Skip to main page content
Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 2006 Jan 1;34(Database issue):D475-8.
doi: 10.1093/nar/gkj061.

WormBase: Better Software, Richer Content

Free PMC article

WormBase: Better Software, Richer Content

Erich M Schwarz et al. Nucleic Acids Res. .
Free PMC article


WormBase (, 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.

Similar articles

  • WormBase: new content and better access.
    Bieri T, Blasiar D, Ozersky P, Antoshechkin I, Bastiani C, Canaran P, Chan J, Chen N, Chen WJ, Davis P, Fiedler TJ, Girard L, Han M, Harris TW, Kishore R, Lee R, McKay S, Müller HM, Nakamura C, Petcherski A, Rangarajan A, Rogers A, Schindelman G, Schwarz EM, Spooner W, Tuli MA, Van Auken K, Wang D, Wang X, Williams G, Durbin R, Stein LD, Sternberg PW, Spieth J. Bieri T, et al. Nucleic Acids Res. 2007 Jan;35(Database issue):D506-10. doi: 10.1093/nar/gkl818. Epub 2006 Nov 11. Nucleic Acids Res. 2007. PMID: 17099234 Free PMC article.
  • WormBase: a comprehensive data resource for Caenorhabditis biology and genomics.
    Chen N, Harris TW, Antoshechkin I, Bastiani C, Bieri T, Blasiar D, Bradnam K, Canaran P, Chan J, Chen CK, Chen WJ, Cunningham F, Davis P, Kenny E, Kishore R, Lawson D, Lee R, Muller HM, Nakamura C, Pai S, Ozersky P, Petcherski A, Rogers A, Sabo A, Schwarz EM, Van Auken K, Wang Q, Durbin R, Spieth J, Sternberg PW, Stein LD. Chen N, et al. Nucleic Acids Res. 2005 Jan 1;33(Database issue):D383-9. doi: 10.1093/nar/gki066. Nucleic Acids Res. 2005. PMID: 15608221 Free PMC article.
  • Using WormBase: A Genome Biology Resource for Caenorhabditis elegans and Related Nematodes.
    Grove C, Cain S, Chen WJ, Davis P, Harris T, Howe KL, Kishore R, Lee R, Paulini M, Raciti D, Tuli MA, Van Auken K, Williams G; WormBase Consortium. Grove C, et al. Methods Mol Biol. 2018;1757:399-470. doi: 10.1007/978-1-4939-7737-6_14. Methods Mol Biol. 2018. PMID: 29761466 Free PMC article.
  • WormBase: methods for data mining and comparative genomics.
    Harris TW, Stein LD. Harris TW, et al. Methods Mol Biol. 2006;351:31-50. doi: 10.1385/1-59745-151-7:31. Methods Mol Biol. 2006. PMID: 16988424 Review.
  • Studying gene function in Caenorhabditis elegans using RNA-mediated interference.
    Maine EM. Maine EM. Brief Funct Genomic Proteomic. 2008 May;7(3):184-94. doi: 10.1093/bfgp/eln019. Epub 2008 Apr 28. Brief Funct Genomic Proteomic. 2008. PMID: 18443013 Review.
See all similar articles

Cited by 44 articles

See all "Cited by" articles


    1. Eeckman F.H., Durbin R. ACeDB and macace. Methods Cell Biol. 1995;48:583–605. - PubMed
    1. Stein L.D., Thierry-Mieg J. Scriptable access to the Caenorhabditis elegans genome sequence and other ACEDB databases. Genome Res. 1998;8:1308–1315. - PMC - PubMed
    1. Chen N., Harris T.W., Antoshechkin I., Bastiani C., Bieri T., Blasiar D., Bradnam K., Canaran P., Chan J., Chen C.K., et al. WormBase: a comprehensive data resource for Caenorhabditis biology and genomics. Nucleic Acids Res. 2005;33:D383–D389. - PMC - PubMed
    1. Chen N., Lawson D., Bradnam K., Harris T.W., Stein L.D. WormBase as an integrated platform for the C.elegans ORFeome. Genome Res. 2004;14:2155–2161. - PMC - PubMed
    1. Stein L.D., Bao Z., Blasiar D., Blumenthal T., Brent M.R., Chen N., Chinwalla A., Clarke L., Clee C., Coghlan A., et al. The genome sequence of Caenorhabditis briggsae: a platform for comparative genomics. PLoS Biol. 2003;1:E45. - PMC - PubMed

Publication types