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WormBase: better software, richer content

Schwarz, Erich M. and Antoshechkin, Igor and Bastiani, Carol and Bieri, Tamberlyn and Blasiar, Darin and Canaran, Payan and Chan, Juancarlos and Chen, Nansheng and Chen, Wen J. and Davis, Paul and Fiedler, Tristan J. and Girard, Lisa and Harris, Todd W. and Kenny, Eimear E. and Kishore, Ranjana and Lawson, Dan and Lee, Raymond and Müller, Hans-Michael and Nakamura, Cecilia and Ozersky, Phil and Petcherski, Andrei and Rogers, Anthony and Spooner, Will and Tuli, Mary Ann and Van Auken, Kimberly and Wang, Daniel and Durbin, Richard and Spieth, John and Stein, Lincoln D. and Sternberg, Paul W. (2006) WormBase: better software, richer content. Nucleic Acids Research, 34 (Databa). D475-D478. ISSN 0305-1048. PMCID PMC1347424. http://resolver.caltech.edu/CaltechAUTHORS:SCHWnar06

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Abstract

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.


Item Type:Article
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https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1347424/PubMed CentralArticle
ORCID:
AuthorORCID
Van Auken, Kimberly0000-0002-1706-4196
Sternberg, Paul W.0000-0002-7699-0173
Additional Information:© 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. Received September 13, 2005. Revised October 6, 2005. Accepted October 6, 2005. P.W.S. is an investigator with the Howard Hughes Medical Institute. WormBase is supported by grant P41-HG02223 from the US National Human Genome Research Institute, and by the British Medical Research Council. Funding to pay the Open Access publication charges for this article was provided by grant P41-HG02223 from the US National Human Genome Research Institute. Conflict of interest statement. None declared.
Issue or Number:Databa
PubMed Central ID:PMC1347424
Record Number:CaltechAUTHORS:SCHWnar06
Persistent URL:http://resolver.caltech.edu/CaltechAUTHORS:SCHWnar06
Alternative URL:http://dx.doi.org/10.1093/nar/gkj061
Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:1221
Collection:CaltechAUTHORS
Deposited By: Archive Administrator
Deposited On:05 Jan 2006
Last Modified:30 Oct 2017 20:35

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