Workshop on Database Issues in Biological Databases DBiBD

Workshop on Database Issues in Biological Databases (DBiBD)

January 8-9, 2005
National e-Science Centre, Edinburgh, Scotland, UK
in conjunction with ICDT

Jointly organized by the European Bioinformatics Institute and the Edinburgh Database Group.


Scope & Objectives | Program | Where & When| Committee

Program

Slides can be found at: www.nesc.ac.uk/action/esi/contribution.cfm?Title=459
Saturday the 8th
9.00 Opens
9.30 Exploring and Exploiting the Biological Maze, Zoe Lacroix
10.00 Towards a Taxonomically Intelligent Phylogentic Database, Rod Page
10.30 MMD-A Mathematically Modelling Database for Cell Signalling Pathways, V. Mahesh,
M. Breit, G. Enzenberg, R. Modre-Osprian and B. Tilg.
11.00 Coffee
11.30 Creating a Medicinal Plant Database, Carsten Kettner, Harold Kosch, Margit Lang,
Janine Lachner, Doris Oborny and Erich Teppan.
12.00 Taxonomy Database as an Enabling Techology for the Tree of Life, Nadia Anwar.
12.30 Lunch
2.00 Using the Functional Data Model to Store and Query Recursive Biological Data,
Graham Kemp, Selpi and Merja Karjalainen.
2.30 The Ensembl Database - A relational database for genome information, Stabenau, A., Andrews, T.D., Bevan, P., Caccamo, M., Chen, Y., Clarke L., Coates, G., Curwen, V., Cutts, T., Down, T., Fernandez-Suarez, X.M., Gane, P., Gilbert, J., Hammond, M., Hotz, H., Iyer, V., Jekosch, K., Kahari, A., Kasprzyk, A., Keefe, D., Lehvaslaiho, H., McVicker, G., Melsopp, C., Meidl, P., Pettet, R., Potter, S., Proctor, G., Rae, M., Rios, D., Searle, S., Slater, G., Smedley, D., Smith, J., Spooner, W., Stalker, J., Storey, R., Ureta-Vidal, A., Woodwark, K.C., Cameron, G., Durbin, R., Cox, A., Hubbard, T.
3.00 Integration of functional genomics data using sets of biological entities, Roland
Barriot, Jerome Poix, Claire Gaugain, Isabelle Dutour and Antoine de Daruvar.
3.30 Coffee
4.00 NCRI Cancer Informatics Initiative: maximising the impact of cancer research using informatics , Peter Kerr, Fiona Reddington, Helen Parkinson, Max Wilkinson, Richard Begent
4.30 BioMart Query Network, Arek Kasprzyk, Andreas Kahari, Darin London, Craig Melsopp, Damian Smedley, Will Spooner, Arne Stabenau, Katerina Tzouvara.
 
Sunday the 9th
9.00 Wormbase, Anthony Rogers and Daniel Lawson.
9.30 Database Issues in Nutritional Genomics, Peter M.D. Gray and Anthony J. Travis.
10.00 Enhancing the Semantics of Links and Paths in Life Science Sources , S. Heymann, F. Naumann, P. Rieger and L. Raschid.
10.30 Coffee
11.00 Well Constructed Workflows in Bioinformatics, Anna Gambin, Jan Hidders, Natalia Kwasnikowska, Slawomir Lasota, Jacek Sroka, Jerzy Tyskiewicz and Jan Van den Bussche.
11.30 A Classification of Biological Data Artifacts, Judice L.Y. Koh, Mong Li Lee, Vladimir
Brusic.
12.00 The ArrayExpress Gene Expression Database: a Software Engineering and Implementation Perspective, Ugis Sarkans, Helen Parkinson, Gonzalo Garcia Lara, Ahmet Oezcimen, Anjan Sharma, Niran Abeygunawardena, Sergio Contrino, Ele Holloway, Philippe Rocca-Serra, Gaurab Mukherjee, Mohammadreza Shojatalab, Misha Kapushesky, Susanna Sansone, Anna Farne, Tim Rayner, and Alvis Brazma.
12.30 Lunch
2.00 Using DataBase ontologies and Related Concepts in SRS 8.1 to find biological data, Jaquie Finn.
2.30 Statistical Data Fusion to prioritize lists of genes, Bert Coessens, Stein Aerts, Bart de Moor.
3.00 Integration of the Biological Databases into Grid-Portal Environments, Michal Kosiedowski, Michal Malecki, Cezary Mazurek, Pawel Spychala and Marcin Wolski.
3.30 Coffee
4.00 MitoNuc and MitoDrome: two databases of nuclear genes encoding for
mitochondrial proteins, F. Licciulli, D. Catalano, A. Turi, G. Grillo, G. Tripoli, D. Porcelli, C. Caggese, C. Saccone and D. D'Elia.
4.30 Proteomics Databases for comparative studies: Transactional and Data Warehouse approaches to solve the needle in a haystack problem, Patricia Rodriguez-Tome, Nicolas Pinaud and Thomas Kowall.

Scope & Objective

It is now more than ten years since the database research community started to look seriously at the problems of biological databases. To what extent has this research paid off, and to what extent is the research "on track"? Also, during those ten years, biologists have started to make extensive use of database technology. What are their experiences, and what new issues have emerged?

The purpose of this meeting is to bring together biologists who are consumers of database technology and database researchers who are interested in the challenges posed by the proliferation of biological databases. The meeting will be an informal workshop whose purpose is to produce a report on the existing and new challenges of biological data.

Where & When

The DBIBD workshop will be held in conjunction with ICDT at January 8-9, 2005 in the National e-Science Centre, which is located in the centre of Edinburgh.

Committee

Organizers Committee
  • Amr El Abbadi, University of California, Santa Barbara, USA
  • Richard Baldock, National e-Science Centre, Edinburgh, UK
  • Susan Davidson, University of Pennsylvania, USA
  • Richard Durbin, The Wellcome Trust Sanger Institute, Cambridge, UK
  • Christoph Freytag, Humboldt-Universität zu Berlin, Germany
  • Stanley Letovsky, Harvard University, USA
  • Victor Markowitz, Lawrence Berkeley National Laboratory, Berkeley, USA
  • Rod Page, University of Glasgow, UK
  • Jignesh Patel, University of Michigan, USA
  • David Searls, GlaxoSmithKline Pharmaceuticals
  • Lincoln Stein, Cold Spring Harbor Laboratory, NY, USA
  • Limsoon Wong, Institute for Infocomm Research, Singapore