Letter to Science about wikifying genome information
The March 21, 2008 issue of Science included a News piece[1] 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.
The letter below was submitted on April 13, 2008, and appeared in the June 6, 2008 issue[2].
The text, references, and initial signers are protected from further editing, but the other sections of this page are editable. <protect>
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We noted with interest the recent correspondence[3] and accompanying news article [1] regarding a proposal to "wikify" GenBank. David Lipman’s fears that "It would be chaos" are widely shared, but should be balanced by recognizing that individual curators cannot fully encompass the collective expertise of the larger scientific community. Serious users of Genbank use it as a starting point for in-depth analysis with new bioinformatic tools and reviews of more recent work. These users often learn more about the data than the initial depositors or curation staff. This valuable information is being lost to future researchers, hidden in notebooks, and rarely published. A parallel wiki-based structure provides one way of capturing this data.
We are working on such systems, including EcoliWiki [4], the community annotation component of PortEco [5] and GONUTS [6], a browser and annotation system for Gene Ontology [7]. We regard these, and similar efforts [8][9][10][11] as experiments to test wiki-based curation. So far, the challenge is not chaos, but lack of participation. Thus, we are also experimenting with curation by undergraduates supervised by an experienced scientist. Integrating annotation and genomics education leverages how we teach critical thinking about the literature, accelerates the pace of curation, and provides institutional incentives for established scientists to participate.
Nevertheless, we understand that changing the GenBank model should not be done lightly. There are well-established expectations, both good and bad, about GenBank, and wikifying it could be quite disruptive. Perhaps GenBank could support an arms length relationship to wikis via the LinkOut service. We look forward to ongoing discussion of how community curation could be added to GenBank. In the meantime, we encourage the 250 signers of the Bidartondo et al. letter to help us build wiki-based fungal curation via GO at GONUTS.
References
See Help:References for how to manage references in EcoliWiki.
- ↑ 1.0 1.1 Pennisi, E (2008) DNA data. Proposal to 'Wikify' GenBank meets stiff resistance. Science 319 1598-9 PubMed
- ↑ Hu, JC et al. (2008) The emerging world of wikis. Science 320 1289-90 PubMed
- ↑ Bidartondo, MI (2008) Preserving accuracy in GenBank. Science 319 1616 PubMed
- ↑ http://ecoliwiki.net
- ↑ http://PortEco.org
- ↑ http://gowiki.tamu.edu
- ↑ Ashburner, M et al. (2000) Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat. Genet. 25 25-9 PubMed
- ↑ Mathivanan, S et al. (2008) Human Proteinpedia enables sharing of human protein data. Nat. Biotechnol. 26 164-7 PubMed
- ↑ Arshinoff, BI et al. (2007) Xanthusbase: adapting wikipedia principles to a model organism database. Nucleic Acids Res. 35 D422-6 PubMed
- ↑ http://www.wikipathways.org
- ↑ http://PDBWiki.org
Submitted signers
- James C. Hu, Texas A&M University
- Rodolfo Aramayo, Texas A&M University
- Dan M. Bolser, The BiO Centre, http://BiO.CC
- Tyrrell Conway, University of Oklahoma Advanced Center for Genome Technology
- Christine Elsik, Georgetown University
- Michael Gribskov, Purdue University
- Thomas Kelder, Maastricht University
- Daisuke Kihara, Biological Sciences/Computer Science, Purdue University, West Lafayette, IN 47907
- Tom Knight, MIT
- Alexander R. Pico, The Gladstone Institutes, San Francisco
- Deborah A. Siegele, Texas A&M University
- Barry L. Wanner, Biological Sciences, Purdue University, West Lafayette, IN 47907
- Roy D. Welch, Syracuse University
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Added after submission
- The Steering Committee of OpenWetWare (openwetware.org)
