Publications

2014

SAFE: Policy Aware SPARQL Query Federation Over RDF Data Cubes. Yasar Khan, Muhammad Saleem, Aftab Iqbal, Muntazir Mehdi, Aidan Hogan, Panagiotis Hasapis, Axel-Cyrille Ngonga Ngomo, Stefan Decker, Ratnesh Sahay. Proceedings of The Semantic Web Applications and Tools for the Life Sciences  (SWAT4LS) 2014, Freie Universtität Berlin, Germany, 2014.

A Formal Investigation of Semantic Interoperability of HCLS Systems. Ratnesh Sahay, Antoine Zimmermann, Ronan Fox, Axel Polleres, Manfred Hauswirth. In Miguel-Angel Sicilia, Pablo Serrano-Balazote (ed.), Interoperability in Healthcare Information Systems: Standards, Management, and Technology, IGI Global. 2014.

A Semantic Web Platform for Automating the Interpretation of Finite Element Bio-simulations. Andre Freitas, Kartik Asooja, Joao Jares, Stefan Decker, Ratnesh Sahay. In proceeding of the Semantic Web Application and Tools for Life Sciences (SWAT4LS) 2014, Berlin, Germany , Freie Universtität Berlin, Germany, 2014.

Discovering Domain-Specific Public SPARQL Endpoints: A Life-Sciences Use-Case. Muntazir Mehdi, Aftab Iqbal, Aidan Hogan, Ali Hasnain, Yasar Khan, Stefan  Decker, Ratnesh Sahay.  18th International Database Engineering & Applications Symposium, Porto, Portugal, Portugal, 2014.

Towards a Semantic Web Platform for Finite Element Simulations. Andre Freitas, Kartik Asooja, Swapnil Soni, Marggie Jones, Panagiotis Hasapis, Ratnesh Sahay. 11th European Semantic Web Conference (ESWC), Springer LNCS Notes , Crete, Greece, Greece, 2014.

Utilizing Domain-Specific Keywords for Discovering Public SPARQL Endpoints: A Life-Sciences Use-Case. Muntazir Mehdi, Aftab Iqbal, Ali Hasnain, Yasar Khan, Stefan Decker, Ratnesh Sahay. Proceedings of the 29th Annual ACM Symposium on Applied Computing, the Semantic Web and Applications (SWA) track, 2014, Gyeongju, Korea, 2014.

2013

Towards a Semantic Representation for Multi-Scale Finite Element Biosimulation Experiments. Andre Freitas, Marrgie Jones, Kartik Asooja, Christos Bellos, Steve Elliott, Stefan Stenfelt, Panagiotis Hasapis, Christos Georgousopoulos, Torsten  Marquardt, Nenad Filipovic, Stefan Decker, Ratnesh Sahay. In 13th IEEE International Conference on BioInformatics and BioEngineering (BIBE) 2013, Chania, Greece.

SIFEM Project: Semantic Infostructure interlinking an open source Finite  Element tool and libraries with a model repository for the multi-scale Modelling of the inner-ear. Christos Bellos, Athanasios Bibas, Dimitrios Kikidis, Steve Elliott, Stefan Stenfelt, Ratnesh Sahay, Konstantina Nikita, Dimitrios Koutsouris, Dimitrios I. Fotiadis. In 13th IEEE International Conference on BioInformatics and BioEngineering (BIBE) 2013, Chania, Greece.

Querying Phenotype-Genotype Associations across Multiple Knowledge Bases using Semantic Web Technologies. Oya Deniz Beyan, Aftab Iqbal, Yasar Khan, Athos Antoniades, John Keane, Panagiotis Hasapis, Christos Georgousopoulos, Myrto Ioannidi, Stefan Decker, Ratnesh Sahay. 13th IEEE International Conference on BioInformatics and BioEngineering, Chania, Greece, 2013.

ReVeaLD: A user-driven domain-specific interactive search platform for biomedical research. Maulik Kamdar, Dimitris Zeginis, Ali Hasnain, Stefan Decker, Helena Deus. Journal of Biomedical Informatics, Elsevier, 2013.

A Bayesian Association Rule Mining Algorithm. David Tian, Ann Gledson, Athos Antoniades, Aristo Aristodimou, Ntalaperas Dimitrios, Ratnesh Sahay, Jianxin Pan, Stavros Stivaros, Goran Nenadic, Xiao-jun Zeng, John Keane.  In IEEE SMC 2013 – IEEE International Conference on Systems, Man, and Cybernetics, Manchester, UK, United Kingdom, 2013.

On-The-Fly Generation of Multidimensional Data Cubes for Web of Things. Muntazir Mehdi, Ratnesh Sahay, Wassim Derguech, Edward Curry. In 17th International Database Engineering & Applications Symposium (IDEAS 2013), ACM Digital Library, Barcelona, Spain, Spain, 2013.

An Ontology for Clinical Trial Data Integration. Ratnesh Sahay, D. Ntalaperas, E. Kamateri, P. Hasapis, Oya Deniz Beyan, M. Strippoli, C. Demetriou, M. Brochhausen, T. Bouras, D. Tian, A. Antoniades, C. Georgousopoulos, Manfred Hauswirth, Stefan Decker. In IEEE SMC 2013 – IEEE International Conference on Systems, Man, and Cybernetics, Manchester, UK, United Kingdom, 2013.

Fostering Serendipity through Big Linked Data. Muhammad Saleem, Maulik Kamdar, Aftab Iqbal, Shanmukha Sampath, Helena Deus, Axel-Cyrille Ngonga in Semantic Web Challenge at ISWC, Australia, 2013.

Advancing Patient Record Safety and EHR Semantic Interoperability. Konstantinos Perakis, Thanasis Bouras, Dimitris Ntalaperas, Panagiotis Hasapis, Christos Georgousopoulos, Ratnesh Sahay, Oya Deniz Beyan, Cristi Potlog, Daniela Usurelu. In IEEE SMC 2013 – IEEE International Conference on Systems, Man, and Cybernetics, Manchester, UK, United Kingdom, 2013.

ReVeaLD: A User-driven Domain specific Interactive Search Platform for Biomedical Research. Maulik Kamdar, Dimitris Zeginis, Ali Hasnain, Stefan Decker, Helena Deus. 10th Summer School on Ontology Engineering and the Semantic Web (SSSW 2013), Cercedilla, Spain, 2013.

Linked2Safety. Aristo Aristodimou, Athos Antoniades, Christos Georgousopoulos, John Keane, Ratnesh Sahay, Nikolaus Forgo, Cristi Potlog, K. Tarabanis, Myrto Ioannidi, Marie-Pierre Strippoli, Christiana Demetriou, Constantinos Pattichis Joint 21st Annual International Conference on Intelligent Systems for Molecular Biology and 12th Annual European Conference on Computational Biology (ISMB/ECCB), ISMB-Open Access, Berlin, Germany , Germany, 2013.

Analyzing Social Behavior of Software Developers Across Different Communication Channels. Aftab Iqbal, Marcel Karnstedt, Michael Hausenblas. 25th International Conference on Software Engineering and Knowledge Engineering (SEKE), Boston, United States, 2013.

2012

Weaving Social Networks with Linked Biomedical Data. Panagiotis Hasapis, Thanassis Bouras, Helena Deus, Ronan Fox, Sabine. Kolvenbach, Wolfgang Prinz Applied Computing 2012, 2012.

Mobile Health Apps – From Singular to Collaborative. Ronan Fox, James Cooley, Matthew McGrath, Manfred Hauswirth Proceeding of pHealth 2012, 2012.

Translating standards into practice – One Semantic Web API for Gene Expression. Helena Deus, Eric Prudhommeaux, Michael Miller, Jun Zhao, James Malone, Tomasz Adamusiak, Jim McCusker, Sudeshna Das, Philippe Rocca Serra, Ronan Fox, M. Scott Marshall. Journal of Biomedical Informatics, in press, Elsevier, 2012.

Emerging best practices for mapping life sciences data to RDF – a case series. M. Scott Marshall, Richard Boyce, Jun Zhao, Egon L Willighagen, Helena Deus, Matthias Samwald, Elgar Pichler, Janos Hajagos, Eric Prudhommeaux, Susie Stephens. Journal of Web Semantics, (accepted), Elsevier, 2012.

2011

Exposing WikiPathways as Linked Open Data. Andra Waagmeester, Helena Deus, Chris T. Evelo Benelux Bioinformatics Conference 2011, 2011.

Translating standards into practice – One Semantic Web API for Gene Expression. Helena Deus, Eric Prud’hommeaux, Michael Miller, Jun Zhao, James Malone, Tomasz Adamusiak, Jim McCusker, Sudeshna Das, Philippe Rocca Serra, Ronan Fox, M. Scott Marshall. Semantic Web Applications and Tools for Life Sciences. London, UK, 2011.

SPARQL Access Policies. Eric PrudHommeaux, Helena Deus. W3C Linked Enterprise Data Patterns Workshop. Workshop at W3C Linked Enterprise Data Patterns Workshop, Boston, 2011.

A Methodological Approach for Ontologising and Aligning Health Level Seven (HL7) Applications. Ratnesh Sahay, Ronan Fox, Antoine Zimmermann, Axel Polleres, Manfred Hauswirth. Proceedings of the International Conference on Massive Information Sharing and Integration (MISI 2011), Special Track on Eletronic Healthcare (SALUS 2011), Vienna, Austria, 2011.

Creating a Virtual Personal Health Record Using Mashups. Ronan Fox, James Cooley, Manfred Hauswirth. IEEE Internet Computing, 15 (4), :23-30, IEEE , 2011.

S3QL: A distributed domain specific language for controlled semantic integration of life sciences data. Helena Deus, Miria Coelho Correa, Romesh Stanislaus, Maria Miragaia, Wolfgang Maass, Herminia de Lencastre, Ronan Fox, Jonas S Almeida. BMC Bioinformatics, 12, (285), BioMed Central, 2011.

Collaborative Development of Trusted Mashups. Ronan Fox, James Cooley, Manfred Hauswirth. Proceedings of the The 12th International Conference on Information. Integration and Web-based Applications & Services (iiWAS2010), conference, 2011.

Collaborative Development of Trusted Mashups. Ronan Fox, James Cooley, Manfred Hauswirth International Journal of Pervasive Computing and Communications (IJPCC), 7 (3), :264 – 288, Emerald Insight, 2011.

2010

Remote Healthcare Delivery with Sqwelch. Ronan Fox, James Cooley, Manfred Hauswirth. Proceedings of the 1st ACM International Health Informatics Symposium, 2010.

Structured Digital Tables on the Semantic Web. Kei-Hoi Cheung, Matthias Samwald, Raymond Auerbach, Mark B. Gerstein. Nature Molecular Systems Biolog, 2010.

Semantic SenseLab: implementing the vision of the Semantic Web in neuroscience. Matthias Samwald, Huajun Chen, Alan Ruttenberg, Ernest Lim, Luis Marenco, Perry Miller, Gordon Shepherd, Kei-Hoi Cheung. Artificial Intelligence in medicine, Elsevier, 2010.

Establishing a distributed system for the simple representation and integration of diverse scientific assertions. Matthias Samwald, Holger Stenzhorn. Journal of Biomedical Semantics, 2010.

2009

Heterogeneity and Context in Semantic-Web-Enabled HCLS Systems. Antoine Zimmermann, Ratnesh Sahay, Ronan Fox, Axel Polleres. Proceedings of the 8th International Conference on Ontologies, DataBases, and Applications of Semantics (ODBASE 2009), Vilamoura, Algarve, Portugal, 2009.

Entrez Neuron RDFa: a pragmatic Semantic Web application for data integration in neuroscience research. Matthias Samwald, Ernest Lim, Peter Masiar, Luis Marenco, Huajun Chen, Thomas Morse, Pradeep Mutalik, Gordon Shepherd, Perry Miller, Kei-Hoi Cheung, K.-P. Adlassnig, B. Blobel, J. Mantas, I. Masic. Proceedings of the International Conference of the European Federation for Medical Informatics, 2009 , Studies in Health Technology and Informatics, 150, 2009.

Creating a Translational Medicine Ontology. Christine Denney, Bosse Andersson, Colin Batchelor, Olivier Bodenreider, Sam Cheng, John Hart, John Hill, Joanne Luciano, John Madden, Mark Musen , Elgar Pichler, Matthias Samwald, Sándor Szalma, Lynn Schriml, Dav The Sixth International Workshop of Data Integration in the Life Sciences, 2009.

Linked Data for Connecting Traditional Chinese Medicine and Western Medicine. Jun Zhao, Anja Jentzsch, Matthias Samwald, Kei-Hoi Cheung. The Sixth International Workshop of Data Integration in the Life Sciences, 2009.

Simple, ontology-based representation of biomedical statements through fine-granular entity tagging and new web standards. Matthias Samwald, Holger Stenzhorn. Bio-Ontologies 2009, 2009.

Life sciences on the Semantic Web: the Neurocommons and beyond. Alan Ruttenberg, Jonathan A. Rees, Matthias Samwald, M. Scott Marshall. Briefings in Bioinformatics, Oxford University Press, 2009.

Federating Distributed Social Data to Build an Interlinked Online Information Society. Alexandre Passant, Matthias Samwald, John Breslin, Stefan Decker. Proceedings of the WebSci’09: Society On-Line, 18-20 March 2009, Athens, Greece., 2009.

semantic Service-Oriented Design And Development Methodology For Enterprise Healthcare Integration. Ratnesh Sahay, Ronan Fox, Manfred Hauswirth 5th International Conference on Web Information Systems and Technologies (WEBIST 2009), Lisbon, Portugal, 2009.

Approaches to Neuroscience Data Integration. Kei-Hoi Cheung, Ernest Lim, Matthias Samwald, Huajun Chen, Luis Marenco, Matthew E. Holford, Thomas M. Morse, Pradeep Mutalik, Gordon M. Shepherd, Perry L. Miller Briefings in Bioinformatics, Tadgh Nagle, 2009.

A journey to Semantic Web query federation in the life sciences. Kei-Hoi Cheung, H. Robert Frost, M. Scott Marshall, Eric Prud’hommeaux, Matthias Samwald, Jun Zhao, Adrian Paschke BMC Bioinformatics, 2009.

2008

Ontologising Interaction Behavior for Service-Oriented Enterprise Healthcare Integration. Ratnesh Sahay, Ronan Fox, Manfred Hauswirth Proceedings of the 6th IEEE European Conference on Web Services (ECOWS 2008), Dublin, Ireland, 2008.

PPEPR for Enterprise Healthcare Integration. Ronan Fox, Ratnesh Sahay, Manfred Hauswirth Proceedings of the eHealth 2008 Conference, City University, London EC1, 2008.

PPEPR: Plug and Play Electronic Patient Records. Ratnesh Sahay, Waseem Akhtar, Ronan Fox. Proceedings of the 23rd Annual ACM Symposium on Applied Computing, the Semantic Web and Applications (SWA) track, Fortaleza, Ceará, Brazil, 2008.

Simplifying Access to Large-Scale Health Care and Life Sciences Datasets. Holger Stenzhorn, Kavitha Srinivas, Matthias Samwald, Alan Ruttenberg. Proceedings of the 5th European Semantic Web Conference (ESWC2008), Springer, 2008.

2007

Entrez Neuron: an OWL/RDFa–based Web Application for Information Exploration and Integration in Neuroscience. Matthias Samwald, Ernest Lim, Peter Masiar, Luis Marenco, Huajun Chen, Thomas Morse, Gordon Shepherd, Perry Miller, Kei Cheung. Sematic Web for Health Care and Life Sciences Workshop Workshop at 17th International World Wide Web Conference, 2007.

2006

Positive Patient Identification using RFID and Wireless Networks. Antonio Aguilar, Wil van der Putten, Gerald Maguire. Proceedings of the HISI 11th Annual Conference and Scientific Symposium, Dublin, Ireland, 2006.

2005

Semantic Interoperability in the context of eHealth. Antonio Aguilar. HP/DERI/CIMRU Research Seminar. Galway, Ireland, 2005.