GeneDB: a generic database for genome resources
By Arnaud Kerhornou
scientific programmer, The Wellcome Trust Sanger Institute
GeneDB (http://www.genedb.org) is a generic database currently being developed by the Pathogen Sequencing Unit (PSU) at Sanger Institute. The goal of this project is to provide a user-driven database, developed and maintained from the research community’s point of view, with data manually annotated and curated by biologists. It also aims to integrate genomic data with experimental results related to genome mapping, gene expression, protein function, protein-protein interactions, antigenic diversity and metabolic pathways.
GeneDB currently houses annotated and curated sequencing data of six organisms, including the fission yeast, Schizosaccharomyces pombe, and the kinetoplastid protozoa Leishmania major and Trypanosoma brucei. The database structure is generic enough to in future integrate datasets for other prokaryotic and eukaryotic organisms being sequenced by both the PSU and other sequencing centres.
To date, a prototype database has been developed, generated from flat files, allowing the user to access DNA and protein sequences, literature searches, similarity information, graphics representation, and summarizing up-to-date domain, motif searches. We are now in the process of integrating the GeneDB prototype with GUS, a relational database system being developed by the Computational Biology and Informatics Laboratory at the University of Pennsylvania (http://www.gusdb.org).