[BiO BB] NETTAB 2007 on A Semantic Web for Bioinformatics

Paolo Romano paolo.romano at istge.it
Fri Oct 20 05:42:53 EDT 2006

This message will be posted to many mailing lists. Sorry for the duplications.

Preliminar announcement

                     Workshop NETTAB 2007 focused on
A Semantic Web for Bioinformatics: Goals, Tools, Systems, Applications

                      June 12-15, 2007, Pisa, Italy


Scientific Programme Overview

NETTAB 2007 workshop intends to focus on the Semantic Web, as it is
defined in the action statements of the WorldWideWeb Consortium (W3C)
(see http://www.w3.org/2001/sw/) and in its possible uses in bioinformatics.
It therefore aims at:
- introducing the basic knowledge of related standards and technologies,
   in a non trivial way through invited lectures
- outlining the promising features of the semantic web in bioinformatics
   through invited lectures and open discussion
- showing some valuable examples in bioinformatics through invited lectures,
   oral communications and posters
- allowing for as much discussion as possible through open discussions and
   a panel discussion
- demonstrating "how it works" practically through tutorials

For these reasons, the workshop will include:
- invited lectures on technological issues, perspectives and examples
   in bioinformatics
- oral communications on applications, tools and examples in bioinformatics
- a panel discussion on perspectives of the Semantic Web in bioinformatics
- a poster session
- tutorials, both on implementation of tools and technologies and on the
   best practice in bioinformatics

Note that, starting from this edition, NETTAB workshops will also include
special sessions devoted both to the general theme of the series of workshops,
i.e. "Network Tools and Applications in Biology", and on further topics
selected by local organizers.
This year, you are therefore welcome to submit your work on any of the
followings topics:

- Main focus theme: Semantic Web applications in bioinformatics
- Adjunct focus themes: Algorithms in bioinformatics
                     and Formal Methods for Systems Biology
- General theme: Network Tools and Applications in Bioinformatics

Biological information is increasing at an impressive rate. An integrated
access to this huge amount of information requires complex searching and
retrieval software. In particular, this integration activity is concerned
with how to link data, how to select and extract information and how to
pipe retrieval and analysis steps. This automated approach requires the
adoption of new technologies and tools and their applications in the
bioinformatics domain.
Some reference points have already been assessed or are now emerging:
the adoption of XML schemas for the creation of the models of the
information, the definition of XML based languages for data representation
and exchange, the implementation of Web Services for the interoperability
of software aiming to an automated access to data and analysis tools,
the creation of computerised pipelines and workflows for the definition
and automated execution of both basic and complex analysis processes of
interest to the researchers.
Workflow enactment portals can also bring some added value by allowing
all researchers, even the non expert ones, access to automated processes.

However, while these first steps towards integration of data and automation
of real processes have been made, little has been made for supporting
semantic integration.
What we need are common definitions of knowledge domains, e.g. ontologies,
association of biological concepts to existing data, metadata information
describing all information sources and searching tools that are able to
make the best use of this additional information.
The definition of common ontologies and their application to software
and database tools may be seen as a first, needed attempt to organize
the information, overcoming heterogeneity of data structures, but the
problem of associating the huge amount of information included in
existing databases and information sources with concepts defined in
these ontologies is a big one.
Anyway, the addition of semantic contents in current databases would
give an essential contribution to the best integration of biological
distributed information.
At the same time, the development of metadata for biological information,
on the basis of Semantic Web standards and tools, and its definition for
all information sources, not only databases, can also be seen as a
promising approach for a future, semantic based integration of biological
Text mining is of a fundamental importance in research since literature
is still the most relevant information source in biomedical research.
It is the most evident example of an unstructured information source
whose content should be integrated with structured data in order to
achieve the best results.


Goals of the Semantic Web for Bioinformatics:
- Roles and uses of ontologies in knowledge discovery, text analysis
   and data mining
- Expected results of adoption of Semantic Web tools in Bioinformatics

Standards, Technologies, Tools:
- Semantic Web standards (RDF, OWL, .)
- RDF Schemas and Query systems
- Biomedical Ontologies and related tools
- Formal approaches to large biomedical controlled terminologies and

- RDF repositories and query systems for life sciences
- Semantically aware biomedical Web Services
- Semantic Biological Data Integration Systems

Existing and perspective applications:
- Case studies, use cases, and scenarios
- Semantic Web applications in life sciences

P. Romano, Bioinformatics, National Cancer Research Institute, Italy
M. Schröder, Biotechnology Centre, TU Dresden, Germany
N. Cannata, Mathematics and Computer Science, University of Camerino, Italy
O. Signore, ISTI, National Research Council, Italy

G. Armano, Electrical and Electronic Engineering Dept, Univ. of Cagliari, IT
C. Baker, Institute for Infocomm Research (I2R), SG
P. Barahona, Department of Informatics, New University of Lisboa, PT
L. Barrio-Alvers, Transinsight GmbH, DE
O. Bodenreider, National Library of Medicine, USA
A. Burger, Department of Computer Science, Heriot-Watt University, UK
M. Cannataro, Experimental and Clinical Medicine Dept, Univ. of
    Catanzaro "Magna Graecia", IT
W. Ceusters, Bioinformatics and Life Sciences, University at Buffalo, USA
M. Cockerill, BioMed Central, UK
M.-D. Devignes, LORIA, Vandoeuvre les Nancy, FR
R. Dieng, INRIA, Sophia Antipolis, FR
L. Grivell, European Molecular Biology Organisation, DE
M. Harris, European Bioinformatics Institute, UK
M. Helmer-Citterich, Biology Dept, University of Rome "Tor Vergata", IT
C. M. Keet, Computer Science Faculty, Free University of Bozen-Bolzano, IT
J. Koehler, Biomathematics and Bioinformatics, Rothamsted Research, UK
M. Krallinger, Spanish National Cancer Research Center (CNIO), ES
L. Krippahl, Department of Informatics, New University of Lisboa, PT
P. Lambrix, Computer and Information Science Dept, Linköping University, SE
U. Leser, Institute for Computer Science, Humboldt-University of Berlin, DE
J. Luciano, Department of Genetics, Harvard Medical School, USA
R. Marangoni, Computer Science Department, University of Pisa, IT
M. Marchiori, Pure and Applied Mathematics Dept, University of Padua, IT
M. Masseroli, Department of BioEngineering, Polytechnic of Milan, IT
G. Mauri, Informatics Systems and Communication Dept, Univ. Milan "Bicocca", IT
E. Merelli, Mathematics and Computer Science Dept, University of Camerino, IT
L. Milanesi, Biomedical Technologies Institute, National Research Council, IT
S. Moeller, Institute of Neuro- and Bioinformatics, University of Lübeck, DE
S. Philippi, Institute for Software Technology, Univ. of Koblenz-Landau, DE
D. Quann, IBM Software Group, USA
D. Rubin, Stanford Medical Informatics, Stanford University Medical Center, USA
S.-A. Sansone, European Bioinformatics Institute, UK
M. Senger, International Rice Research Institute, PH
D. Turi, School of Computer Science, University of Manchester, UK
G. Vetere, IBM Center for Advanced Studies of Rome, IT
D. Zaccagnini, Language and Computing, USA

Paolo Romano (paolo.romano at istge.it)
Bioinformatics and Structural Proteomics
National Cancer Research Institute (IST)
Largo Rosanna Benzi, 10, I-16132, Genova, Italy
Tel: +39-010-5737-288  Fax: +39-010-5737-295

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