Letter to Science about wikifying genome information: Difference between revisions

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Changed my 'affiliation' to something closer to the truth. I like the + by User:Tk. I think this is the way a lot of peope contribute to Wikipedia, using it as a research scratch pad.
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We have been working on wiki-based systems for gene annotation, including EcoliWiki <ref>http://ecoliwiki.net</ref>, the community annotation component of the EcoliHub project <ref>http://ecolihub.org</ref> and GONUTS <ref>http://gowiki.tamu.edu</ref>, a wiki-based browser and annotation engine for the Gene Ontology <ref name='PMID:10802651'/>.  We regard these, and other wiki-based efforts <ref name='PMID:18259167'/><ref name='PMID:17090585'/><ref>http://www.wikipathways.org</ref><ref>http://PDBWiki.org</ref> 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 a 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.  
We have been working on wiki-based systems for gene annotation, including EcoliWiki <ref>http://ecoliwiki.net</ref>, the community annotation component of the EcoliHub project <ref>http://ecolihub.org</ref> and GONUTS <ref>http://gowiki.tamu.edu</ref>, a wiki-based browser and annotation engine for the Gene Ontology <ref name='PMID:10802651'/>.  We regard these, and other wiki-based efforts <ref name='PMID:18259167'/><ref name='PMID:17090585'/><ref>http://www.wikipathways.org</ref><ref>http://PDBWiki.org</ref> 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 a 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.  


Serious users of Genbank typically use that data as a starting point for in-depth analysis including application of new bioinformatic tools and literature reviews of more recent work.  At the end of this process, these users often know more than the initilal depositors or curation staff.  This valuable information is currently being lost to future researchers, hidden in notebooks, and rarely published.  A parallel wiki-based structure provides one way of capturing this data.
Serious users of Genbank typically use that data as a starting point for in-depth analysis including application of new bioinformatic tools and literature reviews of more recent work.  At the end of this process, these users often know more than the initial depositors or curation staff.  This valuable information is currently being lost to future researchers, hidden in notebooks, and rarely published.  A parallel wiki-based structure provides one way of capturing this data.


While these experiments are in progress, 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 of gene function via GO terms at GONUTS.
While these experiments are in progress, 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 of gene function via GO terms at GONUTS.

Revision as of 19:09, 11 April 2008

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.

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[2] and accompanying news article [1] regarding a proposal to "wikify" GenBank. David Lipman’s fears that "It would be chaos" are widely shared. However, we believe that these fears should be balanced by recognizing the fact that the expertise of an individual curator is unlikely to fully encompass the collective expertise of the larger scientific community. 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 [3], the community annotation component of the EcoliHub project [4] and GONUTS [5], a wiki-based browser and annotation engine for the Gene Ontology [6]. We regard these, and other wiki-based efforts [7][8][9][10] 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 a 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.

Serious users of Genbank typically use that data as a starting point for in-depth analysis including application of new bioinformatic tools and literature reviews of more recent work. At the end of this process, these users often know more than the initial depositors or curation staff. This valuable information is currently being lost to future researchers, hidden in notebooks, and rarely published. A parallel wiki-based structure provides one way of capturing this data.

While these experiments are in progress, 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 of gene function via GO terms at GONUTS.

signatures

  • 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
  1. ↑ 1.0 1.1 Pennisi, E (2008) DNA data. Proposal to 'Wikify' GenBank meets stiff resistance. Science 319 1598-9 PubMed
  2. ↑ Bidartondo, MI (2008) Preserving accuracy in GenBank. Science 319 1616 PubMed
  3. ↑ http://ecoliwiki.net
  4. ↑ http://ecolihub.org
  5. ↑ http://gowiki.tamu.edu
  6. ↑ Ashburner, M et al. (2000) Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat. Genet. 25 25-9 PubMed
  7. ↑ Mathivanan, S et al. (2008) Human Proteinpedia enables sharing of human protein data. Nat. Biotechnol. 26 164-7 PubMed
  8. ↑ Arshinoff, BI et al. (2007) Xanthusbase: adapting wikipedia principles to a model organism database. Nucleic Acids Res. 35 D422-6 PubMed
  9. ↑ http://www.wikipathways.org
  10. ↑ http://PDBWiki.org
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