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