[BioinfoKenya] CFP Semantic Web in Bioinformatics

George Githinji georgkam at gmail.com
Sat Dec 2 05:57:38 EST 2006

---------- Forwarded message ----------
From: Paolo Romano <paolo.romano at istge.it>
Date: Dec 2, 2006 1:30 PM
Subject: CFP Semantic Web in Bioinformatics
To: georgkam at gmail.com

Dear George Githinji Kamanu,

I'm sending you the first Call for papers of the seventh NETTAB workshop.
If you feel it can be of interest for the
bioinfokenia.org community, could you please submit it to the list?
Thank you very much in advance.

Ciao. Paolo

                7th International Workshop NETTAB 2007

                            FOCUS THEME
A Semantic Web for Bioinformatics: Goals, Tools, Systems, Applications

                           ADJUNCT THEMES
                    Algorithms in bioinformatics
                 Formal Methods for Systems Biology
            Network Tools and Applications in Bioinformatics

                           June 12-15, 2006
        Department of Computer Science, University of Pisa, Pisa


                        FIRST CALL FOR PAPERS


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, the
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
emerging: the adoption of XML schemas for information models'
specification, the definition of XML based languages for data
representation and exchange, the implementation of Web Services
for automated access to analysis tools and dat , the creation
of computerised pipelines and workflows for the definition
and the execution of basic and complex analysis. Workflow
enactment portals can bring added value, allowing also non
expert researchers to have analysis automation at their disposal.

However, while these first steps towards data integration and
processes automation have been made, little has been made
for supporting semantic integration. What we need are shared
definitions of knowledge domains, i.e. ontologies, association
of biological concepts to existing data, metadata information
describing information sources and search tools able to make
the best use of this additional information.

The definition of 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 information
sources and the huge amount of data with concepts defined in
these ontologies is a big one. The addition of semantic
contents in current databases would give an essential
contribution to the best integration of distributed biological

The development of metadata for biological information, on the
basis of Semantic Web standards, and its definition for all
information sources can also be seen as a promising approach
for a semantic based integration of biological information.
Text mining is of a fundamental importance since literature
still is the most relevant information source in biomedical
research. It is the most clear example of an unstructured
information source whose content should be integrated with
structured data in order to be fully exploited.


This workshop aims at getting together biologists,
bioinformaticians, computer scientists and linguists to
try to answer the following questions:
- Is the Semantic Web of some use for Bioinformatics?
- Which goals should have a Semantic Web for Bioinformatics?
- Which standards, technologies and tools of the Semantic Web
   can most profitably be used in Bioinformatics?
- Which application did the Semantic Web already find
   in Bioinformatics?
- Which current Bioinformatics research problems can be
   solved by the Semantic Web?
- Which are the short, medium and long term perspectives in
   applying Semantic Web technologies to Biinformatics?
The workshop also intends to:
- introduce the basic knowledge of related standards and
   technologies, in a non trivial way through invited lectures
   and tutorials
- outline the promising features of the Semantic Web in
   bioinformatics through invited lectures and open discussion
- show some valuable examples in bioinformatics through
   invited lectures, oral communications and posters
- support as much discussion as possible through open
   discussions and a panel discussion
- practically demonstrate "how it works" through tutorials


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

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 vocabularies

- 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


Starting from this edition, NETTAB workshops will also include
special sessions devoted both to the general theme of the series
of workshops, "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 general adjunct topics:
- Algorithms in bioinformatics
- Formal Methods for Systems Biology
- Network Tools and Applications in Bioinformatics


Submission of oral communications: March 16, 2007
Proposals for tutorials: March 16, 2007
Submission of posters: April 20, 2007
Early Registration Deadline: April 27, 2007


All accepted oral communications and posters will be
published in the abstracts' book.
Selected papers will also be published in an international
peer reviewed journal that will soon be announced.
Further more detailed information will be added to the web
site and in the texts of the Call for Papers presented in
upcoming occasions.


P. Romano, Bioinformatics, Natl Cancer Research Inst., Italy
M. Schröder, Biotechnology Centre, TU Dresden, Germany
N. Cannata, Mathematics & Computer Science Dept, Univ. 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",
E. Merelli, Mathematics and Computer Science Dept, University of Camerino,
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,
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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