WormBase (www.wormbase.org) arose as a web-accessible interface to ACeDB, collecting and presenting data from over 30 years of C. elegans research. As the first large eukaryotic genome sequenced, C. elegans has also become a model system for genome annotation and functional genomics. Thus, in addition to being a central repository of sequence and clone information, WormBase aims to bring the biology to bear on the sequence by developing a highly cross referenced web-accessible database linking mutant phenotypes, to sequences, to predicted proteins, to anatomy.

Five new additions greatly extend the usefulness of WormBase for functional genomics studies: the integration of large-scale genome wide experiments, batch annotation of the existing data, online availability of anatomical information, sequence alignments with C. briggsae, and streamlined access to underlying data.

First, genome-wide studies have been integrated into the extensive functional information already available from WormBase. These studies include systematic RNAi screens to assay the disruption of gene function (1,2), expression profiles under a variety of growth conditions, genetic backgrounds, and life stages (3), and high-density SNPs as a mapping resource (4). Second, ongoing literature curation and sequence annotation continues to expand the extent of functional information in the database. This curation includes the assignment of Gene Ontology terms, precomputed BLASTP homologies, and prominent protein motifs. Third, WormBase contains detailed information on worm anatomy, including a browsable pedigree of the worm lineage, a prototype guide to worm ultrastructure, and searchable pages of the worm nervous system. Fourth, alignments of the nearly complete genomic sequence of the closely related species C. briggsae have been added recently. The alignments promise to increase the accuracy of gene predictions and to be a valuable tool for identifying conserved sequences.

Finally, WormBase offers multiple ways to access the underlying data. These include a web interface that accepts queries in the internal database query language AQL, and new web-based tools that provide customizable database dumps. In addition, WormBase continues to offer scriptable access to the data via the object-oriented AcePerl (stein.cshl.org/AcePerl) module for more extensive queries.