I am a member of the Bioinformatics Core of the Bioinformatics Expertise Center, which acts as a bioinformatics hub for the Leiden University Medical Center. As part of a split appointment, I also coordinate work in Adaptive Information Disclosure (AID). AID combines expertise in information retrieval, machine learning, and semantic web in the context of the Virtual Laboratory e-science project to create an infrastructure for computational experiments and knowledge capture. My current focus is on coordinating efforts to apply Semantic Web tools such as AIDA to support research in biology and medicine, with a special focus on building applications that are useful to participants in the Bioinformatics Expertise Center of the Leiden University Medical Center. I am also co-chairing the W3C Semantic Web for Health Care and Life Sciences Interest Group. I envision a future where scientists share and manipulate knowledge using visual and concept-based interfaces that adapt to their own terminologies and interests. Knowledge provenance that links a given assertion to evidence will allow scientists to explore, analyze, and compare data and hypotheses. Many are working toward this future using the Semantic Web.

Research Interests

• Research goals in the context of a virtual laboratory
• Data Integration through annotation with ontologies
• Knowledge representation for exchange of knowledge and data models
• Semantic Networks and their application to resource management
• Molecular Pathways as a specialized application of graph visualization
• Scalable methods for graph visualization

Activities

• Co-chairing the W3C Semantic Web for Health Care and Life Sciences Interest Group
• Co-organizer of Semantic Web Applications and Tools for the Life Sciences (SWAT4LS) 2009
• Co-organizer of Workshop on Semantic Web Applications in Scientific Discourse (SWASD) at the International Semantic Web Conference (ISWC) 2009.
• Steering group member of Shared Names: an effort to ease data integration by making permanent and reliable names available as URI's.
• W3C Advisory Committee representative for the University of Amsterdam
• Program Committee of the Semantic Web for Health Care and Life Sciences Workshop HCLS2008
• Program Committee of the European Semantic Web Conference ESWC08
• Program Committee of the International Semantic Web Conference and the Asian Semantic Web Conference(ISWC+ASWC'07)
• Program Committee (2005 - present) for the Workshop on Uncertainty Reasoning for the Semantic Web
• Program Committee (2002 & 2003) and Reviewer (2004 & 2005) for IEEE Symposium on Information Visualization
• Program Committee for International Workshop on Graph-Based Tools
• Royere/GVF (Graph Visualization Framework) at gvf.sourceforge.net
• Workshop on the Visualization of relational data (2002)
• GraphML: A workgroup formed at the Graph Drawing Symposium 2000 conference to create an XML standard for the description of graphs.

Publications

• M. Scott Marshall, Marco Roos, Edgar Meij, Sophia Katrenko, Willem Robert van Hage, Pieter W. Adriaans, Semantic disclosure in an e-Science environment, Book Chapter in Huajun Chen, Yimin Wang and Kei Cheung (eds.) - Semantic e-Science, Springer Annals of Information Systems AoIS, Springer, April 2009.
• Marco Roos, M. Scott Marshall, Andrew P. Gibson, Martijn Schuemie, Edgar Meij, Sophia Katrenko, Willem Robert van Hage, Konstantinos Krommydas and Pieter W. Adriaans, Structuring and extracting knowledge for the support of hypothesis generation in molecular biology, BMC Bioinformatics Volume 10 Supplement 10, Oct 2009.
• 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 Volume 10 Supplement 10, Oct 2009.
• Ruttenberg A, Rees JA, Samwald M, Marshall MS. Life sciences on the Semantic Web: The Neurocommons and Beyond. Briefings in Bioinformatics, 10(2): 193-204, Mar 2009[online]
• M. Roos, M. S. Marshall, A.P. Gibson, P. W. Adriaans, Structuring mined knowledge for the support of hypothesis generation in molecular biology, Benelux Bioinformatics Conference, December 2008. [Poster]
• M. Roos, M. S. Marshall, A.P. Gibson, P. W. Adriaans, Structuring mined knowledge for the support of hypothesis generation in molecular biology, Semantic Web Applications and Tools for Life Sciences 2008, November 18, Edinburgh, UK
• M. Scott Marshall, Kasper van den Berg, Kamel Boulebiar, Piter de Boer, Marco Roos, Tristan Glatard, Silvia Olabarriaga, A Metadata Management Approach to fMRI Data, UK e-Science All Hands Meeting (AHM), Edinburgh, UK, September 8- 11, 2008.
• S. Koulouzis, E. Meij, M.S. Marshall, and A. Belloum, Enabling Data Transport between Web Services through alternative protocols and Streaming, In: 4th IEEE International Conference on e-Science, 2008.
• M. Roos, P.T. de Boer, M.S. Marshall, K. van den Berg, S. Katrenko, E. Meij, W.R. van Hage, P.W. Adriaans, Biological applications of AIDA knowledge management components, In: The 16th Annual International Conference on Intelligent Systems for Molecular Biology (ISMB), 2008. [Poster]
• Marshall MS, Prud'hommeaux E. A Prototype Knowledge Base for the Life Sciences (W3C Interest Group Note). http://www.w3.org/TR/hcls-kb/.
• M. Roos, S. Katrenko, W.R. van Hage, E. Meij, F. Verster, M.S. Marshall, P.W. Adriaans, My first BioAID: heuristic support for hypothesis construction from literature, In: The 15th Annual International Conference on Intelligent Systems for Molecular Biology (ISMB) and 6th European Conference on Computational Biology (ECCB), 2007. [Poster]
• Lennart J. G. Post, Marco Roos, M. Scott Marshall, Roel van Driel, and Timo M. Breit, A semantic web approach applied to integrative bioinformatics experimentation: a biological use case with genomics data. Bioinformatics, 23(22):3080-3087, 2007. [online]
• M. Roos, M. S. Marshall, E. Meij, S. Katrenko, W. van Hage, P. W. Adriaans, AIDA: combining text mining and e-Science for bioinformatics, UK e-Science All Hands Meeting (AHM), September 10-13, 2007, Nottingham, United Kingdom
• Keet, C.M., Roos, M. and Marshall, M.S. A survey of requirements for automated reasoning services for bio-ontologies in OWL. Third international Workshop OWL: Experiences and Directions (OWLED 2007), 6-7 June 2007, Innsbruck, Austria. CEUR-WS Vol xxx. abstract
• Advancing translational research with the Semantic Web, Alan Ruttenberg, Tim Clark, William Bug, Matthias Samwald, Olivier Bodenreider, Helen Chen, Donald Doherty, Kerstin Forsberg, Yong Gao, Vipul Kashyap, June Kinoshita, Joanne Luciano, M Scott Marshall, Chimezie Ogbuji, Jonathan Rees, Susie Stephens, Gwendolyn T Wong, Elizabeth Wu, Davide Zaccagnini1, Tonya Hongsermeier, Eric Neumann, Ivan Herman and Kei-Hoi Cheung. BMC Bioinformatics 2007, 8(Suppl 3):S2 http://www.biomedcentral.com/1471-2105/8/S3/S2
• Vipul Kashyap, Kei-Hoi Cheung, Don Doherty, Matthias Samwald, M. Scott Marshall, Joanne Luciano, Susie Stephens, Ivan Herman and Ray Hookway, An Ontology-based approach for Data Integration - An Application in Biomedical Research, Book Chapter in Cardoso, J., Hepp, M., Lytras, M. (Eds.) "Real-world Applications of Semantic Web Technology and Ontologies", Springer 2007. Hardcover ISBN-10: 0-387-48530-9, ISBN-13: 978-0-387-48530-0
• Marshall, M.S., Post, L., Roos, M., Breit, T.M. Using semantic web tools to integrate experimental measurement data on our own terms. Workshop on Knowledge Systems in Bioinformatics (KSinBIT?06), Springer Verlag LNCS 4277, 2006, 679-688.
• S. Katrenko, M. S. Marshall, M. Roos and P. Adriaans., Learning Biological Interactions from Medline Abstracts, Learning Language in Logic (LLL05) Workshop, ICML05, Bonn, Germany, 2005.
• M. Roos, M. G. Jansen, M. S. Marshall, and T. Breit., Future application of ontologies in e-Bioscience, Position paper W3C Workshop on Semantic Web for Life Sciences, 2004.
• U. Brandes, M. Eiglsperger, I. Herman, M. Himsolt, and M. S. Marshall., Graphml progress report: Structural layer proposal, Proceedings of Symposium on Graph Drawing (GD 2001), pp. 501-512, 2001.
• M. S. Marshall, Methods and Tools for the Visualization and Navigation of Graphs ("Méthodes et outils pour la visualisation et la navigation de données relationnelles"), Ph.D. Thesis, Dept. of Mathematics and Computer Science, University of Bordeaux, France, June 2001.
• M. S. Marshall, I. Herman, and G. Melançon, An object-oriented design for graph visualization, Software: Practice & Experience, 31:739-756,2001.
• I. Herman, M. S. Marshall, G. Melançon, Density Functions for Visual Attributes and Effective Partitioning in Graph Visualization, IEEE Information Visualization Symposium 2000, eds. S.F. Roth and D.A. Keim, IEEE CS Press, pp. 49-56, 2000.
• I. Herman and M. S. Marshall, GraphXML - a graph description language, Proceedings of the Symposium on Graph Drawing (GD 2000), Springer Verlag, LNCS 1984, pp. 52-62, 2000. Available on-line. A more detailed version of the specification is in: Reports of the Centre for Mathematics and Computer Sciences, Amsterdam INS-R0009, 2000.
• M. S. Marshall, I. Herman, G. Melançon, Automatic Generation of Interactive Overview Diagrams for the Navigation of Large Graphs, Centre for Mathematics and Computer Sciences, Amsterdam INS-R0014, 2000.
• I. Herman, G. Melançon, M. S. Marshall. Graph Visualization and Navigation in Information Visualisation: a Survey. In: IEEE Transactions on Visualization and Computer Graphics, 6(1), pp. 24-43, 2000.
• I. Herman, M. S. Marshall, G. Melançon, D.J. Duke, M. Delest, J.-P. Domenger. Skeletal Images as Visual Cues in Graph Visualisation. In: Data Visualisation '99, Proceedings of the joint Eurographics and IEEE TCVG Symposium on Visualization, eds. E. Gröller, H. Löffelmann and W. Ribarsky, Springer-Verlag, pp. 13-22, 1999.
• D. Duke, I. Herman, M. S. Marshall, PREMO: A Framework for Multimedia Middleware -- Specification, Rationale, and Java Binding, LNCS Volume 1591, Springer-Verlag, 1999.

Previous Research In 1997/98, I developed a Java implementation of an ISO reference framework for multimedia called PREMO (Presentation Environment for Multimedia Objects) together with Ivan Herman.  I am a co-author of "PREMO: A Framework for Multimedia Middleware -- Specification, Rationale, and Java Binding" © Springer-Verlag written with Ivan Herman and David Duke. The book was published in the Springer-Verlag LNCS series and is available in pdf format here. Documentation for the Java implementation of Premo, including clickable UML diagrams, has been generated using Together software.

Bio

Dr M. Scott Marshall is an Assistant Professor of Bioinformatics at the Leiden University Medical Center. As part of a split appointment, he is responsible for activities in the Adaptive Information Disclosure subprogramme of the Virtual Laboratory for e-Science project, where semantic e-Science applications for health care and life sciences are being developed. Previously, Dr. Marshall has worked at CWI, Glaucus Proteomics, Kiadis Pharma, and the microarray department at the University of Amsterdam in The Netherlands. He is a co-chair of the W3C Semantic Web Health Care and Life Sciences Interest Group. Dr. Marshall received a PhD for his work in graph visualization.