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Program Print

Keynote speakers

 

Schedule

(vcal , ical formats) 

The list of accepted papers is available here

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TimeActivity  
 Wednesday, June 25 (Evry)
09:00 am - 12:00 pm

Bio-ontologies tutorial

Olivier Dameron and Julie Chabalier

 

 

12:00 -
02:00 pm

Lunch 
02:00 -
02:15 pm 
Welcome  PC Chairs
 
02:15 -
03:15 pm

Keynote session
Chair: Amos Bairoch

Keynote: Peter Karp

BioWarehouse: Relational Integration of Eleven Bioinformatics Databases and Formats 

 
03:15 -
04:15 pm

Session 1: Annotation in scientific data integration
Chair:
Amos Bairoch 

  • Integrating Protein-Protein Interactions and text Mining for protein Function Prediction, Samira Jaeger, Sylvain Gaudan, Ulf Leser, Dietrich Rebholz-Schuhmann

  • Integrating Biological Data – The Distributed Annotation System, Andrew M Jenkinson, Mario Albrecht, Ewan Birney, Hagen Blankenburg, Thomas Down, Robert D Finn, Henning Hermjakob, Tim JP Hubbard, Rafael C Jimenez, Philip Jones, Andreas Kahari, Eugene Kulesha, José R Macias, Gabrielle A Reeves and Andreas Prlic

 
04:15 -
04:45 pm
Coffee 
04:45 -
05:15 pm

Flash Session
Chair:
Christine Froidevaux  

  • Analysing Experimental Data in the context of Integrated Biological Networks, Jan Taubert, Jochen Weile, Matthew Hindle, Artem Lysenko, Keywan Hassani-Pak,Catherine Canevet, and Chris Rawlings 

  • Terminizier: An interactive web-based tool for automated detection of ontological terms in unstructured, free-text annotation, David Hancock, Norman Morrison, Giles Velarde, Douglas Kell, and Dawn Field

  • Semantic Mashups with BioXMash, Patrick Ziegler, and Ela Hunt

  • Mixed queries for a functional genomics warehouse, Frederic Lemoine, Bernard Labedan,  and Christine Froidevaux

  • Mapping the NRC dataflow model to the Open Provenance Model, Natalia Kwasnikowska, and Jan Van den Bussche

  • UniMed: Mapping of UniProt entries to disease terminologies, Anais Mottaz, Yum L Yip, Julien Gobeill, Patrick Ruch, and Anne-Lise Veuthey

  • Using a metadata approach to manage similarities and differences between clinical datasets, Irene Papatheodorou, Charles Crichton Lorna Morris, Peter Maccallum, James Brenton and Carlos Caldas

  • Semi-automatic composition of bioinformatics Web services based on task and domain ontologies, Nicolas Lebreton, Olivier Dameron, Christophe Blanchet, and Julie Chabalier
 

06:00 -
08:30 pm

Poster-Demo session 1, Cocktail-Dinner (Hotel All Seasons’)

 
 
 Thursday, June 26 (Evry)
09:00 am - 10:00 pm

Keynote session

Chair: Louiqa Raschid

Keynote: Olivier Bodenreider 

Ontologies and data integration in biomedicine: Success stories and challenging issues

 
10:00 -
10:30 am 
Coffee
 
10:30 am -
12:00 pm

Session 2: Semantic Web for the life sciences
Chair: Olivier Dameron  

  • Analyzing the Evolution of Life Science Ontologies and Mappings
    Michael Hartung, Tor
    alf Kirsten, and Erhard Rahm

  • Ontology Design Principles and Normalization Techniques in the Web
    Xiaoshu Wang, Jonas S. Almeid
    a, and Arlindo L. Oliveira

  • Exploiting Ontology Structure and Patterns of Annotation to Mine Significant Associations between Pairs of Controlled Vocabulary Terms
    Woei-Jyh Lee, Louiqa Raschid, Hassan Sayyadi, and Padmini Srinivasan

 
12:00 -
02:00 pm
Lunch 
02:00 -
03:30 pm

Session 3: Designing and evaluating architectures to integrate biological data
Chair: Bertram Ludaesher 

  • Automatic Methods for Integrating Biomedical Data Sources in a Mediator-Based System
    Fleur Mougin, Anita Burgun, Olivier Bodenreider, Julie Chabalier, Olivier Loréal and Pierre
    Le Beux

  • VisGenome and Ensembl: Usability of Integrated Genome Maps
    Joanna Jakubowska, Ela Hunt, John McClure, Matthew Chalmers, Martin McBride and Anna F. Dominiczak
  • An Entity Resolution Framework for Deduplicating Proteins
    Lucas Lochovsky and Thodoros Topaloglou
 
03:30 -
04:30 pm
Coffee - Poster session 2  
04:30 -
05:50 pm
Session 4: New architectures and experience on using systems 
Chair: Ela Hunt
  • Semantic Representation and Querying of caBIG Data Services
    E. Patrick Shironoshita, Ray M. Bradley, Reginald Jean-Mary, Thomas J. Taylor, Mich
    ael Ryan, and Mansur R. Kabuka

  • SisGen: A CORBA--based data management program for DNA sequencing projects
    Georgios J. Pappas Jr., Robson P. Miranda, Natalia F. Martins, Roberto C
    . Togawa and Marcos M.C. Costa

  • Bgee: Integrating and Comparing Heterogeneous Transcriptome Data Among Species
    Frederic Bastian, Gilles Parmentier, Julien Roux, Sebastien Moretti, Vincent La
    udet and Marc Robinson-Rechavi

  • ENFIN - an integrative structure for Systems Biology
    Florian Reisinger, Manuel Corpas, John Hancock, Henning Hermjakob, Ewan Birney and Pascal Kahlem

 
06:30 pm -
12:00 am

Banquet in Paris on board the Capitaine Fracasse

6:30 pm : Bus to Paris

09:15 pm : Boarding

 
 Friday, June 27
09:30 -
10:30 am

Session 5: New features of major resources for biomolecular data
Chair: Marie-Paule Lefranc

  • UniProtKB/Swiss-Prot: new and future developments
    Amos Bairoch

  • EBI Proteomics Services
    Henning Hermjakob

 
10:30 -
11:00 am
Coffee
 
11:00 am -
12:00 pm

Keynote session
Chair: Ulf Leser

Keynote: Norman Paton

Data Integration in the Life Sciences: Fun, Findings and Frustrations

 
12:00 -
13:30 pm

Lunch

 

13h30 - 14h00 pm

 Best Paper Award
 
02:00 -
03:20 pm

Session 6: Systems using technologies from the Semantic Web for the life sciences
Chair: Thodoros Topaloglou  

  • A System for Ontology-Based Annotation of Biomedical Data
    Clement Jonquet,
    Mark A. Musen, and Nigam Shah

  • Bio2RDF: A Semantic Web Atlas of post genomic knowledge about Human and Mouse
    Francois Belleau, Nicole Tourigny, Benja
    min Good and Jean Morissette

  • OMIE: Ontology Mapping within an Interactive and Extensible environment
    Amel Bouzeghoub, Abde
    ltif Elbyed, and Fariza Tahi

  • Chemical Knowledge for the Semantic Web
    Mykola Konyk, Alexander De Leon, and Michel Dumontier

 
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Session 6: Systng for irated Genoogical data
Chair: Loui-Lis Poupem>

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04:15 -

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