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messages to Data Integration in Life Sciences conf

From: Eric Prud'hommeaux <eric@w3.org>
Date: Thu, 12 Jun 2008 01:15:35 -0400
To: public-semweb-lifesci@w3.org
Message-ID: <20080612051535.GQ5591@w3.org>
Ther's a conf call DILS (program link below:)
  http://dils2008.lri.fr/index.php?option=com_content&task=view&id=16
Of our lot, Michel and Holger might be going (Holger is trying, I
haven't asked Michel). What messages do we have to deliver to
A. the individual sessions
B. the folks who will likely attend
?

Here are my notes from scanning the agenda (and regretting that I
won't be there):

          BioWarehouse: Relational Integration of Eleven
          Bioinformatics Databases and Formats
    
          Session 1: Annotation in scientific data
          integration
    
            • Integrating Protein-Protein Interactions and
              text Mining for protein Function Prediction,
              Samira Jaeger, Sylvain Gaudan, Ulf Leser,
    03:15     Dietrich Rebholz-Schuhmann
    -
    04:15   • Integrating Biological Data – The Distributed
    pm        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,
    04:15     Gabrielle A Reeves and Andreas Prlic

This sounds to me like labeling a text string in HTML, Word, ... with
something that allows them to unify based on that term. Relevent to
Sudeshna's Scientific Collaboration Framework.

    -     Coffee
    04:45  Flash Session
    
            • 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

Perhaps like Therese Vachon (Novartis)'s UltraLink?
    
            • Semantic Mashups with BioXMash, Patrick
              Ziegler, and Ela Hunt

            • Mixed queries for a functional genomics
    04:45     warehouse, Frederic Lemoine, Bernard Labedan,
    -         and Christine Froidevaux

How are the mixing their queries? Some meta-query lang that we can
play with/map to?

    05:15   • 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

Would be fun to get ahold of this data and RDF-ize it.

            • 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

Sounds like they're factoring out info we want for COI.

            • Semi-automatic composition of bioinformatics
              Web services based on task and domain
              ontologies, Nicolas Lebreton, Olivier Dameron,
    06:00     Christophe Blanchet, and Julie Chabalier

How does this compare to Northampton or CWI's semweb service
integration? Would like to show them SPDL.

     Thursday, June 26 (Evry)
          Ontologies and data integration in biomedicine:
          Success stories and challenging issues
    
    10:30 Session 2: Semantic Web for the life sciences
    
            • Analyzing the Evolution of Life Science
              Ontologies and Mappings
              Michael Hartung, Toralf Kirsten, and Erhard
              Rahm

Could support us if their onto-mapping needs line up with SemWeb
strengths (distributed ont development, monotonic interpretation)

    10:30   • Ontology Design Principles and Normalization
    am -      Techniques in the Web
    12:00     Xiaoshu Wang, Jonas S. Almeida, and Arlindo L.
    pm        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,
    12:00     and Padmini Srinivasan

May provide techniques relevent to COI mapping use case (CTO queries
over CPO data)

    -     Lunch
    02:00 Session 3: Designing and evaluating architectures
          to integrate biological data
    
            • Automatic Methods for Integrating Biomedical
              Data Sources in a Mediator-Based System
              Fleur Mougin, Anita Burgun, Olivier
              Bodenreider, Julie Chabalier, Olivier Loréal
    02:00     and Pierre Le Beux
    -
    03:30   • VisGenome and Ensembl: Usability of Integrated
    pm        Genome Maps
              Joanna Jakubowska, Ela Hunt, John McClure,
              Matthew Chalmers, Martin McBride and Anna F.
              Dominiczak
            • An Entity Resolution Framework for
              Deduplicating Proteins
    03:30     Lucas Lochovsky and Thodoros Topaloglou
    -     Coffee - Poster session 2 (to be announced soon)
    04:30 Session 4: New architectures and experience on
          using systems
    
            • 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

ooo, we need ears at this one!

    04:30   • 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

what works for CORBA works for web services.

            • 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
     05:50    Kahlem

Need to talk to them about SPASQL and semantic query federation.
What's happening in ENFIN now?

     Friday, June 27
          Session 5: New features of major resources for
          biomolecular data
    
    09:30   • UniProtKB/Swiss-Prot: new and future
    -         developments
    10:30     Amos Bairoch
    am
            • EBI Proteomics Services
              Henning Hermjakob
    11:00 Data Integration in the Life Sciences: Fun,
    12:00 Findings and Frustrations
    
    02:00 Session 6: Systems using technologies from the
          Semantic Web for the life sciences
    
            • 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

already RDF-y -- and I think Mark has a SPARQL endpoint.

            • 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
    03:20     Dumontier

Michel, can you give us a hint about this presentation?

          Session 7: Mining integrated biological data
    
            • Combining One-Class Classification Models Based
    03:50     on Diverse Biological Data for Prediction of
    -         Protein-Protein Interactions
    04:50     José A. Reyes and David Gilbert
    pm
            • Semi supervised Spectral Clustering for
              regulatory module discovery
              Alok Mishra and Duncan Gillies
-- 
-eric

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Received on Thursday, 12 June 2008 05:16:14 GMT

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