WORMBASE: A CORE DATA RESOURCE FOR C.ELEGANS BIOLOGY

California Institute Of Technology, Pasadena CA

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Abstract

Caenorhabditis elegans is a major model system for basic biological and biomedical research and the first animal for which there is a complete description of its genome, anatomy and development. Three years of funding is requested to extend an existing database, ACeDB, into WormBase, a Model Organism Database (MOD), with complete coverage of core genomic, genetic, anatomical and functional information about this nematode. Such a database is necessary to allow the entire biomedical research community as well as C. elegans researchers to make full use of the 97,000,000 basepair genomic sequence, with its 19,000 genes, and the results of intensive molecular genetic analysis of C. elegans. The two top priorities will thus be data curation and user interface. WormBase will include up-to-date annotation of the genomic sequence, the current genetic and physical maps and many experimental data connected to the function and interactions of cells and genes, as well as development and organismal behavior. Direct access to the sources of biological material, such as the strain collection of the Caenorhabditis Genetics Center and direct links to data sets maintained by others will be provided. Data will be recovered from the existing resources, from direct contribution of the individual laboratories, and from the literature. While WormBase will act as a central forum through which every laboratory will be able to contribute constructively to the global effort to fully comprehend this metazoan organism, WormBase professional curators will ensure detailed attribution of data sources and check consistency and integrity. To facilitate communication WormBase will use wherever possible terminology and style concordant with other model organism databases. WormBase will be Web-based and easy to use. The underlying database manager will remain the object-based Acedb database system, which can also be used locally on any platform. Minor enhancements to Acedb will meet the changing priorities of the data sets. Coordination of the project and the main curation site will be at Caltech under the supervision of a C. elegans biologist. Curation and annotation of genomic sequence will take place at the two sequencing centers, the Sanger Centre and Washington University, that generated the entire genome sequence. The Montpellier team will develop interfaces to new large-scale projects such as systematic inactivation of genes, systematic analysis of gene expression, and the large scale cDNA project of Kohara. Development of new user interfaces will take place at Cold Spring Harbor, currently providing Web-based access to ACeDB.