Publications, talks et cetera
Peer-reviewed articles
2012
[45] Matthias Samwald, Karsten Fehre, Jeroen de Bruin, Klaus-Peter Adlassnig. The Arden Syntax standard for clinical decision support: experiences and directions”. Journal of Biomedical Informatics, accepted (journal article, impact factor 1,7)
[44] M. Scott Marshall, Richard Boyce, Helena Deus, Jun Zhao, Egon Willighagen, Matthias Samwald, Elgar Pichler, Janos Hajagos, Eric Prud’hommeaux. „Emerging practices for mapping and linking life sciences data using RDF – a case series“. Journal of Web Semantics, accepted (journal article, impact factor 2,8)
[43] Matthias Samwald, Adrien Coulet, Iker Huerga, Robert L Powers, Joanne S. Luciano, Robert R. Freimuth, Frederick Whipple, Elgar Pichler, Eric Prud’hommeaux, Michel Dumontier, M. Scott Marshall. „Semantically enabling pharmacogenomic data for the realization of personalized medicine“. Pharmacogenomics, accepted (journal article; impact factor 3,9)
[42] Matthias Samwald, Adrien Coulet, Robert R. Freimuth, Iker Huerga, Joanne Luciano, Elgar Pichler, Robert L. Powers, Eric Prud’hommeaux, Frederick Whipple, Michael Marshall, und Michel Dumontier. „An informatics infrastructure for translating pharmacogenomic knowledge into clinical practice“. In 2012 AMIA Summit on Translational Bioinformatics, accepted (conference article)
2011
[41] Matthias Samwald, Marlene Kritz, Manfred Gschwandtner, Veronika Stefanov, Allan Hanbury. „An open, trustworthy and multilingual search engine for medical practitioners“. In 23rd International Conference of the European Federation for Medical Informatics (MIE2011), User Centred Networked Health Care – A. Moen et al. (Eds.), MIE 2011 / CD / Short Communications, 2011 (conference article)
[40] Matthias Samwald, Holger Stenzhorn, Michel Dumontier, M. Scott Marshall, Joanne Luciano, Klaus-Peter Adlassnig. „Towards an interoperable information infrastructure providing decision support for genomic medicine“. Studies in Health Technology and Informatics 169 (2011): 165-169. Proceedings of Medical Informatics Europe 2011 (MIE2011). (conference article)
PDF, Link to publisher
[39] Matthias Samwald, Marlene Kritz, Manfred Gschwandtner, Veronika Stefanov, Allan Hanbury. „Towards an open, trustworthy and multilingual search engine for medical practitioners: News from the European Khresmoi project“. In Schreier, G., Hayn, D. & Ammenwerth, E. (Eds.) Tagungsband der eHealth2011 – Health Informatics meets eHealth – von der Wissenschaft zur Anwendung und zurück, Grenzen überwinden – Continuity of Care, 26.–27. Mai 2011, Wien, Österreichische Computer Gesellschaft, Wien, 135 – 140 (conference article)
PDF
[38] Matthias Samwald, Anja Jentzsch, Christopher Bouton, Claus Stie Kallesøe, Egon Willighagen, Janos Hajagos, M. Scott Marshall, Eric Prud’hommeaux, Oktie Hassanzadeh, Elgar Pichler, Susie Stephens. „Linked open drug data for pharmaceutical research and development“ Journal of Cheminformatics 3, no. 1 (2011): 19. (journal article)
[37] Joanne S. Luciano, Bosse Andersson, Colin Batchelor, Olivier Bodenreider, Tim Clark, Christine Denney, Christopher Domarew, Thomas Gambet, Lee Harland, Anja Jentzsch, Vipul Kashyap, Peter Kos, Julia Kozlovsky, Timothy Lebo, M. Scott Marshall, James P. McCusker, Deborah L. McGuiness, Chimezie Ogbuji, Elgar Pichler, Robert L. Powers, Eric Prud怙hommeaux, Matthias Samwald, Lynn Schriml, Petev J. Tonellato, Patricia L. Whetzel, Jun Zhao, Susie Stephens, Michel Dumontier. „The Translational Medicine Ontology and Knowledge Base: Driving personalized medicine by bridging the gap between bench and bedside“. Journal of Biomedical Semantics 2, no. 2 (2011): S1. (journal article)
[36] Joanne S. Luciano, Bosse Andersson, Colin Batchelor, Olivier Bodenreider, Tim Clark, Christine Denney, Christine Domarew, Thomas Gambet, Anja Jentzsch, Vipul Kashyap, Peter Kos, Julia Kozlovsky, M. Scott Marshall, James P. McCusker, Deborah L. McGuiness, Timothy Lebo, Chimezie Ogbuji, Elgar Pichler, Robert L. Powers, Eric Prud’hommeaux, Matthias Samwald, Lynn Schriml, Peter J. Tonellato, Patricia L. Wletzel, Jun Zhao, Susie Stephens, Michel Dumontier. „The Translational Medicine Ontology and Knowledge Base: Using Semantic Web Technology in Personalized Medicine for Data Integration“ In Proceedings of the AMIA Summit on Translational Bioinformatics, San Francisco, CA, March 7, 2011. (conference article)
Conference proceedings
[35] Matthias Samwald, Jun Zhao, Michel Dumontier, M. Scott Marshall, Kei Cheung, Joanne S. Luciano. „Translating ethnopharmacological findings into novel drug leads: the potential roles of linked open data and ontologies“. In Proceedings of the AMIA Summit on Translational Bioinformatics, San Francisco, CA, March 7, 2011. (poster)
Conference proceedings
2010
[34] Helena Deus, Jun Zhao, Satya Sahoo, Matthias Samwald, Eric Prud’hommeaux, Michael Miller, M.Scott Marshall, Kei-Hoi Cheung. “Provenance of Microarray Experiments for a Better Understanding of Experiment Results” Proceedings of Second International Workshop on the role of Semantic Web in Provenance Management (SWPM-2010), Shanghai, China (conference article)
[33] Matthias Samwald, Michel Dumontier, Jun Zhao, Joanne Luciano, M Scott Marshall, Kei-Hoi Cheung. “Integrating findings from traditional medicine into modern pharmaceutical research: the potential role of linked open data.” Chinese Medicine 5, No. 1 (2010): 43. (journal article)
[32] Emek Demir, Michael P Cary, Suzanne Paley, Ken Fukuda, Christian Lemer, Imre Vastrik, Guanming Wu, Peter D’Eustachio, Carl Schaefer, Joanne Luciano, Frank Schacherer, Irma Martinez-Flores, Zhenjun Hu, Veronica Jimenez-Jacinto, Geeta Joshi-Tope, Kumaran Kandasamy, Alejandra C Lopez-Fuentes, Huaiyu Mi, Elgar Pichler, Igor Rodchenkov, Andrea Splendiani, Sasha Tkachev, Jeremy Zucker, Gopal Gopinath, Harsha Rajasimha, Ranjani Ramakrishnan, Imran Shah, Mustafa Syed, Nadia Anwar, Özgün Babur, Michael Blinov, Erik Brauner, Dan Corwin, Sylva Donaldson, Frank Gibbons, Robert Goldberg, Peter Hornbeck, Augustin Luna, Peter Murray-Rust, Eric Neumann, Oliver Reubenacker, Matthias Samwald, Martijn van Iersel, Sarala Wimalaratne, Keith Allen, Burk Braun, Michelle Whirl-Carrillo, Kei-Hoi Cheung, Kam Dahlquist, Andrew Finney, Marc Gillespie, Elizabeth Glass, Li Gong, Robin Haw, Michael Honig, Olivier Hubaut, David Kane, Shiva Krupa, Martina Kutmon, Julie Leonard, Debbie Marks, David Merberg, Victoria Petri, Alex Pico, Dean Ravenscroft, Liya Ren, Nigam Shah, Margot Sunshine, Rebecca Tang, Ryan Whaley, Stan Letovksy, Kenneth H Buetow, Andrey Rzhetsky, Vincent Schachter, Bruno S Sobral, Ugur Dogrusoz, Shannon McWeeney, Mirit Aladjem, Ewan Birney, Julio Collado-Vides, Susumu Goto, Michael Hucka, Nicolas Le Novère, Natalia Maltsev, Akhilesh Pandey, Paul Thomas, Edgar Wingender, Peter D Karp, Chris Sander, Gary D Bader. “The BioPAX community standard for pathway data sharing.” Nature Biotechnology 28, Nr. 9 (9, 2010): 935-942. (journal article; impact factor 29,5)
[31] Kei-Hoi Cheung, Matthias Samwald, Raymond K. Auerbach, Mark B. Gerstein. “Structured digital tables on the Semantic Web: toward a structured digital literature”, Nature Molecular Systems Biology 6 (August 24, 2010): 403. (journal article; impact factor 12,2)
[30] 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, Susie Stephens. “The Translational Medicine Ontology: Driving personalized medicine by bridging the gap from bedside to bench” Bio-Ontologies 2010, Proceedings of the 13th Annual Bio-Ontologies Meeting, Boston, USA (conference article)
[29] 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, 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)
[28] Matthias Samwald, 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)
[27] Matthias Samwald, Huajun Chen, Alan Ruttenberg, Ernest Lim, Luis Marenco, Perry Miller, Gordon Shepherd, 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
[26] Anita de Waard, Simon Buckingham Shum, Annamaria Carusi, Jack Park, Matthias Samwald, 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 article)
Conference Proceedings
[25] Matthias Samwald, 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. (conference article)
Article PDF, Presentation PDF
[24] 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)
[23] 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)
[22] 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)
[21] 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
[20] 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)
[19] 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)
[18] 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)
[17] 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
[16] 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
[15] 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
[14] Matthias Samwald, Klaus-Peter Adlassnig. “The bio-zen plus ontology.” Applied Ontology 3, no. 4 (Januar 1, 2008): 213-217. (journal article)
Link
[13] 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)
[12] 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)
[11] Sebastian Schaffert, Julia Eder, Matthias Samwald, Andreas Blumauer. “KiWi – Knowledge in a Wiki.” 5th European Semantic Web Conference (ESWC2008), Tenerife, Spain, 6, 2008. (poster)
[10] 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
[9] Matthias Samwald. “Semantic Web Technology in Neuroscience and Biomedicine. ” University of Vienna; Medical University of Vienna, 2007. (doctoral thesis)
[8] 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)
[7] 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)
[6] 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
[5] 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
[4] 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)
[3] 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
[2] 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)
[1] Matthias Samwald. “Neuromuscular Synapses of the Sympathetic Nervous System” University of Vienna; Medical University of Vienna, 2005. (master thesis)
Articles published without peer-review
Matthias Samwald. “Suchen und Finden” Das Österreichische Gesundheitswesen – ÖKZ, Ausgabe 52.JG 7, 2011.
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.