roos, Jeroen Laros, Barend Mons, Kristina Hettne, Peter A.C 't Hoen
• iCyrus: A Semantic Framework for Biomedical Image Discovery 13-22
  Syed Ahmad Chan Bukhari, Mate Nagy, Paolo Ciccarese, Michael Krauthammer, Christopher J.O Baker
• Linked Functional Annotation For Differentially Expressed Gene (DEG) Demonstrated using Illumina Body Map 2.0 23-32
  Alokkumar Jha, Yasar Khan, Aftab Iqbal, Achille Zappa, Muntazir Mehdi, Ratnesh Sahay, Dietrich Rebholz-Schuhmann
• Towards Shared Hypothesis Testing in the Biomedical Domain 33-37
  Asan Agibetov, Ernesto Jimenez Ruiz, Alessandro Solimando, Giovanna Guerrini, Giuseppe Patanè, Michela Spagnuolo,
• Glycan Pattern Search 38
  Davide Alocci, Julien Mariethoz, Frédérique Lisacek
• VacSeen: A Linked Data-Based Information Architecture to Track Vaccines Using Barcode Scan Authentication 39-48
  Partha Bhattacharjee, Monika Solanki, Rahul Bhattacharyya, Isaac Ehrenberg, Sanjay Sarma
• Suggesting Valid Pharmacogenes by Mining Linked Data 49-58
  Kévin Dalleau, Ndeye Coumba Ndiaye, Adrien Coulet
• ODM on FHIR: Towards Achieving Semantic Interoperability of Clinical Study Data 59-68
  Hugo Leroux, Alejandro Metke, Michael John Lawley
• Wikidata: A Platform for Data Integration and Dissemination for the Life Sciences and Beyond 69-73
  Elvira Mitraka, Andra Waagmeester, Sebastian Burgstaller-Muehlbacher, Lynn M. Schriml, Andrew I. Su, Benjamin M. Good
• Towards the Semantic Standardization of Orthology Content 74-83
  Jesualdo Tomás Fernández-Breis, María Del Carmen Legaz-García, Hirokazu Chiba, Ikuo Uchiyama
• Cell, Chemical and Anatomical Views of the Gene Ontology: Mapping to a Roche Controlled Vocabulary 84-93
  David Osumi-Sutherland, Enrico Ponta, Mélanie Courtot, Helen Parkinson, Laura Badi
• A Highly Literate Approach to Ontology Building 94-107
  Phillip Lord, Jennifer Warrender
• OBOPedia: An Encyclopaedia of Biology Using OBO Ontologies 108-117
  Robert Stevens, Adam Nogradi
• A new Ontology Lookup Service at EMBL-EBI 118-119
  Simon Jupp, Tony Burdett, Catherine Leroy, Helen Parkinson
• Collaborative Ontology Development Using the Webulous Architecture and Google App 120-121
  Simon Jupp, Danielle Welter, Tony Burdett, Helen Parkinson, James Malone
• KnowSense: A Semantically-enabled Pervasive Framework to Assist Clinical Autonomy Assessment 122-131
  Georgios Meditskos, Thanos Stavropoulos, Yiannis Kompatsiaris
• Using Semantics and NLP in Experimental Protocols 132-141
  Olga Giraldo, Alexander Garcia, Oscar Corcho, Jose Figueredo
• R2RML-based Access and Querying to Relational Clinical Data with Morph-RDB 142-151
  Freddy Priyatna, Raul Alonso-Calvo, Sergio Paraiso, Gueton Padron-Sanchez, Oscar Corcho
• D2RQ Mapper 152-154
  Yasunori Yamamoto, Toshiaki Katayama
• Cochrane PICO Annotator and PICOfinder: Using Semantically-enabled Evidence to Find What Works in Health Care 155-156
  Chris Mavergames, Lorne Becker, Irfan Dawood, Anthony Hughes, Julian Everett
• Validata: An Online Tool for Testing RDF Data Conformance 157-166
  Jacob Baungard Hansen, Andrew Beveridge, Roisin Farmer, Leif Gehrmann, Alasdair Gray, Sunil Khutan, Tomas Robertson, Johnny Val
• Exposing Provenance Metadata Using Different RDF Models 167-176
  Gang Fu, Evan Bolton, Núria Queralt, Laura I. Furlong, Vinh Nguyen, Amit Sheth, Olivier Bodenreider, Michel Dumontier

SWAT4LS 2015 Poster Abstracts

• Towards Enabling the Semantic Access of Phenotypic Information in Clinical Letters 177-178
  Shahad Kudama, Rafael Berlanga, Henry Houlden, Ernesto Jimenez-Ruiz, Hallgeir Jonvik, Adam Milward, Huw Morris, Mina Ryten, Jake Saklatvala, Michael Simpson, Nicholas Wood
• OncoCL-KB, a Knowledgebase for Integration of Clinical and Molecular Cancer Data 179-180
  Mary E Dolan
• COPO - Linked Open Infrastructure for Plant Data 181-182
  Felix Shaw, Anthony Etuk, Alejandra Gonzalez-Beltran, Phillip Rocca-Serra, Paul Kersey, Ruth Bastow, Susanna-Assunta Sansone, Vicky Schneider, Robert Davey, David Johnson
• Visualising Ontologies with AberOWL 183-192
  Miguel Ángel Rodríguez-García, Luke Slater, Keiron O'Shea, Paul Schofield, Georgios Gkoutos, Robert Hoehndorf
• Towards an Imaging Biomarker Ontology Based on the Open Biological and Biomedical Ontologies Foundry 193-194
  Emna Amdouni, Yannick Morvan, Bernard Gibaud
• RDF-Based Integration with SPARQL Building System for Life Science Database Archive 195-196
  Atsuko Yamaguchi, Katsuhiko Okubo, Norio Kobayashi, Kouji Kozaki, Sadahiro Kumagai, Kai Lenz, Tomoe Nobusada, Hongyan Wu, Yasunori Yamamoto, Hideki Hatanaka
• From Letters to Pixels 197-198
  Kenneth McLeod, Albert Burger, Christopher Armit, Bill Hill, Richard Baldock
• Performance Evaluation of Human Resources in a Hospital 199-200
  Angel Esteban-Gil, Jesualdo Tomás Fernandez-Breis, Clara Miranda-Lopez
• Digital Dr. House: A Semantic Alerting Platform for the ICU 201-202
  Femke Ongenae, Bram Gadeyne, Femke De Backere, Liesbet De Bus, Pieter Depuydt, Johan Decruyenaere, Filip De Turck
• Automated Generation of SADI Web Services for Clinical Intelligence using Ruled-Based Semantic Mappings 203-204-
  Mohammad Sadnan Al Manir, Alexandre Riazanov, Harold Boley, Artjom Klein, Christopher J.O. Baker
• Exposing French Agronomic Resources as Linked Open Data 205-207
  Aravind Venkatesan, Nordine El Hassouni, Florian Philippe, Cyril Pommier, Hadi Quesneville, Manuel Ruiz, Pierre Larmande
• Feasibility of Modeling HL7 FHIR Profiles Using RDF Shape Expressions Language 208-209
  Harold Solbrig, Eric Prud'hommeaux, Deepak Sharma, Christopher Chute, Guoqian Jiang
• RDF-based Data Sharing of Bio-resource Related Information 210-211
  Hiroshi Masuya, Terue Takatsuki, Mikako Saito, Eiki Takayama, Kazuya Ohshima, Nozomu Ohshiro, Kai Lenz, Nobuhiko Tanaka, Hiroshi Mori, Shuichi Kawashima, Norio Kobayashi
• Semantic-Web Access to Patent Annotations 212-213
  Anna Gaulton, Lee Harland, Mark Davies, George Papadatos, Antonis Loizou, Nathan Dedman, Daniela Digles, Stian Soiland-Reyes, Valery Tkachenko, Stefan Senger, John Overington, Nick Lynch
• SCRY: Enabling Quantitative Reasoning in SPARQL Queries 214-215
  Bas Stringer, Albert Meroño-Peñuela, Antonis Loizou, Sanne Abeln, Jaap Heringa
• Automatic Synthesis of Bioconductor Pipelines: A Domain Modeling Challenge 216-217
  Anna-Lena Lamprecht, Tiziana Margaria
• SPANG: A Command-line Client Supporting Query Generation for Distributed SPARQL Endpoints 218-219
  Hirokazu Chiba, Ikuo Uchiyama
• Using BioPortal as a Repository for Mediating Ontologies in Ontology Alignment 220-221
  Weiguo Xia, Ernesto Jimenez-Ruiz, Valerie Cross
• RIKEN Meta Database: A Life-science Metadata Database Based on the Semantic Web 222-223-
  Norio Kobayashi, Kai Lenz, Hiroshi Masuya
• Exploring the Capacity of Open, Linked Data Sources to Assess Adverse Drug Reaction Signals 224-226
  Pantelis Natsiavas, Vasileios Koutkias, Nicos Maglaveras
• UniProt-GOA: A Central Resource for Data Integration and GO Annotation 227-228
  Mélanie Courtot, Aleksandra Shypitsyna, Elena Speretta, Alexander Holmes, Tony Sawford, Tony Wardell, Maria J. Martin, Claire O'Donovan
• Dem@Care: Ambient Sensing and Intelligent Decision Support for the Care of Dementia 229-230
  Thanos Stavropoulos, Georgios Meditskos, Ioannis Kompatsiaris, Stelios Andreadis
• Information from Semantic Integration of Texts and Databases 231-240
  Erik van Mulligen, Wytze Vlietstra, Rein Vos, Jan Kors
• Measuring the Usability of Triple Stores for Knowledge Management on Trauma Care Organizations 241-242
  Joseph Utecht, Mathias Brochhausen