NETTAB 2007 Workshop: Presentations


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*

Presentations

Here, all presentations from authors that agreed to have them published in the NETTAB site will be made available. They are grouped by session, and sessions are listed cronologically.
All presentations are formatted as PDF files. You are kindly requested to make a personal use only, cite the source and the authors and do not redistribute, unless an explicit consensus from the authors is granted.
Not all presentations are currently linked, some of them will be added to the site later. Stay tuned!

Tutorials

RDF standard and technologies
Heiko Stoermer, University of Trento, Italy
Modelling Biological Knowledge in OWL (slides and demo movies)
Georgina Moulton and Robert Stevens, University of Manchester, United Kingdom
BioPAX: OWL based biological pathway exchange format
Gary Bader, University of Toronto, Canada
Reasoning on ontologies - How to use Protégé and RacerPro together
Maurizio Iacovella, Epistematica, Italy
The Unified Medical Language System (UMLS) and the Semantic Web
Olivier Bodenreider, National Library of Medicine, USA

Opening session

Introduction to workshop's aims and structure
Paolo Romano, National Cancer Research Institute, Genoa, Italy,
Pathway Commons: A public library of biological pathways on the semantic web (INVITED LECTURE!)
Gary Bader, University of Toronto, Canada

Focus Session 1: Goals of the Semantic Web in Bioinformatics

On the integration of biomedical knowledge bases: problems and solutions
Luca Vassalli, University of Genova, Italy
Intuitive and machine-understandable organization of the bioinformatics domain and related resources with Resourceomes
Nicola Cannata, University of Camerino, Italy
Exploiting text mining of biological annotations to extract protein interactions for the Semantic web
Martin Krallinger, CNIO, Spain
Semantic Web for Health Care and Life Science Interest Group: A Vision for Advancing Research Communities (INVITED LECTURE!)
Eric Neumann, Teranode Co., USA,

General Theme Session 1: From Components to Processes in Bioinformatics

Webservices and Workflows on the Bielefeld Bioinformatics Server: Practices and Problems (three versions available: PDF from PowerPoint, Keynote for Mac only, Quicktime movie)
Sven Hartmeier, University of Bielefeld, Germany
Bio-jETI: a Service Integration, Design, and Provisioning Platform for Orchestrated Bioinformatics Processes
Bernhard Steffen, University of Dortmund, Germany
Variations of GeneFisher as Processes in Bio-jETI
Anna-Lena Lamprecht, University of Göttingen, Germany
A Workflow for Retrieving Orthologous Promoters and Implications for Workflow Management Systems. A Case Study.
Martin Haubrock, University of Göttingen, Germany

Adjunct Theme Session 1: Algorithms in Bioinformatics

Algorithmica and molecular biology: the Pisan experience
Fabrizio Luccio, University of Pisa, Italy
A Grammatical Inference approach to Transmembrane domain prediction
Piedachu Peris, Polytechnic University of Valencia, Spain
Reconstructing networks of pathways via significance analysis of their intersections
Gastone Castellani, University of Bologna, Italy

General Theme Session 2: Network Tools and Applications in Biology

Biohealth in EELA
Stefano Troiani, CIEMAT, Spain
Scientific Grid Computing via Community-Controlled Autobuilding of Software Packages Across Architectures
Steffen Möller, University of Lubeck, Germany

Focus Session 2: Semantic Web Technologies and Tools

Publishing ontologies on the Web (INVITED LECTURE!)
Antoine Isaac, University of Amsterdam, The Netherlands
An ontological modeling approach to neurovascular disease study: the NEUROWEB case
Giuseppe Frisoni, University of Milan "Bicocca", Italy
Ontology-Based Mediation in the Amine System Project
Ismael Navas-Delgado, University of Malaga, Spain
Bio-ontologies: The cream in the Semantic Web layer cake (INVITED LECTURE!)
Olivier Bodenreider, National Library of Medicine, USA

Adjunct Theme Session 2: Formal Methods for Systems Biology

Formal Executable Descriptions of Biological Systems
Pierpaolo Degano, University of Pisa, Italy
A Toolkit Supporting Formal Reasoning about Causality inMetabolic Networks
Davide Chiarugi, University of Siena, Italy
In silico stochastic simulation of Ca triggered synaptic release
Andrea Bracciali, University of Pisa, Italy
Executable Symbolic Models of Neural Processes
Enrico Cataldo, University of Pisa, Italy

Flash posters session

Towards Using Explicit Semantics in Life Science Workflows
Ismael Navas-Delgado, University of Malaga, Spain
Ontology-guided Data Preparation for Discovering Genotype-Phenotype Relationships
Adrien Coulet, LORIA, France
Data-induced Domain Models for Information Extraction from Patients' Clinical Data
Agnieszka Mykowiecka, Polish Academy of Sciences, Poland
GraphBlast: multi-feature graphs database searching
Rosalba Giugno, University of Catania, Italy
A personalized integrated system for rice functional genomic
Pierre Larmande, CIRAD, France

Focus Session 3: Applications of Semantic Web in Bioinformatics

Sealife: A Semantic Grid Browser for the Life Sciences Applied to the Study of Infectious Diseases (INVITED LECTURE!)
Michael Schroeder, Biotec TU Dresden, Germany,
Albert Burger, Heriot-Watt University, Scotland, United Kingdom, and
Robert Stevens, University of Manchester, United Kingdom
Document navigation: Ontology or Knowledge Organisation System?
Simon Jupp, University of Manchester, United Kingdom
FungalWeb: A semantic web for exploring knowledge-based bioinformatics
Greg Butler, Concordia University, Canada