Worm Breeder's Gazette 17(4): 15 (May 1, 2003)

These abstracts should not be cited in bibliographies. Material contained herein should be treated as personal communication and should be cited as such only with the consent of the author.

www.wormgenes.org , a new gene centered database.

Danielle et Jean Thierry-Mieg1,2,3, Michel Potdevin2, Mark Sienkiewicz1, Vahan Simonyan1, Tadasu Shin-i3, Yuji Kohara3

1 NCBI, NIH, Bethesda, USA
2 CNRS Montpellier, France
3 NIG, Mishima, Japan

Wormgenes is a new resource for C.elegans offering a detailed summary about each gene and a powerful query system.

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The interface is very simple: you ask a question, you get a list of genes. If you open a gene, the information will come as a single little illustrated story, with paragraphs about function, expression, interactions and so on, and the selected biblio at the bottom. From there, you can jump to a second page, where we annotated the mRNA variants and proteins. You can query across the database for proteins sharing a motif or belonging to the same family. The database can of course be queried by name, but also by content, using natural language. For example you may ask for 'mitotic spindle orientation', 'expressed in nerve' 'protruding vulva and essential', 'axon guid', 'stress response', 'growth factor and transduct' or 'membrane protein in endoplasmic reticulum'. The system looks everywhere for the simultaneous presence of all these (possibly truncated) words and returns a list of genes. If you find a gene missing from the list, please send us a note, so that we can improve our annotation.

It is also possible to use a blast interface, in which case you will get the best matches to your query in worm, human, and soon arabidopsis and drosophila, the 4 species for which so far we offer a similar integrated annotation of all the genes we reconstruct from alignment on the genome of the entire mRNA and EST dataset in Genbank. In the worm, we are limited now to the genes with complete mRNAs from Genbank.

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The data are derived in part from a selection of CGC and Wormbase, in part from our own annotations, in part from direct contributions. Wormgenes (also called AceView at NCBI) offers direct links to Yuji Kohara's NextDB in situ hybridization, to Marc Vidal's WorfDB, to Tony Hyman's RNAi sites and to various other places including Wormbase. The bibliography leads to Leon Avery's site and to Medline. The site is updated quarterly in synchrony with the worm sections of the NCBI Refseq and Locuslink resources.

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We would be very pleased to receive your comments and suggestions on the interface, but mostly to integrate under your name any addition to the data that you might like to contribute.

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Acknowledgments: A database is only as good as the data it presents, and we are grateful to the whole worm community for their experimental results, to the CGC, Wormbase and the other sites for data gathering, and to all our friends who helped over the years in the development of acedb.