The FlyBase Database of the Drosophila Genome Projects and community literature

Abstract

The FlyBase Drosophila genetics database and the public interfaces of the Berkeley Drosophila Genome Project (BDGP) and European Drosophila Genome Project (EDGP) are in the process of integrating.At present, the data of these projects are available from independent, but hyperlinked, WWW sites (FlyBase URL, http://flybase.bio.indiana.edu/; BDGP URL, http://fruitfly.berkeley.edu/; EDGP URL, http://edgp.ebi.ac.uk/ ).Because of the considerable overlap of data classes between the contributions of the Drosophila genome projects and the Drosophila community, the new and enlarged FlyBase consortium views the implementation of a single integrated Drosophila genomics/genetics server as essential to the scientific community.This integration will occur in a stepwise fashion over the next 1-2 years.In this report, the salient features of the current databases and how to interrogate and navigate the extensive data sets are discussed. BACKGROUNDThe fruit fly, Drosophila melanogaster, is one of the most studied eukaryotic organisms and a central model for the human genome project.Introduced as an experimental organism in the early years of this century, the genetic prowess of D.melanogaster has placed this fly at the forefront of many areas of research, notably gene regulation, chromosome behavior, developmental biology, cell biology, neurobiology, population biology, ecology and evolution.Beginning in 1992, data on the genetics and genomics of D.melanogaster and related species have been electronically available over the Internet through the funded FlyBase, BDGP and EDGP informatics groups.These groups recognize that many (perhaps all) genome project and community data types overlap considerably, and that it would be of great value to present the scientific community with an integrated view of these data.Beginning in 1998, the BDGP, EDGP and FlyBase have begun the process of merging their data distribution efforts into a single project.In the short term, however, the data will be accessible only through independent servers, and so it is the purpose of this report to describe current aspects of the FlyBase, BDGP and EDGP public databases.However, it should be realized that the merger is in progress, and the specific aspects of database access will be in flux for the next several months.Some new merged efforts are also discussed. SCOPE The classes of dataThe taxonomic scope of FlyBase is the family Drosophilidae.However, the vast majority of data concerns the one species D.melanogaster. FlyBase curation of community literatureFlyBase represents abstracted and value-added curated genetic and genomic data from the Drosophila 'literature', i.e., from the published scientific literature, accessions from nucleic acids, protein and other databases, written personal communications, and bulk submissions.All information in FlyBase is attributed, meaning that it is attached to a specific bibliographic citation.The current view of the D.melanogaster genome and the functions of individual genes is necessarily incomplete.Given this incompleteness, and the heterogeneity of the literature, it is an important function of FlyBase to attempt to integrate the literature, particularly by the use of structured terminology (controlled vocabularies and nomenclature).The genetic data sets.FlyBase organizes genetic data in terms of chromosomal locations in the genome, and in terms of the products that the genes encode.Gene descriptions therefore include recombinational, cytogenetic, physical and sequence level information on map locations, functional, expression pattern and structural information on gene products, and biological roles