Publications, talks et cetera
Peer-reviewed articles
2010
Kei-Hoi Cheung, Matthias Samwald, Raymond Auerbach and Mark B. Gerstein. “Structured Digital Tables on the Semantic Web”, Nature Molecular Systems Biology, accepted (journal article; impact factor 12,2)
Michel Dumontier, Bosse Andersson, Colin Batchelor, Christine Denney, Christopher Domarew, Anja Jentzsch, Joanne Luciano, Elgar Pichler, Eric Prud’hommeaux, Patricia Whetzel, Olivier Bodenreider, Tim Clark, Lee Harland, Vipul Kashyap, Peter Kos, Julia Kozlovsky, James McGurk, Chimezie Ogbuji, Matthias Samwald, Lynn Schriml, Peter J. Tonellato, Jun Zhao and Susie Stephens. “The Translational Medicine Ontology: Driving personalized medicine by bridging the gap from bedside to bench” Bio-Ontologies 2010, co-located with ISMB2010, accepted (conference article)
Patricia L. Whetzel, Colin Batchelor, Elgar Pichler, Bosse Andersson, Olivier Bodenreider, Tim Clark, Christopher Domarew, Michel Dumontier, Anja Jentzsch, Vipul Kashyap, Julia Kozlovsky, Joanne Luciano,
Chimezie Ogbuji, Matthias Samwald, Jun Zhao and Susie Stephens. “Translational Medicine Ontology: A Patient-Centric Ontology for Drug Development and Clinical Practice” Proceedings of the Summit on Translational Bioinformatics 2010, San Francisco, USA. (poster)
Matthias Samwald and Holger Stenzhorn. “Establishing a distributed system for the simple representation and integration of diverse scientific assertions.” Journal of Biomedical Semantics 1, Nr. 1 (2010): S5. (journal article)
Matthias Samwald, Huajun Chen, Alan Ruttenberg, Ernest Lim, Luis Marenco, Perry Miller, Gordon Shepherd and Kei-Hoi Cheung. “Semantic SenseLab: implementing the vision of the Semantic Web in neuroscience” Artificial Intelligence in Medicine 48, no. 1 (January 2010): 21-28. (journal article; impact factor 1,96)
2009
Anita de Waard, Simon Buckingham Shum, Annamaria Carusi, Jack Park, Matthias Samwald and Ágnes Sándor. “Hypotheses, Evidence and Relationships: The HypER Approach for Representing Scientific Knowledge Claims” Proceedings of the Workshop on Semantic Web Applications in Scientific Discourse (SWASD 2009), co-located with the 8th International Semantic Web Conference (ISWC-2009). Conference Proceedings (conference article)
Matthias Samwald and Holger Stenzhorn. “Simple, ontology-based representation of biomedical statements through fine-granular entity tagging and new web standards” Bio-Ontologies 2009, co-located with ISMB2009. Article PDF, Presentation PDF (conference article)
Kei-Hoi Cheung, H. Robert Frost, M. Scott Marshall, Eric Prud’hommeaux, Matthias Samwald, Jun Zhao and Adrian Paschke. “A Journey to Semantic Web Query Federation in Life Sciences“ BMC Bioinformatics, BMC Bioinformatics 10, no. Suppl 10 (2009): S10 (journal article; impact factor 3,78)
Kei-Hoi Cheung, Ernest Lim, Matthias Samwald, Huajun Chen, Luis Marenco, Matthew E. Holford, Thomas M. Morse, Pradeep Mutalik, Gordon M. Shepherd and Perry L. Miller. “Approaches to Neuroscience Data Integration” Briefings in Bioinformatics, 10, no. 4 (July 2009): 345-353 (journal article; impact factor 4,63)
Alan Ruttenberg, Jonathan A. Rees, Matthias Samwald and M. Scott Marshall. “Life sciences on the semantic web: the neurocommons and beyond” Briefings in Bioinformatics, 10, no. 2 (March 2009): 193-204 (journal article; impact factor 4,63)
Anja Jentzsch, Jun Zhao, Oktie Hassanzadeh, Kei-Hoi Cheung, Matthias Samwald and Bo Andersson. “Linking Open Drug Data” In Proceedings of Linking Open Data Triplification Challenge at the I-Semantics 2009, 2009. (conference paper)
Jun Zhao, Anja Jentzsch, Matthias Samwald and Kei-Hoi Cheung. „Linked Data for Connecting Traditional Chinese Medicine and Western Medicine” The Sixth International Workshop of Data Integration in the Life Sciences (Poster&Demo), Manchester, UK, 2009 (poster)
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, David Sedlock, Larisa Soldatova, Koji Sonoda, David Statham, Holger Stenzhorn, Trish Whetzel, Elizabeth Wu and Susie Stephens. „Creating a Translational Medicine Ontology” The Sixth International Workshop of Data Integration in the Life Sciences (Poster&Demo), Manchester, UK, 2009 (poster)
Christine Denney, Colin Batchelor, Olivier Bodenreider, Sam Cheng, John Hart, Jon Hill, John Madden, Mark Musen, Elgar Pichler, Matthias Samwald, Sándor Szalma, Lynn Schriml, David Sedlock, Larisa Soldatova, Koji Sonoda, David Statham, Patricia L. Whetzel, Elizabeth Wu and Susie Stephens. „Creating a Translational Medicine Ontology” Proceedings of the First International Conference on Biomedical Ontology (ICBO 2009) 2009:164 (poster)
Matthias Samwald, Ernest Lim, Peter Masiar, Luis Marenco, Huajun Chen, Thomas Morse, Pradeep Mutalik, Gordon Shepherd, Perry Miller and Kei-Hoi Cheung. “Entrez Neuron RDFa: a pragmatic Semantic Web application for data integration in neuroscience research“ Studies in Health Technology and Informatics 150 (2009): 317-321.
Presented at the International Conference of the European Federation for Medical Informatics, 2009 (conference article)
Alexandre Passant, Matthias Samwald, John Breslin and Stefan Decker. “Federating Distributed Social Data to Build an Interlinked Online Information Society.” In Proceedings of the WebSci’09: Society On-Line, 2009. Link PDF (conference article)
Holger Stenzhorn and Matthias Samwald. “Das Semantic Web als Werkzeug in der biomedizinischen Forschung.” In Social Semantic Web: Web 2.0 - Was nun? Heidelberg, Germany: Springer, 2009. (book chapter)
2008
Matthias Samwald and Klaus-Peter Adlassnig. “The bio-zen plus ontology.” Applied Ontology 3, no. 4 (Januar 1, 2008): 213-217. http://dx.doi.org/10.3233/AO-2008-0053 (journal article)
Holger Stenzhorn, Kavitha Srinivas, Matthias Samwald and Alan Ruttenberg. “Simplifying Access to Large-Scale Health Care and Life Sciences Datasets.” In Proceedings of the 5th European Semantic Web Conference (ESWC2008). Tenerife, Spain: Springer, 2008. (conference article)
Matthias Samwald, Ernest Lim, Peter Masiar, Luis Marenco, Huajun Chen, Thomas Morse, et al. “Entrez Neuron: an OWL/RDFa–based Web Application for Information Exploration and Integration in Neuroscience.” World Wide Web Conference, Beijing, China, 2008. (conference article)
Matthias Samwald and Kei-Hoi Cheung. “Experiences with the conversion of SenseLab databases to RDF/OWL (W3C Interest Group Note).” World Wide Web Consortium, 6, 2008. http://www.w3.org/TR/hcls-senselab/. (W3C interest group note)
Sebastian Schaffert, Julia Eder, Matthias Samwald, and Andreas Blumauer. “KiWi - Knowledge in a Wiki.” 5th European Semantic Web Conference (ESWC2008), Tenerife, Spain, 6, 2008. (poster)
Christian Morbidoni, Danh Le Phuoc, Axel Polleres, Matthias Samwald and Giovanni Tummarello. “Previewing Semantic Web Pipes.” In Proceedings of the 5th European Semantic Web Conference (ESWC2008). Tenerife, Spain: Springer, 2008. (conference article)
2007
Matthias Samwald. “Semantic Web Technology in Neuroscience and Biomedicine. ” University of Vienna; Medical University of Vienna, 2007. (doctoral thesis)
Alan Ruttenberg, Tim Clark, William Bug, Matthias Samwald, Olivier Bodenreider, Helen Chen, et al. “Advancing translational research with the Semantic Web.”
BMC Bioinformatics 8 Suppl 3 (2007): S2. doi:1471-2105-8-S3-S2. (journal article)
Matthias Samwald, William Bug, Jonathan Rees, Chris Mungall, John Barkley, Ray Hookway, et al. “The Semantic Web Health Care and Life Sciences Interest Group work in progress: A large scale, OBO inspired, repository of biological knowledge based on Semantic Web technologies.” (Poster) International Conference on Intelligent Systems for Molecular Biology (ISMB2007), Vienna, Austria, 2007. (poster)
Vipul Kashyap, Kei-Hoi Cheung, Donald Doherty, Matthias Samwald, M. Scott Marshall, Joanne Luciano, et al. “Ontology-Based Data Integration For Biomedical Research.” In The Semantic Web: Real-World Applications from Industry, 97-122, 2007. (book chapter)
Matthias Samwald. “Branchenreport: Semantische Technologien in den Life Sciences (Industry Report: Semantic Technologies in the Life Sciences).” Branchenreport der Semantic Web School. Vienna, Austria: Semantic Web School, 2007. (industry white paper)
2006
Matthias Samwald. “Classes Versus Individuals: Fundamental Design Issues for Ontologies on the Biomedical Semantic Web.” In Proceedings of the European Federation for Medical Informatics, Special Topic Conference. Timisoara, Romania, 2006. (conference article)
Matthias Samwald, Isabella Hinterleitner and Klaus-Peter Adlassnig. “Semantic web technology for database integration in neuroscience.” In FENS Forum Abstracts, 3: Vienna, Austria, 2006. (conference article)
Matthias Samwald and Alan Ruttenberg. “Representation and resolution of digital resources on the semantic web – an ontology-based approach.” Athens, Georgia, USA, 2006. (conference article)
2005
Matthias Samwald and Klaus-Peter Adlassnig. “Bringing Neuroscience to the Semantic Web: The Semantic Synapse Project.” In Proceedings of the International Conference on Intelligent Agents, Web Technologies & Internet Commerce. Vienna, Austria, 2005. (conference article)
Matthias Samwald. “Neuromuscular Synapses of the Sympathetic Nervous System” University of Vienna; Medical University of Vienna, 2005. (master thesis)
Articles published without peer-review
Alexandre Passant, Matthias Samwald, John G. Breslin, and Stefan Decker. “Federating Distributed Social Data to Build an Interlinked Online Information Society.” IEEE Intelligent Systems 24, no. 6 (11, 2009): 44-48.
Matthias Samwald. “Extracting conclusion sections from PubMed abstracts for rapid key assertion integration in biomedical research” September 2009. Available from Nature Precedings: http://precedings.nature.com/documents/3775/version/1 (pre-print article)
Matthias Samwald. “Review: Dystroglycan in the Nervous System” June 2007. Available from Nature Precedings: http://precedings.nature.com/documents/196/version/1. (pre-print article)
Invited talks
“High-level knowledge representation on the Semantic Web: the Concept Web Alliance and related efforts”, held at the BioHackathon Symposium 2010, February 2010, Tokyo, Japan.
“Scientific Information Integration”, held at the Hypotheses, Evidence and Relations (Hyp-ER) project meeting, May 2009, Elsevier Offices, Amsterdam, Netherlands.
“Making progress in making progress”, held at the Konrad Lorenz Institute for Evolution and Cognition Research, February 2009, Altenberg, Austria.
Program committee memberships
The Future of the Web for Collaborative Science, co-located with WWW2010, April 2010, Raleigh, USA.
Semantic Web Applications and Tools for Life Sciences (SWAT4LS), November 2009, Amsterdam, Netherlands.
International Semantic Web Conference 2009 (ISWC2009), October 2009, Washington, USA.
Workshop on Semantic Web Applications in Scientific Discourse, co-located with ISWC2009, October 2009, Washington, USA.
NETTAB 2009: Technologies, Tools and Applications for Collaborative and Social Bioinformatics Research and Development, June 2009, Catania, Sicily, Italy.
I-Semantics 2009: International Conference on Semantic Systems, September 2009, Graz, Austria.
Bio-Ontologies 2009: Knowledge in Biology at the International Conference on Intelligent Systems for Molecular Biology 2009 (ISMB2009)
Workshop for Semantic Web Health Care and Life Sciences at the 3rd Asian Semantic Web Conference, December 2008, Bangkok, Thailand.
Semantic Web Applications and Tools for Life Sciences (SWAT4LS) workshop, November 2008, Edinburgh, Scotland, UK.
Semantic Web for Health Care and Life Sciences Workshop (HCLS2008), Beijing, China.
OWL: Experiences and Directions 2008 workshop (OWLED2008), October 26-27 2008, Karlsruhe, Germany.
1st international workshop on Identity and Reference on the Semantic Web (IRSW2008), June 2 2008, Tenerife, Spain.
3rd Workshop on Semantic Wikis (SemWiki2008), June 2 2008, Tenerife, Spain.