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SWAT4LS Workshop

Semantic Web Applications and Tools for Life Sciences

November 28, 2008,
e-Science Institute, Edinburgh, Scotland, UK

Scientific Programme Overview

SWAT4LS workshop focused on Semantic Web Applications and Tools for Life Sciences.

The workshop included:

  • two invited lectures
  • eight oral communications on applications, tools and use cases, selected from submissions
  • a poster/demo session (four posters were selected for flash oral presentations)
  • a tutorial
  • a panel discussion on perspectives of the Semantic Web in life sciences

Invited Lectures

  • Semantic web technology in translational cancer research
    Michael Krauthammer, Department of Pathology, Yale University School of Medicine, USA
    Michael Krauthammer received his M.D. degree at the University of Zurich, Switzerland. After board certification (general practitioner), he obtained a Ph.D. in biomedical informatics at Columbia University in New York and joined the Yale Pathology Informatics program in July, 2004. His main research interests are the design of large scale text and image mining systems and research in translational informatics.
    He is the co-director of the bioinformatics core of the Yale SPORE in skin cancer, a large translational research program, and member of the Yale Cancer Center (YCC) informatics steering committee. He is the Yale PI for adopting caBIG's caTISSUE specimen tracking system across the Yale Medical Campus, enabling Yale researcher to manage their tissue banks and share data via the caGRID infrastructure.
    He is involved, on a national level, in enabling the collaboration among existing skin SPORE programs using caBIG technology. The project, termed "melaGRID", that is carried out by using semantic web technologies, will allow for the sharing of clinical, tissue and omics data, and will be instrumental for performing cross-institutional biomarker studies in melanoma.
  • Web 2.0 + Web 3.0 = Web 5.0? Using Ontologies to bring Web Services on to the Semantic Web
    Mark Wilkinson, University of British Columbia, Vancouver, Canada
    Mark is an Assistant Professor of Medical Genetics at the University of British Columbia, in Vancouver. He is also PI in Bioinformatics at the Heart & Lung Research Institute at St. Paul's Hospital. His primary research interests relate to the construction and use of Semantic systems in the biomedical domain, and in particular the role of mass-collaboration in the development and maintenance of Semantic Web technologies and frameworks. He is founder and leader of the BioMoby project and founder and leader of the SHARE project.
    He will be discussing the BioMoby project and how it opened his eyes to what the Semantic Web could look like, and what mistakes were made along the way. He will then go on to discuss plans for the next generation of Moby Semantic Web Services, where he attempt to make Web Service access completely transparent, such that the "Deep Web" can be queried just like any other Semantic Web resource.


  • Introduction to the W3C for Semantic Web Health Care and Life Sciences Interest Group
    M. Scott Marshall, W3C Semantic Web for Health Care and Life Sciences Interest Group
    The W3C Semantic Web for Health Care and Life Sciences Interest Group (HCLS IG) was recently rechartered for the next three years to continue its mission to develop, advocate for, and support the use of Semantic Web technologies for biological science, translational medicine and health care. Membership in the group has grown to 89 participants, with a wide range of representation from industry and academia. The HCLS tutorial will discuss the challenges and opportunities at hand. An overview of the activities of the each of the current task forces in HCLS will be provided, along with a description of how specific Semantic Web technologies are being applied. Some new developments and the recent Face2Face meeting will also be discussed, as well as how interested parties can participate.

Scientific Programme

Friday November 28, 2008
09.00 - 09.30 Registration and poster hang up
09.30 - 10.00 Keynote lecture
Semantic web technology in translational cancer research,
M. Krauthammer
10.00 - 11.00 Session on Experiences
11.00 - 11.30 Coffee break
11.30 - 12.30 Session on Applications (Tools, Methods, Data)
12.30 - 13.00 Flash poster presentations session (5' each)
13.00 - 14.00 Lunch break
14.00 - 14.45 Tutorial
Introduction to the W3C for Semantic Web Health Care and Life Sciences Interest Group,
M. Scott Marshall
14.45 - 15.30 Poster/Demo Session
15.30 - 16.00 Coffee break
16.00 - 16.45 Session on Perspectives (Tools, Methods, Data)
16.45 - 17.15 Keynote lecture
Using Ontologies to bring Web Services on to the Semantic Web,
M. Wilkinson
17.15 - 18.15 Panel discussion
If the semantic web is so good, how come most people use OBO for ontologies and perl for data integration?
Phil Lord (Chair)

Accepted demos

  • BioGateway: Query architecture and visualisation of results
    Erick Antezana, Ward Blondé, Mikel Egaña, Alistair Rutherford, Robert Stevens, Bernard De Baets, Vladimir Mironov and Martin Kuiper.

Accepted posters


Presentations of oral communications and selected posters are available in the eSI site. Click here.

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