CfP - Semantic Web Applications and Tools for the Life Sciences (SWAT4LS 2012)

[With the usual apologies for cross-posting... ]

Call for Papers

5th International Workshop on Semantic Web Applications and Tools for the Life Sciences (SWAT4LS 2012)
http://www.swat4ls.org/workshops/paris2012

Overview

Since 2008, SWAT4LS is a workshop that has provided a platform for the presentation and discussion of the benefits and limits of applying web-based information systems and semantic technologies in the domains of health care and life sciences.
SWAT4LS has been in Edinburgh (2008), Amsterdam (2009), Berlin (2010) and London (2011). 
Growing steadily each year as Semantic Web applications have become more widespread, the program of SWAT4LS has grown to include associated events.
The next edition of SWAT4LS will be held in Paris, on November 30th 2012, and it will be preceded by two days of tutorials and hackathons.

We are confident that the next edition of SWAT4LS will provide the same open and stimulating environment that brought together researchers, developers, and users, from various fields including biomedical informatics, systems biology, computational biology, drug discovery, bioinformatics and biocomputing, to discuss goals, current limits and real experiences in
the use of Semantic Web technologies in Life Sciences.
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Rationale

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. 
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Topics

Topics of interest include, but are not limited to: 
Standards, Technologies, Tools for the Semantic Web
Big Metadata
Semantic Web standards and new proposals (e.g.: RDF, OWL, SKOS, SPIN, RuleML, Microformats) 
Tools for ontology editing, annotation, versioning and provenance management
RDF stores, NoSQL, reasoners, query and visualization systems
Knowledge representation for biomedical knowledge bases
Query federation systems for distributed knowledge and data discovery
Tools for semantics-enabled web publication

Systems for a Semantic Web for Bioinformatics
Biomedical knowledge bases on the Semantic Web
Semantic biomedical Web Services
Semantics-enabled biomedical information systems and solutions
Linked Data for biomedical research

Existing and prospective applications of the Semantic Web for Bioinformatics
Semantic Wikis
Semantic collaborative research environments
Semantic crowdsourcing and collective intelligence
Alternative approaches to biomedical metadata generation and management
Methods for data sharing and open data
Approaches to data privacy and security
Case studies, use cases, and scenarios
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Type of contributions

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

Previous proceedings of SWAT4LS have appeared in the past in CEUR, Nature Preceedings or ACM. 
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Special issue

Authors of accepted contributions to the upcoming edition of SWAT4LS will be
invited to submit to a special issue of the BMC Journal of Biomedical Semantics.

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Deadlines

Expression of interest for tutorials: 		5th July 2012 (closed)
Submission opening: 				3rd September 2012
Papers submission deadline (abstracts): 	28th September 2012
Papers submission deadline (full text):	9th October 2012
Early registration deadline: 			15th October 2012 
Posters and demos submission deadline: 	22nd October 2012 
Communication of acceptance: 		29th October 2012 
PDF ready: 					23rd November 2012
Hackathon, Tutorials				28-29th November 2012			
Workshop day:				30th November 2012

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Instructions: 

All papers and posters must be in English 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.

Please refer to the SWAT4LS website for detailed formatting instructions prior to submission.
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Submission

All submissions will be handled via the EasyChair submission system (to be opened in the beginning of September).
To ensure high quality, submitted papers will be carefully peer-reviewed by at least three members of the Scientific Committee. 

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Scientific Committee (provisional, more to be confirmed):

Erick Antezana, Bayer CropScience, Ghent, Belgium
Christopher J. O. Baker, Department of Computer Science and Applied Statistics, University of Brunswick, Canada
Olivier Bodenreider, National Library of Medicine, Bethesda, MD, United States of America
Matt-Mouley Bouamrane, Centre for Population and Health Sciences, College of Medical, Veterinary and Life Sciences, University of Glasgow, United Kingdom
Werner Ceusters, SUNY at Buffalo, Buffalo, United States of America
Tim Clark, Massachusetts General Hospital / Harvard Medical School, Boston, United Sates of America
Olivier Dameron, INSERM U936, University of Rennes 1, France
Helena F. Deus, DERI, Galway, Ireland
Michel Dumontier, Carleton University, Ottawa, Ontario, Canada
Patty Kostkova, City eHealth Research Centre, City University, London, UK
Martin Kuiper, Norwegian University of Science and Technology, Trondheim, Norway
Patrick Lambrix, Department of Computer and Information Science, Linköping University, Linköping, Sweden
Chris Mungall, Lawrence Berkeley National Laboratory, Berkeley, United States of America
Alan Ruttenberg, School of Dental Medicine, University at Buffalo, Buffalo, NY, United States of America
Nigam Shah, Center for Biomedical Informatics Research, Stanford, United States of America
Michael Schroeder, Biotechnology Centre, TU Dresden, Dresden, Germany
Luca Toldo, Merck Serono, Darmstadt, Germany

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, IRCCS AOU San Martino – IST National Cancer Research Institute, Genova, Italy
M. Scott Marshall, MAASTRO clinic, The Netherlands
Andrea Splendiani, intelliLeaf, UK and DERI, IE

Helena F. Deus, PhD
Unit Leader, Bioinformatics and Computational Biology
Digital Enterprise Research Institute
helena.deus@deri.org
+353 91 495 270