Sequence Databases and Ontologies Workshop

Organized by IMPG and PBIL

September 26, 2003

Institut Pasteur
Amphithéâtre Jacques Monod
Paris, France


As the number of biological sequences and their associated data is exponentially growing, the need to structure and organize huge amounts of information is stronger than ever. Even if hundreds of databases are already available, many problems remain open: how to represent, structure and integrate heterogeneous data such as sequences, alignments, gene families, 3D structures or expression tags? What kind of curation systems is it possible to develop to ensure the maintenance and the reliability of the information stored? How to provide efficient ways to query and retrieve relevant data subsets?

In the framework of the European Conference on Computational Biology (2003) we organize a mini-satellite event on sequence databases and ontologies. From the submissions we received, ten have been selected for 20 minutes talks, the others being selected as posters that will be presented in the ECCB poster sessions. All the abstracts we received will appear in the workshop proceedings which will be printed locally and distributed to the registered participants.


REGISTRATION

If you wish to attend to this workshop, you only need to send an e-mail to perriere@biomserv.univ-lyon1.fr. No registration fees are required but the number of attendants will be limited to 100 due to space restrictions.

Important: registration is now closed, as we reached the maximum number of seats available in the Jacques Monod lecture hall.


ACCESS

The workshop will be held in Jacques Monod lecture hall at Institut Pasteur, 25 rue du Docteur Roux, 75724 Paris. This lecture hall is located in the Jacques Monod building (see the map of the campus). Information on how to get to the Institut Pasteur is available here.


PROGRAM

Here is the final program for this event. Note that some last minute changes can still happen, so check regularly te schedule on this web page.


9h00-9h30 Registration
9h30-9h40 Welcoming speech
9h40-10h30 Invited talk: Protein domain databases and the use of
large scale analysis of protein modularity - D. Kahn
10h30-10h50 Standardization of format and content in the SWISS-PROT
protein knowledgebase - A. Gattiker, E. Gasteiger,
A. Bairoch
10h50-11h10 Coffee break
11h10-11h30 Databases of homologous gene families: New developments
and Web interfaces - S. Penel, J. Grassot, L. Duret, M.
Gouy, G. Perrière
11h30-11h50 HOPPSIGEN: A database dedicated to comparative analysis
of homologous processed pseudogenes - A. Khelifi, L. Duret,
D. Mouchiroud
11h50-12h10 Databases on eukaryotic gene regulation: TRANSFAC®,
TRANSCompel®, and TRANSPATH®. Annotation, information
processing, and application for analysis of gene expression
data - O. Kel-Margoulis, V. Matys, C. Choi, I. Reuter, E.
Goessling, N. Voss, M. Krull, S. Pistor., S. Thiele, E. Fricke,
S. Land, A. Potapov, D. Tchekmenev, B. Lewicki-Potapov,
A. Kel, E. Wingender
12h10-12h30 A Human-machine platform for 3D visualization and
management of genomic databases - P.E. Gros, J. Hérisson,
R. Gherbi
12h30-14h00 Lunch break
14h00-14h50 Invited talk: Ensembl: An information infrastructure for
genomes - E. Birney
14h50-15h10 Mouse phenotype ontology development and application -
E.C.J. Green, G.V. Gkoutos, A.M. Mallon, S. Greenaway,
A. Blake, M. Simon, J.M. Hancock, D. Davidson
15h10-15h30 GeMCore: A mammalian comparative mapping database -
V. Navratil, G. Bronner, B. Spataro, T. Faraut, D.
Mouchiroud, C. Gautier
15h30-15h50 Coffee break
15h50-16h10 ISYMOD: A knowledge base for integrated system modeling -
J. Chabalier, Y. Quentin, C. Capponi, G. Fichant
16h10-16h30 IMGT-ONTOLOGY and IMGT-ML for immunogenetics and
immunoinformatics - D. Chaume, V. Giudicelli, K. Combres,
M.P. Lefranc
16h30-16h50 MADCAP: MicroArray data characterization and profiling.
A tool for profiling lists of genes with different expression
patterns - J. Lozach, R. Sasik, S. Ogawa, C.K. Glass
16h50-17h00 Closing remarks