CfPart: Semantic Web Applications and Tools for Life Sciences (SWAT4LS)

Dear all,


this is the final Call for Participation for the 1st workshop on

Semantic Web Applications and Tools for Life Sciences (SWAT4LS).


The program has been enriched, as you can see at .

We welcome you all in Edinburgh quite soon.


Best regards,


Adrian Paschke






                   International Workshop on

Semantic Web Applications and Tools for Life Sciences (SWAT4LS)

              28th November 2008, Edinburgh, UK



Call for Participation


Please note that space is limited and participants will be allocated

on a first-come, first-served basis.

A limited number of places are reserved for students, for whom the

workshop fees are waived.


Interested participants should register following the instructions at:


Registration Deadline: 21 November 2008





This workshop will provide a showcase and a space for discussion of

benefits and limits of the adoption of Semantic Web technologies

and tools in biomedical informatics and computational biology.


It will provide:

    * two keynotes

    * a tutorial

    * oral communications on applications, tools and use cases

    * a poster/demo session (some posters will be selected for flash

      oral presentations)

    * a panel discussion on perspectives of the Semantic Web

      in Life Sciences




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


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

attempts to make Web Service access completely transparent,

such that the "Deep Web" can be queried just like any other Semantic

Web resource.




The W3C Interest Group on Semantic Web Technologies for Health

Care and Life Sciences

M. S. Marshall, W3 HCLS IG co-chair


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 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.


Accepted papers


* Robert Bossy, Alain Kotoujansky, Sophie Aubin and Claire


Close Integration of ML and NLP Tools in BioAlvis for Semantic

Search in Bacteriology


* Nadia Anwar, Ela Hunt, Walter Kolch and Andrew Pitt.

Semantic Data Integration for Francisella tularensis novicida

Proteomic and Genomic Data


* George Zheng and Athman Bouguettaya.

PathExplorer: Service Mining for Biological Pathways on the Web


* Heiko Dietze and Michael Schroeder.

GoWeb: A semantic search engine for the life science web


* Erick Antezana, Ward Blonde, Mikel Egana, Alistair

Rutherford, Robert Stevens, Bernard De Baets, 

Vladimir Mironov and Martin Kuiper.

Structuring the life science resourceome for Semantic Systems

Biology: lessons from the BioGateway project


* Simon Jupp, Robert Stevens, Sean Bechhofer, Yeliz Yesilada and

Patty Kostkova.

Knowledge Representation for Web Navigation


* Antonio Jimeno, Ernesto Jimenez-Ruiz, Rafael Berlanga and

Dietrich Rebholz-Schuhmann

Use of shared lexical resources for efficient ontological



* Maria del Mar Roldan-Garcia, Ismael Navas-Delgado, Amine Kerzazi,

Othmane Chniber, Joaquin Molina and Jose F Aldana Montes.

KASBi: Knowledge-Based Analysis in Systems Biology



Accepted highlight posters


* Erick Antezana, Ward Blond¡î¨Ï, Mikel Ega¡î¡¾a, Alistair

Rutherford, Robert Stevens, Bernard De Baets, Vladimir Mironov

and Martin Kuiper.

BioGateway: integrated RDF for life science queries


* Anna-Lena Lamprecht, Tiziana Margaria and Bernhard Steffen.

Supporting Process Development in Bio-jETI by Model Checking and



* Marco Roos, M. Scott Marshall, Andrew Gibson and Pieter Adriaans.

Structuring mined knowledge for the support of hypothesis

generation in molecular biology


* Dongeun Sun and Seongbin Park.

Knowledge management using Wikipedia


* Wee Tiong Ang, Rajaraman Kanagasabai and Christopher Baker.

Knowledge Translation: Computing the query potential of bio- ontologies


For a full list of contributions accepted please 

visit: .


Workshop Chairs


Albert Burger, School of Mathematical and Computer Sciences,

Heriot-Watt University, and MRC Human Genetics Unit, Edinburgh,

United Kingdom


Adrian Paschke, Corporate Semantic Web, Free University Berlin,



Paolo Romano, Bioinformatics, National Cancer Research Institute,

Genova, Italy


Andrea Splendiani, Medical Informatics Department, University of

Rennes 1, Rennes, France


Programme Committee


+ Giulio Armano, University of Cagliari, Italy

+ Christopher Baker, Institute for Infocomm Research (I2R), Singapore

+ Pedro Barahona, New University of Lisboa, Portugal

+ Liliana Barrio-Alvers, Transinsight GmbH, Germany

+ Virendra C. Bhavsar, University of New Brunswick, Canada

+ Olivier Bodenreider, National Library of Medicine, Bethesda, USA

+ Matt-Mouley Bouamrane, University of Machester, United Kingdom

+ Werner Ceusters, University at Buffalo, USA

+ Kei Cheung, Yale Center for Medical Informatics, USA

+ Marie-Dominique Devignes, LORIA, Vandoeuvre les Nancy, France

+ Michel Dumontier, Carleton University, Canada

+ C. Maria Keet, Free University of Bozen-Bolzano, Italy

+ Graham Kemp, Chalmers University of Technology, Sweden

+ Jacob Tilman Koehler, University of Troms¡î¢³, Norway

+ Ludwig Krippahl, New University of Lisboa, Portugal

+ Patrick Lambrix, Link¡î¡Óping University, Sweden

+ Phillip Lord, University of Newcastle, United Kingdom

+ M. Scott Marshall, University of Amsterdam, The Netherlands

+ Lyndon Nixon, STI International, Austria

+ Stephan Philippi, University of Koblenz-Landau, Germany

+ Alan Ruttenberg, Science Commons, USA

+ Matthias Samwald, DERI, Galway, Ireland, and Semantic Web Company,


+ Nigam Shah, Center for Biomedical Informatics Research, USA

+ Michael Schr¡î¡Óder, TU Dresden, Germany

+ Robert Stevens, University of Manchester, United Kingdom

+ Luca Toldo, Merck Serono, Germany

+ Tetsuro Toyoda, RIKEN, Japan

+ Jano van Hemert, University of Edinburgh, United Kingdom




In Co-operation with:


- National Cancer Research Institute, Genova, Italy

- Corporate Semantic Web, Free University Dresden, Germany

- Biotechnology Centre, TU Dresden, Dresden, Germany

- School of Mathematical and Computer Sciences, Heriot-Watt

  University, Edinburgh, United Kingdom

- Universite de Rennes 1, Rennes, France

- e-Science Institute, Edinburgh, Scotland, United Kingdom

- SeaLife Project, European Commission Information Society and Media

- Laboratory for Interdisciplinary Technologies in Bioinformatics

  (LITBIO), Italy



The workshop is hosted by and located at the


         e-Science Institute,

         15 South College Street

         Edinburgh, EH8 9AA, UK



The workshop is sponsored by:



- Labage SA (

- Leaf Bioscience (

- Textsensor Ltd. (



Received on Tuesday, 18 November 2008 18:37:37 UTC