[DL] CFP: SWAT4LS: Semantic Web applications and Tools for Life Sciences

Adrian Paschke adrian.paschke at gmx.de
Thu Sep 23 09:57:46 CEST 2010

[With apologies for cross-posting]


Submissions are now open for the 3rd Int. Semantic Web Applications and
Tools for Life Sciences
Berlin, 10th December 2010
 <http://www.swat4ls.org/2010/> http://www.swat4ls.org/2010/

* Special issue in BMC Bioinformatics
* Nature proceedings / CEUR Proceedings
* 2 keynotes
* Tutorial day on Semantic Web Services, Linked Data, D2RQ, 

* Semantic Web Meetup in Semantic Life Sciences and Chemistry
* Panel discussion



SWAT4LS is a workshop that provides a venue to present and discuss benefits
and limits of the adoption of Web based information systems and semantic
technologies in life sciences, biomedical informatics and computational


The web is a key medium for information publishing, and web based
information systems play a key role in biomedical information exchange and
integration. At the same time, the variety and complexity of biomedical
information call for the adoption of semantic-based solutions. The Semantic
Web provides a set of technologies and standards that are key to support
semantic markup, ontology development, distributed information resources and
collaborative social environments. Altogether the adoption of the web-based
semantic-enabled technologies in the Life Sciences has potential impact on
the future of publishing, biological research and medicine. This workshop
will provide a venue to present and discuss benefits and limits of the
adoption of these technologies and tools in biomedical informatics and
computational biology. It will showcase experiences, information resources,
tools development and applications. It will bring together researchers, both
developers and users, from the 
various fields of Biology, Bioinformatics and Computer Science, to discuss
goals, current limits and some real use cases for Semantic Web technologies
in Life Sciences. 


Topics of interest include, but are not limited to: 
• Standards, Technologies, Tools for the Semantic Web
o Semantic Web standards and new proposals (RDF, OWL, SKOS, Linked Data, 
o Biomedical Ontologies and related tools
o Alternative approaches to integrate semantic representations and web based
o Formal approaches to large biomedical knowledge bases
• Systems for a Semantic Web for Bioinformatics
o RDF stores, Reasoners, query and visualization systems for life sciences
o Semantic biomedical Web Services
o Semantics aware Biological Data Integration Systems
• Existing and prospective applications of the Semantic Web for
o Semantics aware application tools
o Semantic Wikis
o Semantic collaborative research environments
o Case studies, use cases, and scenarios

Type of contributions

The following possible contributions are sought: 
• Research papers
• Position papers
• Posters
• Software demos



All accepted communications will be published in the proceedings, either
Nature Proceedings or via CEUR-WS ( <http://ceur-ws.org/>

Special issue

Authors of accepted contributions to the 2010 edition of SWAT4LS will be
invited to submit extended and revised contributions for a special issue in
BMC Bioinformatics.


• Submission openinig: 13 September 2010
• Papers submission deadline: 12 October 2010
• Posters and demo submission deadline: 1 November 2010
• Communication of acceptance: 8 November 2010
• Camera ready: 21 November 2010


All papers and posters must be in English, formatted according to LNCS
format (http://www.springer.de/comp/lncs/authors.html) and submitted in pdf
• Submissions for papers should report original research, and should be
between 8 and 15 pages.
• Submissions for position papers should report qualified opinions,
recommendations or conclusions, and should be between 3 and 6 pages.
• Submissions for posters should be between 2 and 4 pages.
• Submissions for software demo proposals should also be between 2 and 4


All submissions will be handled via the EasyChair submission system. A link
will be provided when registrations open.
To ensure high quality, submitted papers will be carefully peer-reviewed by
at least three members of the Scientific Program Committee. 

Full Program

(more detailed information available at


Wednesday 8th December 2010
Location: Free University of Berlin

-           Tutorial: Semantic Web meets Cloud Computing
            Presenter: Jonas Almedia (Univ. Texas MDAnderson Cancer Center,
Huston, USA)
-           Free Hackathon

Thursday 9th December 2010
Location: Free University of Berlin or Harnak Hause (to be confirmed)

-           Tutorial: Interoperable Semantic Web services
-           Presenters: Jon Ison (EMBL-EBI, Hinxton, U.K.), Matus Kalas
(Bergen Center for Computational Science, Bergen, Norway)
-           Tutorial: Producing Linked Data
            Presenters: TBD
-           Tutorial: D2RQ
            Presenters: Radoslaw Oldakowski (Free University of Berlin)
-           7th Berlin Semantic Web Meetup - Semantic Health Care and Life
            Presentations from Meetup participants
-           SWAT4LS / Meetup Dinner + poster session

Friday 10th December 2010
Location: Harnak Hause
The workshop will run from 9.00 to 19.00, followed by the optional social
It will feature:

-           Keynotes:

            -           Christopher Baker: A renaissance for the point
mutation: from legacy data to semantic web service
            -           Jonas Almeida: Development of Integrative
Bioinformatics Applications using Cloud Computing resources and Knowledge
Organization Systems (KOS).

-           Accepted papers presentations

-           Flash presentations

-           Poster session

-           Demo session

-           Panel discussion (Confirmed participants: Chris Baker, Jonas
Almeida, Chirs Bizer)


Workshop Chairs
• Adrian Paschke, Corporate Semantic Web, Freie Universitaet Berlin, Germany
• Albert Burger, School of Mathematical and Computer Sciences, Heriot-Watt
University, and Human Genetics Unit, Medical Research Council, Edinburgh,
Scotland, United Kingdom
• Paolo Romano, Bioinformatics, National Cancer Research Institute, Genova,
• M. Scott Marshall, Adaptive Information Disclosure Group, University of
Amsterdam, The Netherlands
• Andrea Splendiani, Biomathematics and Bioinformatics dept., Rothamsted
Research, UK




Scientific Program committee (more to be confirmed):

            • Erick Antezana, Bayer CropScience, Ghent, Belgium

            • Pedro Barahona, Department of Informatics, New University of
Lisboa, Lisboa, Portugal

            • Olivier Bodenreider, National Library of Medicine, Bethesda,
MD, United States of America

            • Werner Ceusters, NY CoE in Bioinformatics and Life Sciences,
University at Buffalo, Buffalo, NY, United States of America

            • Kei Cheung, Center for Medical Informatics, Yale University
School of Medicine, New Haven, United States of America

            • Tim Clark, Massachuttes General Hospital and Harvard Medical
School, Boston, United States of America

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

            • Olivier Dameron, INSERM U936, University of Rennes 1, France

            • Asuman Dogac, Department of Computer Eng., Middle East
Technical University, Ankara ,Turkey

            • Michel Dumontier, Carleton University, Ottawa, Ontario, Canada

            • Toshiaki Katayama, Human Genome Center (HGC), University of
Tokyo, Japan

            • C. Maria Keet, Faculty of Computer Science, Free University of
Bozen-Bolzano, Bolzano, Italy

            • Graham Kemp, Chalmers University of Technology, Sweden

            • Michael Krauthammer, Department of Pathology, Yale University
School of Medicine, United States of America

            • Patrick Lambrix, Department of Computer and Information
Science, Linköping University, Linköping, Sweden

            • Phillip Lord, School of Computing Science, Newcastle
University, Newcastle-upon-Tyne, United Kingdom

            • Alistair Miles, Centre for Genomics and Global Health, The
Wellcome Trust Centre for Human Genetics, Oxford, Uk

            • Stephan Philippi, Institute for Software Technology,
University of Koblenz-Landau, Koblenz, Germany

            • Marco Roos, Instituut voor Informatica, University of
Amsterdam, The Netherlands

            • Alan Ruttenberg, Science Commons, Cambridge, MA, United States
of America

            • Matthias Samwald, DERI, Galway, Ireland, and Konrad Lorenz
Institute for Evolution and Cognition Research, Altenberg, Austria

            • Nigam Shah, Center for Biomedical Informatics Research,
Stanford, United States of America

            • Michael Schroeder, Biotechnology Centre, TU Dresden, Dresden,

            • Robert Stevens, School of Computer Science, University of
Manchester, Manchester, United Kingdom

            • Tetsuro Toyoda, Genomic Sciences Center, RIKEN, Yokohama,






The deadline for early bird registration is October 8th. 




As spaces are limited, we encourage interested participants to register in


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