Letter to Science about wikifying genome information: Difference between revisions
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Please help us edit the text and add your signature if you want to go on record with us. Limit is 300 words | Please help us edit the text and add your signature if you want to go on record with us. Limit is 300 words | ||
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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'/>. While David Lipman’s fears that "It would be chaos." are widely held, the expertise of GenBank's single full-time staff mycologist is unlikely to be superior on average to the collective, albeit intermittently applied, expertise of the 250 signers of the Bidartondo et al. letter, | 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'/>. While David Lipman’s fears that "It would be chaos." are widely held, the expertise of GenBank's single full-time staff mycologist is unlikely to be superior on average to the collective, albeit intermittently applied, expertise of the scientists who might participate in community curation, including the 250 signers of the Bidartondo et al. letter,. But although the time has come for serious discussion about alternative models, 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. | ||
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 <ref name='PMID:18259167'/><ref name='PMID:17090585'/> as experiments to assess the performance of wiki-based community curation. | 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 <ref name='PMID:18259167'/><ref name='PMID:17090585'/> as experiments to assess the performance of wiki-based community curation. In our experience so far with community curation, the biggest problem is not chaos, it's lack of participation. Thus, we are also experimenting with literature-based curation done by undergraduates under the supervision of a more experienced scientist. Incorporating wiki-based annotation as part of genomics undergraduate education leverages the way we teach students critical thinking about the literature, accelerates the pace of curation, and provides institutional incentives for established scientists to participate more actively in curation. | ||
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. | |||
While these experiments are in progress, perhaps GenBank could support an arms length relationship to wikis via the LinkOut service. We look forward to | |||
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Revision as of 17:14, 7 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
draft
We noted with interest the recent correspondence from Bidartondo et al[2] regarding a proposal to "wikify" GenBank and the accompanying news article by Elizabeth Pennisi [1]. While David Lipman’s fears that "It would be chaos." are widely held, the expertise of GenBank's single full-time staff mycologist is unlikely to be superior on average to the collective, albeit intermittently applied, expertise of the scientists who might participate in community curation, including the 250 signers of the Bidartondo et al. letter,. But although the time has come for serious discussion about alternative models, 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.
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 [3][4] as experiments to assess the performance of wiki-based community curation. In our experience so far with community curation, the biggest problem is not chaos, it's lack of participation. Thus, we are also experimenting with literature-based curation done by undergraduates under the supervision of a more experienced scientist. Incorporating wiki-based annotation as part of genomics undergraduate education leverages the way we teach students critical thinking about the literature, accelerates the pace of curation, and provides institutional incentives for established scientists to participate more actively in curation.
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.
- ↑ 1.0 1.1 Pennisi, E (2008) DNA data. Proposal to 'Wikify' GenBank meets stiff resistance. Science 319 1598-9 PubMed
- ↑ Bidartondo, MI (2008) Preserving accuracy in GenBank. Science 319 1616 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