WormBase: better software, richer content

Schwarz, E. M., Antoshechkin, I., Bastiani, C., Bieri, T., Blasiar, D., Canaran, P., Chan, J., Chen, N., Chen, W. J., Davis, P., Fiedler, T. J., Girard, L., Harris, T. W., Kenny, E. E., Kishore, R., Lawson, D., Lee, R., Muller, H. M., Nakamura, C., Ozersky, P., Petcherski, A., Rogers, A., Spooner, W., Tuli, M. A., Van Auken, K., Wang, D., Durbin, R., Spieth, J., Stein, L. D., Sternberg, P. W. (January 2006) WormBase: better software, richer content. Nucl. Acids Res., 34 (suppl_). D475-478.

URL: https://www.ncbi.nlm.nih.gov/pubmed/16381915
DOI: 10.1093/nar/gkj061

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: Paper
Uncontrolled Keywords: Animals Caenorhabditis elegans genetics physiology Caenorhabditis elegans Proteins chemistry genetics DNA Complementary chemistry Databases Genetic Expressed Sequence Tags chemistry Genome Helminth Genomics Internet Polymorphism Single Nucleotide RNA Interference Software User Computer Interface
Subjects: organism description > animal > C elegans
bioinformatics > genomics and proteomics > databases > database optimization
bioinformatics > genomics and proteomics > databases > database search and retrieval
bioinformatics > genomics and proteomics > genetics & nucleic acid processing > DNA, RNA structure, function, modification > RNAi
bioinformatics > genomics and proteomics > genetics & nucleic acid processing > DNA, RNA structure, function, modification > cDNA
bioinformatics > genomics and proteomics > computers > computer software
bioinformatics > genomics and proteomics > databases > databases
CSHL Authors:
Communities: CSHL labs > Stein lab
Depositing User: CSHL Librarian
Date: 1 January 2006
Date Deposited: 09 Dec 2011 15:34
Last Modified: 27 Apr 2018 15:43
PMCID: PMC1347424
Related URLs:
URI: http://repository.cshl.edu/id/eprint/22895

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