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December 28, 2005Nucleic Acids Research86 citationsOpen Access

WormBase: better software, richer content

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ESErich M. SchwarzCornell University

Key Points

  • The goal is to enhance WormBase for better performance and to expand the available biological content.
  • Restructured software for improved data performance and user experience.
  • Integrated complex queries through Textpresso and WormMart.
  • Merged cDNA and expressed sequence tag data with gene predictions.
  • Loading times for central data pages, including the Gene page, were significantly reduced.
  • Increased ability to execute complex user-defined queries on genomic data.
  • Richer biological content was provided by reconciling gene data and clarifying key genetic features.

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.

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Cite This Study

Erich M. Schwarz (2005) studied this question.

synapsesocial.com/papers/6a15b8385347fbb173a02fachttps://doi.org/10.1093/nar/gkj061
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