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A wiki for the life sciences where authorship matters

Abstract

WikiGenes is the first wiki system to combine the collaborative and largely altruistic possibilities of wikis with explicit authorship. In view of the extraordinary success of Wikipedia there remains no doubt about the potential of collaborative publishing, yet its adoption in science has been limited. Here I discuss a dynamic collaborative knowledge base for the life sciences that provides authors with due credit and that can evolve via continual revision and traditional peer review into a rigorous scientific tool.

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Figure 1: Authorship tracking and reputation system.
Figure 2: Citation of scientific terminology and references.

References

  1. 1

    Butler, D. Science in the web age: joint efforts. Nature 438, 548–549 (2005).

    CAS  Article  PubMed  Google Scholar 

  2. 2

    Waldrop, M.M. Science 2.0. Sci. Am. 298, 68–73 (2008).

    Article  PubMed  Google Scholar 

  3. 3

    Westerhoff, H.V. & Palsson, B.O. The evolution of molecular biology into systems biology. Nat. Biotechnol. 22, 1249–1252 (2004).

    CAS  Article  PubMed  Google Scholar 

  4. 4

    Taipale, J. & Beachy, P.A. The Hedgehog and Wnt signalling pathways in cancer. Nature 411, 349–354 (2001).

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  5. 5

    Patterson, S.D. & Aebersold, R.H. Proteomics: the first decade and beyond. Nat. Genet. 33 (Suppl.), 311–323 (2003).

    CAS  Article  PubMed  Google Scholar 

  6. 6

    Pruitt, K.D., Tatusova, T. & Maglott, D.R. NCBI reference sequences (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins. Nucleic Acids Res. 35 (Database issue), D61–D65 (2007).

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  7. 7

    Brooksbank, C., Cameron, G. & Thornton, J. The European Bioinformatics Institute's data resources: towards systems biology. Nucleic Acids Res. 33 (Database issue), D46–D53 (2005).

    CAS  Article  PubMed  Google Scholar 

  8. 8

    The UniProt Consortium. The universal protein resource (UniProt). Nucleic Acids Res. 36 (Database issue), D190–D195 (2008).

  9. 9

    Hamosh, A., Scott, A.F., Amberger, J.S., Bocchini, C.A. & McKusick, V.A. Online Mendelian Inheritance in Man (OMIM), a knowledgebase of human genes and genetic disorders. Nucleic Acids Res. 33 (Database issue), D514–D517 (2005).

    CAS  Article  PubMed  Google Scholar 

  10. 10

    Baumgartner, W.A. Jr, Cohen, K.B., Fox, L.M., Acquaah-Mensah, G. & Hunter, L. Manual curation is not sufficient for annotation of genomic databases. Bioinformatics 23, i41–i48 (2007).

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  11. 11

    Salzberg, S.L. Genome re-annotation: a wiki solution? Genome Biol. 8, 102 (2007).

    Article  PubMed  PubMed Central  Google Scholar 

  12. 12

    Wang, K. Gene-function wiki would let biologists pool worldwide resources. Nature 439, 534 (2006).

    CAS  Article  PubMed  Google Scholar 

  13. 13

    Mons, B. et al. Calling on a million minds for community annotation in WikiProteins. Genome Biol. 9, R89 (2008).

    Article  PubMed  PubMed Central  Google Scholar 

  14. 14

    Huss, J.W. et al. A gene wiki for community annotation of gene function. PLoS Biol. 6, e175 (2008).

    Article  PubMed  PubMed Central  Google Scholar 

  15. 15

    Check, E. More biologists but tenure stays static. Nature 448, 848–849 (2007).

    CAS  Article  PubMed  Google Scholar 

  16. 16

    Lehmann, S., Jackson, A.D. & Lautrup, B.E. Measures for measures. Nature 444, 1003–1004 (2006).

    CAS  Article  PubMed  Google Scholar 

  17. 17

    Giles, J. Internet encyclopaedias go head to head. Nature 438, 900–901 (2005).

    CAS  Article  PubMed  Google Scholar 

  18. 18

    Adler, B.T., de Alfaro, L. A content-driven reputation system for the Wikipedia in Proc. WWW., 261–270 (ACM Press, New York, 2007).

    Google Scholar 

  19. 19

    Giles, J. Wikipedia rival calls in the experts. Nature 443, 493 (2006).

    CAS  Article  PubMed  Google Scholar 

  20. 20

    Spier, R. The history of the peer-review process. Trends Biotechnol. 20, 357–358 (2002).

    CAS  Article  PubMed  Google Scholar 

  21. 21

    Kassirer, J.P. & Campion, E.W. Peer review. Crude and understudied, but indispensable. J. Am. Med. Assoc. 272, 96–97 (1994).

    CAS  Article  Google Scholar 

  22. 22

    Cokol, M., Iossifov, I., Rodriguez-Esteban, R. & Rzhetsky, A. How many scientific papers should be retracted? EMBO Rep. 8, 422–423 (2007).

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  23. 23

    Conte, R. & Paolucci, M. Reputation in Artificial Societies: Social Beliefs for Social Order. (Kluwer Academic Publishers, Boston, 2002).

    Google Scholar 

  24. 24

    Resnick, P., Zeckhauser, R., Friedman, E. & Kuwabara, K. Reputation systems. Comm. ACM Conf. 43, 45–48 (2000).

    Article  Google Scholar 

  25. 25

    Friedman, E. & Resnick, P. The social cost of cheap pseudonyms. J. Econ. Manage. Strategy 10, 173–199 (2001).

    Article  Google Scholar 

  26. 26

    Kling, R. Computerization and Controversy: Value Conflicts and Social Choices 2nd edn. (Academic Press, San Diego, 1996).

    Google Scholar 

  27. 27

    Chen, M. & Singh, J.P., Computing and using reputations for internet ratings, in Proc. ACM Conf. Electronic Commerce. 154–162 (ACM Press, New York, 2001).

    Google Scholar 

  28. 28

    Rodriguez, M.A., Bollen, J. & Van de Sompel, H. The convergence of digital libraries and the peer-review process. J. Inf. Sci. 32, 149–159 (2006).

    Article  Google Scholar 

  29. 29

    McKusick, V.A. HUGO news. The Human Genome Organisation: history, purposes, and membership. Genomics 5, 385–387 (1989).

    CAS  Article  PubMed  Google Scholar 

  30. 30

    Little, P. Human genome annotation—a possible role for HUGO? Human Genome Organisation. Nat. Genet. 19, 222 (1998).

    CAS  Article  PubMed  Google Scholar 

  31. 31

    de Lichtenberg, U., Jensen, L.J., Brunak, S. & Bork, P. Dynamic complex formation during the yeast cell cycle. Science 307, 724–727 (2005).

    CAS  Article  PubMed  Google Scholar 

  32. 32

    Campbell, S.L., Khosravi-Far, R., Rossman, K.L., Clark, G.J. & Der, C.J. Increasing complexity of Ras signaling. Oncogene, 17 (11 Reviews),1395–1413 (1998).

    CAS  Article  PubMed  Google Scholar 

  33. 33

    von Bubnoff, A. & Cho, K.W. Intracellular BMP signaling regulation in vertebrates: pathway or network? Dev. Biol. 239, 1–14 (2001).

    CAS  Article  PubMed  Google Scholar 

  34. 34

    Anonymous. Compete, collaborate, compel. Nat. Genet. 39, 931 (2007).

  35. 35

    Heber, J. Print and perish? Nat. Mater. 7, 512–514 (2008).

    CAS  Article  PubMed  Google Scholar 

  36. 36

    Hoffmann, R. & Valencia, A. A gene network for navigating the literature. Nat. Genet. 36, 664 (2004).

    CAS  Article  PubMed  Google Scholar 

  37. 37

    Berners-Lee, T. & Hendler, J. Publishing on the semantic web. Nature 410, 1023–1024 (2001).

    CAS  Article  PubMed  Google Scholar 

  38. 38

    Searls, D.B. Data integration: challenges for drug discovery. Nat. Rev. Drug Discov. 4, 45–58 (2005).

    CAS  Article  PubMed  Google Scholar 

  39. 39

    Anonymous. Let data speak to data. Nature 438, 531 (2005).

  40. 40

    Wheeler, D.L. et al. Database resources of the National Center for Biotechnology Information. Nucleic Acids Res. 36 (Database issue), D13–D21 (2008).

    CAS  Article  Google Scholar 

  41. 41

    Roberts, L., Davenport, R.J., Pennisi, E. & Marshall, E. A history of the Human Genome Project. Science 291, 1195 (2001).

    CAS  Article  PubMed  Google Scholar 

  42. 42

    Frazer, K.A. et al. A second generation human haplotype map of over 3.1 million SNPs. Nature 449, 851–861 (2007).

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  43. 43

    Cotton, R.G. et al. Recommendations of the 2006 Human Variome Project meeting. Nat. Genet. 39, 433–436 (2007).

    CAS  Article  PubMed  Google Scholar 

  44. 44

    Anonymous. Join a social revolution. Nature 436, 1066 (2005).

  45. 45

    Lipscomb, C.E. Medical Subject Headings (MeSH). Bull. Med. Libr. Assoc. 88, 265–266 (2000).

    CAS  PubMed  PubMed Central  Google Scholar 

  46. 46

    Hoffmann, R. & Valencia, A. Implementing the iHOP concept for navigation of biomedical literature. Bioinformatics 21 (Suppl. 2), ii252–ii258 (2005).

    CAS  PubMed  Google Scholar 

  47. 47

    Terry, S.F., Terry, P.F., Rauen, K.A., Uitto, J. & Bercovitch, L.G. Advocacy groups as research organizations: the PXE International example. Nat. Rev. Genet. 8, 157–164 (2007).

    CAS  Article  PubMed  Google Scholar 

  48. 48

    Anonymous. What is the human variome project? Nat. Genet. 39, 423 (2007).

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Acknowledgements

This work was supported in part by the Branco Weiss Fellowship, Society in Science. I am thankful to the Memorial Sloan-Kettering Cancer Center for hosting the iHOP information resource, C. Sander and M. Ramirez-Gaite for helpful discussion, and T. Berners-Lee and D. Weitzner for their support.

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Correspondence to Robert Hoffmann.

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Hoffmann, R. A wiki for the life sciences where authorship matters. Nat Genet 40, 1047–1051 (2008). https://doi.org/10.1038/ng.f.217

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