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.
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.
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.
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 |