Preface
The 5th International Workshop on Semantic Web Applications and Tools for the
Life Sciences (SWAT4LS 2012) was devoted to research and developments on
practical distributed semantic technologies and web-based information systems
operating in the context of Biomedical Informatics and Computational Biology.

Growing steadily each year as Semantic Web applications become more
widespread, SWAT4LS (http://www.swat4ls.org/) has been in Edinburgh 2008,
Amsterdam 2009, Berlin 2010 and London (2011), with the first SWAT4LS School
organized in Aveiro in 2012. The 2012 edition of SWAT4LS in Paris was an
exciting venue to exchange new ideas, practical developments and experiences on
issues related to the engineering, management, integration, interoperation and
interchange of semantic data and tools in life sciences. It provided an open and
stimulating environment that brought together researchers, both developers and
users, from the various fields of Biology, Bioinformatics and Computer Science,
who discussed goals, current limits and real experiences in the use of Semantic
Web technologies in Life Sciences.

SWAT4LS 2012 received 47 original submissions from contributors around the
world. The organizers of this event took advantage of the very strong international
program committee, who rigorously reviewed the submissions. Finally, the
workshop program included ten full papers, which presented solid work in
advancing and assessing the state of the art in semantic systems; and eight position
papers, which presented innovative ideas, approaches, and implementations. To
place emphasis on the practical use of semantic technologies in the life science
domain the program also had a poster session with demos and poster papers. This
session offered participants the opportunity to demonstrate their commercial and
open source tools, use cases, and applications.
Further highlights of the three day program of SWAT4LS 2012 included:

- Four plenary keynotes given by world-class practitioners and researchers
featuring foundational topics of semantic computing and industrial success stories:
     1. Mark A. Musen, M.D., Ph.D: Semantic Technology Goes Mainstream:
         The NCBO Experience
     2. C. Michael Gibson, M.S., M.D., FRCP, FAHA, FSCAI, FACC: The
         World is Flat, but the Earth is Round
     3. Christine Golbreich, Ph.D: Formal ontologies for the Semantic Web ?
     4. Ann Marie Martin, Principal Scientific Manager, Knowledge
         Management, European Innovative Medicine Initiative : Joining private
         and public forces to boost innovation in healthcare: the innovative
         medicines initiative and knowledge management
- Six Tutorials

    1.   Interconnecting Linked Open Data and R with the SPARQL package for
         Linked Science
    2.   Biologial Pathways and the Semantic Web
    3.   Using SPARQL to Query BioPortal Ontologies and Metadata
    4.   Drug-discovery knowledge integration and analysis using OWL and
         reasoners
    5.   Thorough introduction to SPARQL for anyone in the Life Sciences
    6.   Use of the BioQueries collaborative portal

- a Hackathon Day: SWAT4LS Hackathon
- a Scientific Poster Exibition
- an Industry Track: Linked Life Data: Increasing Research Scope without
Integration Headaches
- Scientific Paper Presentations
- Social events to promote networking among the SWAT4LS delegates in an
   informal setting.

The SWAT4LS 2012 organizers wish to thank the excellent program committee for
their hard work in reviewing the submitted papers. Their criticism and very useful
comments and suggestions invaluably helped us to maintain high quality of
publications. We also thank the symposium authors for submitting good papers,
responding to the reviewers’ comments and keeping to our production schedule.
We further wish to thank the keynote speakers who have found time in their busy
schedules to come and give very interesting talks. Finally, we thank the sponsors,
whose financial support helped to offer the event at this exiting place, and whose
technical support allowed to attract many high quality submissions.


December 22, 2012

Adrian Paschke, Albert Burger, Paolo Romano, M. Scott Marshall, Andrea
Splendiani