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SWAT4LS: Semantic Web applications and Tools for Life Sciences and Semantic Chemistry

From: Adrian P.
Sent on: Thursday, September 23, 2010 10:38 AM

Berlin Semantic Web Meetup on Semantic Health Care, Life Sciences, Chemistry

Berlin, 9th December 2010




3rd Int. Semantic Web Applications and Tools for Life Sciences
Berlin, 10th December 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 biology.


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 solutions
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 Bioinformatics
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 (

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 ( and submitted in pdf format. 
• 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 pages.


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 Sciences
            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 dinner. 
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, Italy
• 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, Link?ping University, Link?ping, 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, Germany

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

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






The deadline for early bird registration is October 8th.


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


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