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Nucleic Acids Research 2006 34(Database Issue):D475-D478; doi:10.1093/nar/gkj061
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Nucleic Acids Research, 2006, Vol. 34, Database issue D475-D478
© The Author 2006. Published by Oxford University Press. All rights reserved
The online version of this article has been published under an open access model. Users are entitled to use, reproduce, disseminate, or display the open access version of this article for non-commercial purposes provided that: the original authorship is properly and fully attributed; the Journal and Oxford University Press are attributed as the original place of publication with the correct citation details given; if an article is subsequently reproduced or disseminated not in its entirety but only in part or as a derivative work this must be clearly indicated. For commercial re-use, please contact journals.permissions{at}oxfordjournals.org

Article

WormBase: better software, richer content

Erich M. Schwarz1,*, Igor Antoshechkin1, Carol Bastiani1, Tamberlyn Bieri3, Darin Blasiar3, Payan Canaran4, Juancarlos Chan1, Nansheng Chen4, Wen J. Chen1, Paul Davis5, Tristan J. Fiedler4, Lisa Girard1, Todd W. Harris4, Eimear E. Kenny1, Ranjana Kishore1, Dan Lawson5, Raymond Lee1, Hans-Michael Müller1, Cecilia Nakamura1, Phil Ozersky3, Andrei Petcherski1, Anthony Rogers5, Will Spooner4, Mary Ann Tuli5, Kimberly Van Auken1, Daniel Wang1, Richard Durbin5, John Spieth3, Lincoln D. Stein4 and Paul W. Sternberg1,2

1Division of Biology 156-29 California Institute of Technology Pasadena, CA, 91125, USA 2Howard Hughes Medical Institute, California Institute of Technology Pasadena, CA, 91125, USA 3Genome Sequencing Center, Washington University School of Medicine St Louis, MO 63108, USA 4Cold Spring Harbor Laboratory 1 Bungtown Road, Cold Spring Harbor, NY, 11724, USA 5Sanger Institute Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, CB10 1SA, UK

*To whom correspondence should be addressed. Tel: +1 626 394 7078; Fax: +1 626 568 8012; Email: emsch{at}its.caltech.edu

Received September 13, 2005. Revised October 6, 2005. Accepted October 6, 2005.

WormBase (http://wormbase.org), the public database for genomics and biology of Caenorhabditis elegans, has been restructured for stronger performance and expanded for richer biological content. Performance was improved by accelerating the loading of central data pages such as the omnibus Gene page, by rationalizing internal data structures and software for greater portability, and by making the Genome Browser highly customizable in how it views and exports genomic subsequences. Arbitrarily complex, user-specified queries are now possible through Textpresso (for all available literature) and through WormMart (for most genomic data). Biological content was enriched by reconciling all available cDNA and expressed sequence tag data with gene predictions, clarifying single nucleotide polymorphism and RNAi sites, and summarizing known functions for most genes studied in this organism.


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