Program of the 2004 East Coast Worm Meeting - Caenorhabditis ...

31. WormBase: What’s New and What’s Next?
Nansheng Chen 1 , Lincoln D. Stein 1 , WormBase Consortium 2
1 Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, NY 11724
2 Californica Institute of Technology, Wellcome Trust Sanger Center, Washingtown University at
St. Louis, Cold Spring Harbor Laboratory
As a data and software resource for nematode biology and genomics, WormBase
(http://www.wormbase.org) continues to grow and improve. In this presentation, I will highlight the
growth and improvement in the past year from three major aspects: the database, user interface,
and bioinformatics support. The growth of the database was highlighted by the incorporation,
expansion and integration of new large-scale datasets including microarray, SAGE, interactome,
3D protein structure, ORFeome and RNAi data. Significant changes also included our continued
effort in curation of sequence data, literature, gene expression and antibodies, gene ontology,
phenotype ontology, and anatomy ontology. On the user interface side, much effort was made to
make various web pages uniform, informative and stable. Textpresso, a literature search tool, is a
new and useful feature added last year. New bioinformatics support includes batch downloads
(’Batch Genes’ and ’Batch Sequences’ pages), remote access to WormBase databases (ACeDB
database and Bio::DB::GFF MySQL databases), and periodic genome freezes. Looking ahead,
WormBase will continue to grow and improve in all these aspects. WormBase data models and
software architecture are being reorganized and optimized to accommodate the genomics and
biology data from more nematode species, including the three Caenorhabditis species whose
genomes are currently sequenced.