Publications, talks et cetera
Peer-reviewed articles
2013
[51] Marlene Kritz, Manfred Gschwandtner, Veronika Stefanov, Allan Hanbury, Matthias Samwald. „Utilisation and perceived problems of online medical resources and search tools among different groups of European physicians“ Journal of Medical Internet Research, in press (journal article, impact factor 4,7)
[22] Kei-Hoi Cheung, H. Robert Frost, M. Scott Marshall, Eric Prud’hommeaux, Matthias Samwald, Jun Zhao, Adrian Paschke. “A Journey to Semantic Web Query Federation in Life Sciences“ BMC Bioinformatics, 10, no. Suppl 10 (2009): S10 (journal article; impact factor 3,78)
[21] 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. “Approaches to Neuroscience Data Integration” Briefings in Bioinformatics, 10, no. 4 (July 2009): 345-353 (journal article; impact factor 4,63)
[20] Alan Ruttenberg, Jonathan A. Rees, Matthias Samwald, 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)
[19] Anja Jentzsch, Jun Zhao, Oktie Hassanzadeh, Kei-Hoi Cheung, Matthias Samwald, Bo Andersson. “Linking Open Drug Data” In Proceedings of Linking Open Data Triplification Challenge at the I-Semantics 2009, 2009. (conference paper)
Article PDF
[18] Jun Zhao, Anja Jentzsch, Matthias Samwald, 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)
[17] 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, Susie Stephens. „Creating a Translational Medicine Ontology” The Sixth International Workshop of Data Integration in the Life Sciences (Poster&Demo), Manchester, UK, 2009 (poster)
[16] 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, Susie Stephens. „Creating a Translational Medicine Ontology” Proceedings of the First International Conference on Biomedical Ontology (ICBO 2009) 2009:164 (poster)
[15] Matthias Samwald, Ernest Lim, Peter Masiar, Luis Marenco, Huajun Chen, Thomas Morse, Pradeep Mutalik, Gordon Shepherd, Perry Miller, 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)
Link, Article PDF
[14] Alexandre Passant, Matthias Samwald, John Breslin, Stefan Decker. “Federating Distributed Social Data to Build an Interlinked Online Information Society.” In Proceedings of the WebSci’09: Society On-Line, 2009. (conference article)
Link, Article PDF
[13] Holger Stenzhorn, 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
[12] Matthias Samwald, Klaus-Peter Adlassnig. “The bio-zen plus ontology.” Applied Ontology 3, no. 4 (Januar 1, 2008): 213-217. (journal article)
Link
[11] Holger Stenzhorn, Kavitha Srinivas, Matthias Samwald, 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)
[10] Matthias Samwald, 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)
[9] Sebastian Schaffert, Julia Eder, Matthias Samwald, Andreas Blumauer. “KiWi – Knowledge in a Wiki.” 5th European Semantic Web Conference (ESWC2008), Tenerife, Spain, 6, 2008. (poster)
[8] Christian Morbidoni, Danh Le Phuoc, Axel Polleres, Matthias Samwald, Giovanni Tummarello. “Previewing Semantic Web Pipes.” In Proceedings of the 5th European Semantic Web Conference (ESWC2008). Tenerife, Spain: Springer, 2008. (conference article)
2007
[7] 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, impact factor 3.43)
[6] 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)
[5] 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)
2006
[4] 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)
Article PDF
[3] Matthias Samwald, Isabella Hinterleitner, Klaus-Peter Adlassnig. “Semantic web technology for database integration in neuroscience.” In FENS Forum Abstracts, 3: Vienna, Austria, 2006. (conference article)
[2] Matthias Samwald, Alan Ruttenberg. “Representation and resolution of digital resources on the semantic web – an ontology-based approach.” Athens, Georgia, USA, 2006. (conference article)
2005
[1] Matthias Samwald, 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)
Master’s and doctoral theses
Matthias Samwald. “Semantic Web Technology in Neuroscience and Biomedicine. ” University of Vienna; Medical University of Vienna, 2007. (doctoral thesis)
Matthias Samwald. “Neuromuscular Synapses of the Sympathetic Nervous System” University of Vienna; Medical University of Vienna, 2005. (master’s thesis)
Articles published without peer-review
Matthias Samwald. “Suchen und Finden” Das Österreichische Gesundheitswesen – ÖKZ, Ausgabe 52.JG 7, 2011. Article PDF
Alexandre Passant, Matthias Samwald, John G. Breslin, 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. “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)
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
“Semantic Technologies for Biomedical Decision Support”, held at the EMBL-EBI Industry Programme Workshop, European Bioinformatics Institute, May 18, 2011, Hinxton/Cambridge, UK.
“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.
Program committee memberships
ICBO 2012: 3rd International Conference on Biomedical Ontology, July 2012, Graz, Austria.
Bio-Ontologies SIG, co-located with ISMB2011, July 2011, Vienna, Austria.
OWL Experiences and Directions 2011 (OWLED2011), June 2011, San Francisco, USA.
SePublica, May 2011, Heraklion, Greece.
Semantic Web Applications and Tools for Life Sciences (SWAT4LS), December 2010, Berlin, Germany.
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), co-located with the World Wide Web Conference 2008 (WWW2008), April 22 2008, 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.
Workshop for Semantic Web for Health Care and Life Sciences Data Integration, co-located with the World Wide Web Conference 2007 (WWW2007), May 8 2007, Banff, Canada.