Matthias Samwald obtained his doctorate from the University of Vienna and the Medical University of Vienna. He has a background in biomedical informatics. The aim of his work is the use of novel web technologies, ontologies, large-scale data integration and information retrieval techniques to speed up progress in pharmaceutical R&D and medical practice. He worked for the Yale Center for Medical Informatics, Science Commons, the Semantic Web Company, the Konrad Lorenz Institute for Evolution and Cognition Research and DERI Galway. He is an active member of the World Wide Web Consortium (W3C) Health Care and Life Science Interest Group.

Education

2005-2008   PhD thesis at the Section on Medical Expert and
                    Knowledge-Based Systems of the Medical University
                    of Vienna. Topic: Semantic Web technologies in neuroscience
                    and biomedicine

2005            Master's thesis at the Austrian Center for Brain Research,
                    Division of Biochemistry and Molecular Biology, group for
                    cellular neurophysiology. Finished May 2005 with honors

2000-2005   Undergraduate studies at the University of Vienna. Focus on
                    experimental neuroscience and neuropharmacology

2000            Graduation (Matura) with honors

Professional Career

since 11/2010       Information Retrieval Facility (IRF), Vienna
                             Post-doctoral Research Fellow (part-time)

since 10/2007       Digital Enterprise Research Institute, Galway, Ireland
                             Researcher (part-time)

12/2008-10/2010 Konrad Lorenz Institute for Evolution and Cognition
                             Research, Altenberg, Austria
                             Researcher

1/2008-12/2008   Semantic Web Company, Austria
                             Project manager, technologist and biomedical expert

7/2007-3/2008     Yale Center for Medical Informatics, New Haven, USA
                             Consultant 

6/2007-9/2007     Science Commons, MIT, Cambridge, USA. Sponsored by
                             Google
                             Developer

4/2007-7/2007     Yale Center for Medical Informatics, New Haven, USA
                             Visiting scientist 

2006                     Konrad Lorenz Institute for Evolution & Cognition
                             Research, Altenberg, Austria
                             Developer

Professional Activities
 

• Member of the World Wide Web Consortium (W3C) since 10/2006, participant in the Semantic Web for Health Care and Life Science Interest Group of the W3C

Qualifications relevant to the Khresmoi project 
 

• Applying semantic technologies and ontologies in biomedical research and health care, experience with building large integrated knowledge bases in the biomedical and health care domain.
• Excellent biomedical domain knowledge; experience with mediating between persons with backgrounds in healthcare/biomedicine and IT.
• Semantic repositories (e.g. Ontotext OWLIM).
• Information retrieval technologies (e.g. Apache Lucene / Solr) and entity extraction.
• Working in international consortia and European research projects.
• Good scientific track record and experience with grant application writing (e.g. for follow-up projects).
• Fluent English; native German speaker.

Peer-reviewed articles

2010

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, and 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)

Kei-Hoi Cheung, Matthias Samwald, Raymond K. Auerbach and Mark B. Gerstein. “Structured Digital Tables on the Semantic Web”, Nature Molecular Systems Biology 6 (August 24, 2010): 403. (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 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. (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. (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)