Bio-ontologies tutorial

Olivier Dameron and Julie Chabalier

12:00 -
02:00 pm

Keynote session
Chair: Amos Bairoch

Keynote: Peter Karp

BioWarehouse: Relational Integration of Eleven Bioinformatics Databases and Formats 

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

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’)

Keynote session

Chair: Louiqa Raschid

Keynote: Olivier Bodenreider 

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

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

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

• Ontology Design Principles and Normalization Techniques in the Web
  Xiaoshu Wang, Jonas S. Almeida, 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

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

• Semantic Representation and Querying of caBIG Data Services
  E. Patrick Shironoshita, Ray M. Bradley, Reginald Jean-Mary, Thomas J. Taylor, Michael 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 Laudet and Marc Robinson-Rechavi

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

Banquet in Paris on board the Capitaine Fracasse

6:30 pm : Bus to Paris

09:15 pm : Boarding

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

Keynote session
Chair: Ulf Leser

Keynote: Norman Paton

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

Lunch

13h30 - 14h00 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, Benjamin Good and Jean Morissette

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

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

Session 7: Mining integrated biological data

Chair: Anne Poupon 

• Combining One-Class Classification Models Based on Diverse Biological Data for Prediction of Protein-Protein Interactions
  José A. Reyes and David Gilbert

• Semi supervised Spectral Clustering for regulatory module discovery
  Alok Mishra and Duncan Gillies

Closing session