Letter to Science about wikifying genome information

The March 21, 2008 issue of Science included a News piece stimulated by an open letter from a large group of fungal researchers about using wiki models for improving GenBank. We thought we should send a letter to Science in response.

Please help us edit the text and add your signature if you want to go on record with us. Limit is 300 words. Plan is to submit by April 11, 2008

draft

We noted with interest the recent correspondence and accompanying news article regarding a proposal to "wikify" GenBank. While David Lipman’s fears that "It would be chaos." are widely shared, the expertise of GenBank's single staff mycologist is unlikely to be superior to the collective, albeit intermittently applied, expertise of the scientists who might participate in wiki curation, including the 250 signers of the Bidartondo et al. letter. Nevertheless, we understand that changing the GenBank model should not be done lightly. There are now well-established expectations, both good and bad, about GenBank and RefSeq, and wikifying them could be quite disruptive.

We have been working on wiki-based systems for gene annotation, including EcoliWiki (http://ecoliwiki.net), the community annotation component of the EcoliHub project (http://ecolihub.org) and GONUTS (http://gowiki.tamu.edu), a wiki-based browser and annotation engine for the Gene Ontology. We regard these, and other wiki-based efforts as experiments to determine whether wiki-based community curation will work. So far, the biggest problem is not chaos, but lack of participation. Thus, we are also experimenting with literature-based curation by undergraduates under the supervision of a more experienced scientist and as part of the study of an specific scientific topic. Incorporating wiki-based annotation as part of genomics undergraduate education leverages how we teach critical thinking about the literature, accelerates the pace of curation, and provides institutional incentives for established scientists to participate.

While these experiments are in progress, perhaps GenBank could support an arms length relationship to wikis via the LinkOut service. We look forward to the ongoing discussion of the future of how community curation could be added to GenBank. In the meantime, we encourage the signers of the Bidartondo et al. letter to help us build wiki-based fungal curation of gene function via GO at GONUTS.

signatures

• James C. Hu, Texas A&M University
• Michael Gribskov, Purdue University
• Tyrrell Conway, University of Oklahoma Advanced Center for Genome Technology
• Rodolfo Aramayo, Texas A&M University (jim, delete my name if you see fit)
• Barry L. Wanner, Biological Sciences, Purdue University, West Lafayette, IN 47907

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