RiceWiki: a wiki-based database for community curation of rice genes.

Zhang Zhang, Jian Sang, Lina Ma, Gang Wu, Hao Wu, Dawei Huang, Dong Zou, Siqi Liu, Ang Li, Lili Hao, Ming Tian, Chao Xu, Xumin Wang, Jiayan Wu, Jingfa Xiao, Lin Dai, Ling-Ling Chen, Songnian Hu, Jun Yu
Author Information
  1. Zhang Zhang: CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China, Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Fuyang, Zhejiang 311400, China, School of Computer Science and Technology, Beijing Institute of Technology, Beijing 100081, China and College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China.

Abstract

Rice is the most important staple food for a large part of the world's human population and also a key model organism for biological studies of crops as well as other related plants. Here we present RiceWiki (http://ricewiki.big.ac.cn), a wiki-based, publicly editable and open-content platform for community curation of rice genes. Most existing related biological databases are based on expert curation; with the exponentially exploding volume of rice knowledge and other relevant data, however, expert curation becomes increasingly laborious and time-consuming to keep knowledge up-to-date, accurate and comprehensive, struggling with the flood of data and requiring a large number of people getting involved in rice knowledge curation. Unlike extant relevant databases, RiceWiki features harnessing collective intelligence in community curation of rice genes, quantifying users' contributions in each curated gene and providing explicit authorship for each contributor in any given gene, with the aim to exploit the full potential of the scientific community for rice knowledge curation. Based on community curation, RiceWiki bears the potential to make it possible to build a rice encyclopedia by and for the scientific community that harnesses community intelligence for collaborative knowledge curation, covers all aspects of biological knowledge and keeps evolving with novel knowledge.

References

  1. Nucleic Acids Res. 2012 Jan;40(Database issue):D1262-9 [PMID: 22110029]
  2. BMC Bioinformatics. 2008 May 28;9 Suppl 6:S18 [PMID: 18541053]
  3. Nucleic Acids Res. 2012 Jan;40(Database issue):D1308-12 [PMID: 22140107]
  4. Science. 2002 Apr 5;296(5565):92-100 [PMID: 11935018]
  5. Annu Rev Plant Biol. 2002;53:399-419 [PMID: 12221982]
  6. Nucleic Acids Res. 2012 Jan;40(Database issue):D9-12 [PMID: 22144683]
  7. Nucleic Acids Res. 2012 Jan;40(Database issue):D1313-7 [PMID: 22086956]
  8. Genome Res. 2002 Oct;12(10):1599-610 [PMID: 12368253]
  9. Nucleic Acids Res. 2013 Jan;41(Database issue):D1199-205 [PMID: 23193278]
  10. PLoS Biol. 2004 Nov;2(11):e309 [PMID: 15383839]
  11. Amino Acids. 2009 Apr;36(4):615-7 [PMID: 18594947]
  12. Nucleic Acids Res. 2011 Jan;39(Database issue):D141-5 [PMID: 21062808]
  13. Genome Biol. 2007;8(1):102 [PMID: 17274839]
  14. Bioinformatics. 2013 Jul 15;29(14):1837-9 [PMID: 23732274]
  15. Nucleic Acids Res. 2012 Jan;40(Database issue):D1301-7 [PMID: 22096230]
  16. Nature. 2010 Nov 18;468(7322):359-60 [PMID: 21085149]
  17. BMC Bioinformatics. 2009 May 06;10 Suppl 5:S5 [PMID: 19426462]
  18. Nucleic Acids Res. 2012 Jan;40(Database issue):D1270-7 [PMID: 22064863]
  19. Nucleic Acids Res. 2007 Jan;35(Database issue):D883-7 [PMID: 17145706]
  20. Brief Bioinform. 2009 Jan;10(1):1-10 [PMID: 18842678]
  21. Nucleic Acids Res. 2012 Jan;40(Database issue):D1278-87 [PMID: 22096228]
  22. Nucleic Acids Res. 2012 Jan;40(Database issue):D1255-61 [PMID: 22075991]
  23. Database (Oxford). 2012 May 02;2012:bas024 [PMID: 22554788]
  24. Nat Genet. 2010 Nov;42(11):961-7 [PMID: 20972439]
  25. Database (Oxford). 2010 Jul 06;2010:baq009 [PMID: 20624717]
  26. Nature. 2007 Feb 15;445(7129):691 [PMID: 17301755]
  27. Genome Res. 2010 May;20(5):646-54 [PMID: 20305017]
  28. Genome Res. 2005 Dec;15(12):1643-50 [PMID: 16339361]
  29. Genome Biol. 2008;9(5):R89 [PMID: 18507872]
  30. Science. 2008 Mar 21;319(5870):1616 [PMID: 18356505]
  31. Nucleic Acids Res. 2012 Jan;40(Database issue):D130-5 [PMID: 22121212]
  32. Nature. 2012 Sep 6;489(7414):19 [PMID: 22962702]
  33. OMICS. 2012 Jun;16(6):357-62 [PMID: 22702248]
  34. Mol Plant. 2008 Sep;1(5):715-9 [PMID: 19825575]
  35. Nature. 2008 Sep 4;455(7209):22-5 [PMID: 18769412]
  36. PLoS One. 2013;8(2):e56961 [PMID: 23451119]
  37. Plant Cell Physiol. 2013 Feb;54(2):e6 [PMID: 23299411]
  38. Nucleic Acids Res. 2012 Jan;40(Database issue):D1250-4 [PMID: 22139927]
  39. Nat Genet. 2008 Sep;40(9):1047-51 [PMID: 18728691]
  40. Nucleic Acids Res. 2012 Jan;40(Database issue):D1295-300 [PMID: 22058131]
  41. Nucleic Acids Res. 2013 Jan;41(Database issue):D48-55 [PMID: 23203987]
  42. Nature. 2008 Sep 4;455(7209):47-50 [PMID: 18769432]
  43. Nucleic Acids Res. 2013 Jul;41(Web Server issue):W518-22 [PMID: 23703206]
  44. Genome Biol. 2008;9(8):R121 [PMID: 18673581]
  45. Nat Biotechnol. 2011 Dec 11;30(1):105-11 [PMID: 22158310]
  46. Science. 2002 Apr 5;296(5565):79-92 [PMID: 11935017]
  47. Science. 2008 Jun 6;320(5881):1289-90 [PMID: 18535227]
  48. Nature. 2012 Oct 25;490(7421):497-501 [PMID: 23034647]
  49. Nucleic Acids Res. 2004 Jan 1;32(Database issue):D377-82 [PMID: 14681438]
  50. Nature. 2005 Dec 15;438(7070):900-1 [PMID: 16355180]

MeSH Term

Cooperative Behavior
Databases, Genetic
Genes, Plant
Internet
Oryza

Links to CNCB-NGDC Resources

Database Commons: DBC000312 (RiceWiki)

Word Cloud

Similar Articles

Cited By