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Network Tools and Applications in Biology
NETTAB 2007 focused on:
A Semantic Web for Bioinformatics:
Goals, Tools, Systems, Applications
June 12-15, 2007, University of 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

Invited Lectures

  • Opening lecture: Pathway Commons: A public library of biological pathways on the semantic web
    Gary Bader, University of Toronto, Canada
    Gary D. Bader works on biological network analysis and pathway information resources as an Assistant Professor at the Terrence Donnelly Centre for Cellular and Biomolecular Research (CCBR) at the University of Toronto.
    He recently completed post-doctoral work in the group of Chris Sander in the Computational Biology Center (cBio) at Memorial Sloan-Kettering Cancer Center in New York. Gary developed the Biomolecular Interaction Network Database (BIND) during his Ph.D. in the lab of Christopher Hogue in the Department of Biochemistry at the University of Toronto and the Samuel Lunenfeld Research Institute at Mount Sinai Hospital in Toronto. He completed a B.Sc. in Biochemistry at McGill University in Montreal.
    Biological pathways represent knowledge about molecules, processes and their interactions, the cellular wiring diagram. Biological researchers use pathway maps to design and analyze experiments and to make predictions about the behavior of biological systems. Pathway information is, unfortunately, extremely difficult for biologists to use in its current fragmented and incomplete state. This roadblock to biological research can be overcome by developing the Pathway Commons Research Resource. Pathway Commons benefits researchers as a convenient single point of access to diverse biological pathway information from public sources, translated to the common BioPAX data language.

  • The Semantic Web for Health Care and Life Science Interest Group and its Goals
    Eric Neumann, Teranode Co., USA, and Chair of the Health Care & Life Science Interest Group, W3C
    Eric K. Neumann is a Senior Strategist for Teranode Corporation, a company developing next generation systems for pharmaceutical companies. He is also founder and co-chair for the W3C Semantic Web Healthcare and Life Science Interest Group (HCLSIG) that is bringing together industry leaders to identify domain-specific applications that will benefit from semantic web technologies. He has also formed the Clinical Semantics Group, a consultancy group specializing in the development of intelligent applications for clinical trials informatics. Prior to this, Dr. Neumann was Global Head of Knowledge Management for Scientific and Medical Affairs within Sanofi-Aventis, covering all of global R&D. While in that position, he had developed BioDash, the first Drug Discovery Semantic Web dashboard. Dr. Neumann has also held executive positions at Beyond Genomics, 3rd Millenium, and Netgenics, and was an NSF-funded researcher for 6 years while at and Bolt, Beranek, and Newman. Dr. Neumann is an expert in knowledge-based methods for the pharmaceutical industry, and has been in the biotechnology industries for the past 16 years.
    Topics of this talk will include: i) The Vision for the communities, ii) The group's Scope and Participants, iii) Current Activities and Demonstrations: Data Aggregation, Science Collaborations, and Knowledge Mining

  • Publishing ontologies on the Web
    Guus Schreiber, University of Amsterdam, The Netherlands
    Guus Schreiber is a professor of Intelligent Information Systems at the Free University Amsterdam. He acts as chair of the W3C Semantic Web Deployment Working Group and was former chair of W3C's Web Ontology Working Group. He is also Scientific Director of the IST Network of Excellence "Knowledge Web". His research projects focus on semantic annotation and search within large virtual collections, in particular in the cultural-heritage field. or more information see http://www.cs.vu.nl/~guus/.
    This talk will discuss ongoing activities within the W3C Semantic Web Deployment (SWD) Working. The group is currently working on a recommendation for SKOS, which will simplify the RDF/OWL representation of ontologies. SWD is also working on recipes for publishing ontologies on the Web and on "actual-practice" guidelines for ontology maintenance. Recent work on RDFa, which enables embedding of RDF in HTML will also be addressed.

  • Bio-ontologies: The cream in the Semantic Web layer cake
    Olivier Bodenreider, National Library of Medicine, USA
    Olivier Bodenreider is a Staff Scientist in the Cognitive Science Branch of the Lister Hill National Center for Biomedical Communications at the U.S. National Library of Medicine. His research interests include terminology, knowledge representation and ontology in the biomedical domain, both from a theoretical perspective and in their application to natural language understanding, reasoning, information visualization and integration.
    Dr. Bodenreider is a Fellow of the American College of Medical Informatics. He received a M.D. degree from the University of Strasbourg, France in 1990 and a Ph.D. in Medical Informatics from the University of Nancy, France in 1993. Before joining NLM in 1996, he was an assistant professor for Biostatistics and Medical Informatics at the University of Nancy, France, Medical School.
    In this lecture, Olivier Bodenreider will show that ontologies hold the Semantic Web together, and will present examples taken from biomedicine.

  • Sealife: A Semantic Grid Browser for the Life Sciences Applied to the Study of Infectious Diseases
    Michael Schroeder, Biotechnological Centre, Technische Universität Dresden, Germany,
    Albert Burgea, School of Mathematical and Computer Sciences, Heriot-Watt University, Scotland, UK, and
    Robert Stevens, School of Computer Sciences, Manchester University, UK,
    Michael Schroeder is a professor of bioinformatics at the Techical University Dresden, Germany. His group works on protein interactions extracted from literature and 3D protein structures. He developed an ontology-based literature search engine, GoPubMed, which is an example of a semantic web application. He also is coordinator of the bioinformatics group of the REWERSE project which develops rule-based approaches for the semantic web.
    Albert Burger is a Bioinformatics Research Scientist with the MRC Human Genetics Unit in Edinburgh and Senior Lecturer in Computer Science at Heriot-Watt University. He is a member of the Database Group and the Image Systems Engineering Laboratory (ISEL). His current research interests include: Bioinformatics, Ontologies, Knowledge Representation and Evolutionary Computing.
    Robert Stevens received an honours degree in biochemistry from Bristol; an M.Sc. in computational biology from York and a D.Phil. in computer science from York. He is currently a lecturer in bioinformatics within the BioHealth Informatics Group of the School of Computer Science at the University of Manchester. Principal research interests are in knowledge representation within biology and the use of Human Computer Interaction methods to improve the usability of bioinformatics tools. He is involved in projects such as Tambis, Gong, myGrid, which focus on the integration of distributed biomedical information using grid-technologies and ontologies.
    The idea behind the Sealife project is to build a browser, which uses ontologies and text-mining to link bioinformatics services to relevant entities on the fly.

Detailed Scientific Programme

Tuesday June 12, 2007
09.00 - 19.00 Registration and poster hang up
09.00 - 11.00 Tutorial T1
RDF standard and technologies
Heiko Stoermer, Dept of Information and Communication Technologies, University of Trento, Italy
11.00 - 11.15 Coffee break
11.15 - 12.45 Tutorial T2
Modelling Biological Knowledge in OWL
Georgina Moulton and Robert Stevens, University of Manchester, UK
12.45 - 14.00 Time for free lunch
14.00 - 15.30 Tutorial T3
BioPAX: OWL based biological pathway exchange format
Gary Bader, University of Toronto, Canada
15.30 - 15.45 Break
15.45 - 17.15 Tutorial T4
Reasoning on ontologies - How to use Protégé and RacerPro together
Maurizio Iacovella, Epistematica, Italy
17.15 - 17.30 Coffee break
17.30 - 19.00 Tutorial T5
The Unified Medical Language System (UMLS) and the Semantic Web
Olivier Bodenreider, National Library of Medicine, USA
Wednesday June 13, 2007
09.15 - 10.45 Opening Session

Marco Pasquali, Dean of Pisa University
Giorgio Levi, Director Departmentt of Computer Science, University of Pisa
Roberto Marangoni, Chair Local Organizing Committee, Computer Science Department, University of Pisa

Introduction to workshop's aims and structure
Paolo Romano, National Cancer Research Institute, Genoa, Italy,
Michael Schroeder, Biotec TU Dresden, Germany,
Oreste Signore, ISTI, National Research Council, Pisa, Italy,
Nicola Cannata, Computer Science Department, University of Camerino, Italy

Opening Lecture
  • Pathway Commons: A public library of biological pathways on the semantic web
    Gary Bader, University of Toronto, Canada
10.45 - 11.15 Coffee break
11.15 - 13.00 Focus Session 1: Goals of the Semantic Web in Bioinformatics

Oral communications
  • On the integration of biomedical knowledge bases: problems and solutions
    Marco Fato, Enrico Giunchiglia, Ivan Porro, Luca Vassalli
  • Intuitive and machine-understandable organization of the bioinformatics domain and related resources with Resourceomes
    Nicola Cannata, Flavio Corradini, Sergio Gabrielli, Luana Leoni, Emanuela Merelli, Francesca Piersigilli, Leonardo Vito
  • Exploiting text mining of biological annotations to extract protein interactions for the Semantic web
    Martin Krallinger, Carlos Rodriguez Penagos, Florian Leitner, Alfonso Valencia
Invited Lecture
  • The Semantic Web for Health Care and Life Science Interest Group and its Goals
    Eric Neumann, Teranode Co., USA, and Chair of the Health Care & Life Science Interest Group, W3C
13.00 - 14.30 Free time for lunch
14.30 - 16.00 General Theme Session 1: From Components to Processes in Bioinformatics

Oral communications
  • Bio-jETI: a Service Integration, Design, and Provisioning Platform for Orchestrated Bioinformatics Processes
    Christian Kubczak, Tiziana Margaria, Bernhard Steffen
  • Variations of GeneFisher as Processes in Bio-jETI
    Anna-Lena Lamprecht, Tiziana Margaria, Bernhard Steffen
  • Webservices and Workflows on the Bielefeld Bioinformatics Server: Practices and Problems
    Sven Hartmeier, Jan Krüger, Robert Giegerich
  • Requirements of a workflow system for systems biology
    Martin Haubrock, Tilman Sauer, Knut Schwarzer, Stephan Waack, Edgar Wingender, Torsten Crass
16.00 - 16.30 Coffee break
16.30 - 18.00 Adjunct Theme Session 1: Algorithms in Bioinformatics

Invited Lecture
  • Algorithmica and molecular biology: the Pisan experience
    Fabrizio Luccio, University of Pisa, Italy
Oral communications
  • A Grammatical Inference approach to Transmembrane domain prediction
    Piedachu Peris, Damiá López, Marcelino Campos
  • Reconstructing networks of pathways via significance analysis of their intersections
    Mirko Francesconi, Daniel Remondini, Nicola Neretti, John Sedivy, Ettore Verondini, Luciano Milanesi, Leon Cooper, Gastone Castellani
18.00 - 19.00 Flash posters session

Short presentations of up to 10 posters, 5' each
Thursday June 14, 2007
09.00 - 10.30 General Theme Session 2: Network Tools and Applications in Biology

Oral communications
  • Biohealth in EELA
    Vicente Hernández, Ignacio Blanquer, Raúl Isea, Juan Luis Chaves, Henry Ricardo Mora, Manuel Fernández, Fernando Blanco, Rafael Mayo, Gabriel Aparicio, Álvaro Hernández, Daniel López,
  • Scientific Grid Computing via Community-Controlled Autobuilding of Software Packages Across Architectures
    Steffen Möller, Daniel Bayer, David Vernazobres, Albrecht Gebhardt, Dirk Eddelbuettel
  • Network Alignment Tools for Novel Insight in Cellular Machinery
    Anup Bhatkar, Gautam Lihala, Yash Dave
10.30 - 10.50 Coffee break
10.50 - 13.00 Focus Session 2: Semantic Web Technologies and Tools

Invited Lecture
  • Publishing ontologies on the Web
    Guus Schreiber, University of Amsterdam, The Netherlands
Oral communications
  • An ontological modeling approach to neurovascular disease study: the NEUROWEB case
    Gianluca Colombo, Daniele Merico, Giuseppe Frisoni, Marco Antoniotti, Flavio De Paoli, Giancarlo Mauri
  • Ontology-Based Mediation in the Amine System Project
    Ismael Navas-Delgado, Raul Montanez, Aurelio A. Moya-Garcí, Jose Luis Urdiales, José F. Aldana-Montes, Francisca Sanchéz-Jiménez
Invited Lecture
  • Bio-ontologies: The cream in the Semantic Web layer cake
    Olivier Bodenreider, National Library of Medicine, USA
13.00 - 14.30 Free time for lunch
14.30 - 16.00 Adjunct Theme Session 2: Formal Methods for Systems Biology

Invited Lecture
  • Formal Methods in Systems Biology
    Pierpaolo Degano, University of Pisa, Italy
Oral communications
  • A Toolkit Supporting Formal Reasoning about Causality inMetabolic Networks
    Chiara Bodei, Andrea Bracciali, Davide Chiarugi
  • In silico stochastic simulation of Ca triggered synaptic release
    Andrea Bracciali, Marcello Brunelli, Enrico Cataldo, Pierpaolo Degano
  • Executable Symbolic Models of Neural Processes
    Sriram M Iyengar, Carolyn Talcott, Riccardo Mozzachiodi, Enrico Cataldo, Douglas A Baxter
16.00 - 16.30 Coffee break
16.30 - 18.30 Posters' session (including the following software demo)
  • Visualization of moving biomolecules: a new approach based on professional 3D animation software
    Yuri Porozov, Raluca Andrei, Monica Zoppè
(see the list of posters)
18.30 - 19.30 Social activity (to be defined)
20.30 - 22.30 Social Dinner
Friday June 15, 2007
09.00 - 10.30 Focus Session 3: Applications of Semantic Web in Bioinformatics

Invited Lecture
  • Sealife: A Semantic Grid Browser for the Life Sciences Applied to the Study of Infectious Diseases
    Michael Schroeder, Biotec TU Dresden, Germany,
    Albert Burger, Heriot-Watt University, Scotland, UK, and
    Robert Stevens, University of Manchester, UK
Oral communications
  • FungalWeb: A semantic web for exploring knowledge-based bioinformatics
    Greg Butler, CJO Baker
  • Document navigation: Ontology or Knowledge Organisation System?
    Simon Jupp, Robert Stevens, Sean Bechhofer, Patty Kostkova, Yeliz Yesilada
10.30 - 11.00 Coffee break
11.00 - 13.00 Closing Session

Panel discussion
  • Goals and perspectives of a Semantic Web for Bioinformatics
    All speakers and chairs, with contributions from the audience

Presentation of NETTAB 2008 Workshop
  • Bioinformatics Methods for Biomedical Complex System Applications
    Luciano Milanesi, ITB, National Research Council, Milan, Italy, and
    Paolo Romano, National Cancer Research Institute, Genoa, Italy

Closure of the workshop and Farewell

Abstracts of all submissions

Abstracts will be added to the site quite soon.


Presentations of invited lectures, oral communications, selected posters and tutorials are available in a separate file. Click here.

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