WormBase: better software, richer content.

Erich M. Schwarz; Igor Antoshechkin; Carol Bastiani; Tamberlyn Bieri; Darin Blasiar; Payan Canaran; Juancarlos Chan; Nansheng Chen; Wen J. Chen; Paul Davis; Tristan J. Fiedler; Lisa Girard; Todd W. Harris; Eimear E. Kenny; Ranjana Kishore; Dan Lawson; Raymond Lee; Hans Michael Müller; Cecilia Nakamura; Phil Ozersky; Andrei Petcherski; Anthony Rogers; Will Spooner; Mary Ann Tuli; Kimberly Van Auken; Daniel Wang; Richard Durbin; John Spieth; Lincoln D. Stein; Paul W. Sternberg

doi:10.1093/nar/gkj061

WormBase: better software, richer content.

Erich M. Schwarz, Igor Antoshechkin, Carol Bastiani, Tamberlyn Bieri, Darin Blasiar, Payan Canaran, Juancarlos Chan, Nansheng Chen, Wen J. Chen, Paul Davis, Tristan J. Fiedler, Lisa Girard, Todd W. Harris, Eimear E. Kenny, Ranjana Kishore, Dan Lawson, Raymond Lee, Hans Michael Müller, Cecilia Nakamura, Phil OzerskyAndrei Petcherski, Anthony Rogers, Will Spooner, Mary Ann Tuli, Kimberly Van Auken, Daniel Wang, Richard Durbin, John Spieth, Lincoln D. Stein, Paul W. Sternberg

Research output: Contribution to journal › Article › peer-review

66 Scopus citations

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.

Original language	English
Pages (from-to)	D475-478
Journal	Nucleic Acids Research
Volume	34
Issue number	Database issue
DOIs	https://doi.org/10.1093/nar/gkj061
State	Published - 1 Jan 2006
Externally published	Yes

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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., Müller, H. M., Nakamura, C., ... Sternberg, P. W. (2006). WormBase: better software, richer content. Nucleic Acids Research, 34(Database issue), D475-478. https://doi.org/10.1093/nar/gkj061

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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.",

author = "Schwarz, {Erich M.} and Igor Antoshechkin and Carol Bastiani and Tamberlyn Bieri and Darin Blasiar and Payan Canaran and Juancarlos Chan and Nansheng Chen and Chen, {Wen J.} and Paul Davis and Fiedler, {Tristan J.} and Lisa Girard and Harris, {Todd W.} and Kenny, {Eimear E.} and Ranjana Kishore and Dan Lawson and Raymond Lee and M{\"u}ller, {Hans Michael} and Cecilia Nakamura and Phil Ozersky and Andrei Petcherski and Anthony Rogers and Will Spooner and Tuli, {Mary Ann} and {Van Auken}, Kimberly and Daniel Wang and Richard Durbin and John Spieth and Stein, {Lincoln D.} and Sternberg, {Paul W.}",

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doi = "10.1093/nar/gkj061",

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Schwarz, EM, Antoshechkin, I, Bastiani, C, Bieri, T, Blasiar, D, Canaran, P, Chan, J, Chen, N, Chen, WJ, Davis, P, Fiedler, TJ, Girard, L, Harris, TW, Kenny, EE, Kishore, R, Lawson, D, Lee, R, Müller, HM, Nakamura, C, Ozersky, P, Petcherski, A, Rogers, A, Spooner, W, Tuli, MA, Van Auken, K, Wang, D, Durbin, R, Spieth, J, Stein, LD & Sternberg, PW 2006, 'WormBase: better software, richer content.', Nucleic Acids Research, vol. 34, no. Database issue, pp. D475-478. https://doi.org/10.1093/nar/gkj061

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AU - Canaran, Payan

AU - Chan, Juancarlos

AU - Chen, Nansheng

AU - Chen, Wen J.

AU - Davis, Paul

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AU - Girard, Lisa

AU - Harris, Todd W.

AU - Kenny, Eimear E.

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AU - Lee, Raymond

AU - Müller, Hans Michael

AU - Nakamura, Cecilia

AU - Ozersky, Phil

AU - Petcherski, Andrei

AU - Rogers, Anthony

AU - Spooner, Will

AU - Tuli, Mary Ann

AU - Van Auken, Kimberly

AU - Wang, Daniel

AU - Durbin, Richard

AU - Spieth, John

AU - Stein, Lincoln D.

AU - Sternberg, Paul W.

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SP - D475-478

JO - Nucleic Acids Research

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ER -

WormBase: better software, richer content.

Abstract

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