- 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
office: +1.617.258.5741 32-G528, MIT, Cambridge, MA 02144 USA
mobile: +1.617.599.3509
(eric@w3.org)
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Received on Thursday, 12 June 2008 05:16:14 UTC