Letter to Science about wikifying genome information: Difference between revisions

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The March 21, 2008 issue of ''Science'' included a [http://www.sciencemag.org/cgi/content/full/319/5870/1598 News piece]<ref name='PMID:18356493'/> 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 March 21, 2008 issue of ''Science'' included a [http://www.sciencemag.org/cgi/content/full/319/5870/1598 News piece]<ref name='PMID:18356493'/> 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.  
The letter below was submitted on  April 13, 2008, and [http://www.sciencemag.org/cgi/content/full/320/5881/1289b appeared] in the June 6, 2008 issue<ref name='PMID:18535227'/>.
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We noted with interest the recent correspondence from Bidartondo et al<ref name='PMID:18356505'/> regarding a proposal to "wikify" GenBank and the accompanying news article by Elizabeth Pennisi <ref name='PMID:18356493'/>, describing the resistance of GenBank management to the idea.  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 GenBank could be quite disruptive to the user community.  Nevertheless, while our anecdotal evidence suggests that David Lipman’s fears that "It would be chaos." are widely held, it is worth pondering whether the expertise of GenBank's single full-time staff mycologist is a superior on average to the  collective, but intermittently applied, expertise of the 250 signers of the Bidartondo et al. letter, plus the many other members of the scientific community who, like us, would have signed the letter if we had known about it.


We have been working for some time on wiki-based systems for gene annotation, including EcoliWiki (http://ecoliwiki.net), the community annotation component of the NIGMS funded 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 the similar wiki-based efforts of other groups (refs) as experimental, as the actual performance of wiki-based community curation has not been established.  However, the scalability, error propagation, and cost problems alluded to in Elizabeth Pennisi's article mean that these are important experiments to perform.
The text, references, and initial signers are protected from further editing, but the other sections of this page are editable.
<protect>
==Text==
We noted with interest the recent correspondence<ref name='PMID:18356505'/> and accompanying news article <ref name='PMID:18356493'/> 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 <ref>http://ecoliwiki.net</ref>, the community annotation component of PortEco <ref>http://PortEco.org</ref> and GONUTS <ref>http://gowiki.tamu.edu</ref>, a browser and annotation system for Gene Ontology <ref name='PMID:10802651'/>.  We regard these, and similar efforts <ref name='PMID:18259167'/><ref name='PMID:17090585'/><ref>http://www.wikipathways.org</ref><ref>http://PDBWiki.org</ref> 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.  


Current databases are growing at an impressive rate and this situation is not likely to change in the near future. The value of GenBank is directly related to the quality of the information there stored. Incorrect or incomplete annotations can have negative ripple effects on information processing. The time has come to start a serious discussion about alternative models of genome annotation that without the need of a publication, would allow the scientific community to make changes and corrections to GenBank or genome databases, while preserving the highest possible scientific standards.
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.


Towards this end, we are currently experimenting with literature-based curation done by students under the supervision of a more experienced scientist as a component of undergraduate research education. Properly designed and conducted, these experiments could change genomics undergraduate education by introducing these future scientists to the huge amount of information already available, and by training them to think and to evaluate the annotated record with that of the published information. When applied to gene families and pathways within and between genomes, this exercise also forces students to think about the evolutionary relationships of the players involved. We think that, if properly conducted, this student-driven engine could change the pace of genome annotation or at least generate a rich testing field for new models for gene and genome annotation. Regardless, an easily accessible public repository of community-driven curated information is urgently needed and the Wiki model offers a good start point.
==References==
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<references />


While these experiments are in progress, perhaps GenBank could support an arms length relationship to wikis via the LinkOut service. We look forward to participating in 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.
==Submitted signers==
<references/>
* 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)

Latest revision as of 00:37, 1 July 2011

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.

Text

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

[back to top]


See Help:References for how to manage references in EcoliWiki.

  1. ↑ 1.0 1.1 Pennisi, E (2008) DNA data. Proposal to 'Wikify' GenBank meets stiff resistance. Science 319 1598-9 PubMed
  2. ↑ Hu, JC et al. (2008) The emerging world of wikis. Science 320 1289-90 PubMed
  3. ↑ Bidartondo, MI (2008) Preserving accuracy in GenBank. Science 319 1616 PubMed
  4. ↑ http://ecoliwiki.net
  5. ↑ http://PortEco.org
  6. ↑ http://gowiki.tamu.edu
  7. ↑ Ashburner, M et al. (2000) Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat. Genet. 25 25-9 PubMed
  8. ↑ Mathivanan, S et al. (2008) Human Proteinpedia enables sharing of human protein data. Nat. Biotechnol. 26 164-7 PubMed
  9. ↑ Arshinoff, BI et al. (2007) Xanthusbase: adapting wikipedia principles to a model organism database. Nucleic Acids Res. 35 D422-6 PubMed
  10. ↑ http://www.wikipathways.org
  11. ↑ 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


Added after submission

  • The Steering Committee of OpenWetWare (openwetware.org)
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