Adventures in data citation: Sorghum genome data exemplifies the new gold standard

BMC Research Notes

Volumn 5, Issue , 2012, Pages

  Edmunds, Scott C ^a   Pollard, Tom J ^b,c,d   Hole, Brian ^b,e   Basford, Alexandra T ^a  

^a GigaScience   (Hong Kong)

^b Ubiquity Press   (United Kingdom)

^c UNIVERSITY COLLEGE LONDON   (United Kingdom)

^d UNIVERSITY COLLEGE HOSPITAL   (United Kingdom)

^e UNIVERSITY COLLEGE LONDON   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; GENETICS; GENOMICS; INFORMATION DISSEMINATION; INFORMATION SERVICE; INFORMATION SYSTEM; METHODOLOGY; PLANT GENOME; PUBLISHING; SORGHUM; STANDARD; STATISTICS;

GENOME, PLANT; GENOMICS; INFORMATION DISSEMINATION; INFORMATION SERVICES; INFORMATION SYSTEMS; PUBLISHING; SORGHUM;

EID: 84860877608     PISSN: None     EISSN: 17560500     Source Type: Journal    
DOI: 10.1186/1756-0500-5-223     Document Type: Article

References (44)

1. Genomics in C. elegans: so many genes, such a little worm. Hillier LW, Coulson A, Murray JI, Bao Z, Sulston JE, Waterston RH, Genome Research 2005 15 1651 1660 10.1101/gr.3729105 16339362 (Pubitemid 41780394)
2. The human genome project: lessons from large-scale biology. Collins FS, Morgan M, Patrinos A, Science 2003 300 286 290 10.1126/science.1084564 12690187 (Pubitemid 36433711)
3. Bermuda rules: community spirit. Marshall E, With Teeth. Science 2001 291 1192
4. Genome.gov | February 2003 Data Release Policies. http://www.genome.gov/ 10506537
5. Prepublication data sharing. Toronto International Data Release Workshop Authors, Nature 2009 461 168 170 http://www.nature.com/nature/journal/v461/ n7261/full/461168a.html 19741685
6. Data archiving is a good investment. Piwowar HA, Vision TJ, Whitlock MC, Nature 2011 473 285 21593853
7. Sharing detailed research data is associated with increased citation rate. Piwowar HA, Day RS, Fridsma DB, PLoS ONE 2007 2 308 10.1371/journal.pone. 0000308 17375194
8. The Enduring Value of Social Science Research: The Use and Reuse of Primary Research Data. Pienta AM, Alter GC, Lyle JA, 2010 http://hdl.handle.net/ 2027.42/78307
9. Credit where credit is overdue. Nat Biotech 2009 27 579 http://www.nature.com/nbt/journal/v27/n7/full/nbt0709-579.html
10. Cancer trial errors revealed. Samuel Reich E, Nature 2011 469 139 140 10.1038/469139a 21228842
11. Report finds massive fraud at Dutch universities. Callaway E, Nature 2011 479 15 10.1038/479015a 22051650
12. Open data and the social contract of scientific publishing. Vision TJ, BioScience 2010 60 330 331 10.1525/bio.2010.60.5.2
13. Genome-wide patterns of genetic variation in sweet and grain sorghum (Sorghum bicolor). Zheng L-Y, Guo X-S, He B, Sun L-J, Peng Y, Dong S-S, Liu T-F, Jiang S, Ramachandran S, Liu C-M, Jing H-C, Genome Biology 2011 12 114 10.1186/gb-2011-12-11-r114 22104744
14. Genome data from sweet and grain sorghum (Sorghum bicolor). Zheng L-Y, Guo X-S, He B, Sun L-J, Peng Y, Dong S-S, Liu T-F, Jiang S, Ramachandran S, Liu C-M, Jing H-C, GigaScience 2011 http://dx.doi.org/10.5524/100012
15. GigaScience. http://www.gigasciencejournal.com/
16. GigaDB. http://gigadb.org/
17. BGI Homepage. http://en.genomics.cn/navigation/index.action
18. BioMed Central. http://www.biomedcentral.com/
19. DataCite UK User Group Meeting. http://www.ariadne.ac.uk/issue67/ datacite-2011-rpt/
20. Making Datasets Visible and Accessible: DataCites First Summer Meeting http://www.ariadne.ac.uk/issue64/datacite-2010-rpt/]
21. DataCite Members. http://datacite.org/members
22. isCitedBy: A Metadata Scheme for DataCite. Starr J, Gastl A, D-Lib Magazine 2011 17 http://dx.doi.org/10.1045/january2011-starr (ISSN:1082-9873)
23. DOI News-Revised DOI cost-sharing model. http://www.doi.org/news/ DOINewsApr11.html#3
24. Pangaea: Data Publisher for Earth & Environmental Science. http://www.pangaea.de/
25. Southern hemisphere water mass conversion linked with north atlantic climate variability. Pahnke K, Zahn R, Science 2005 307 1741 1746 10.1126/science.1102163 15774752 (Pubitemid 40388610)
26. Dryad Digital Repository. http://datadryad.org/
27. Mean stable carbon isotope ratios of Cibicidoides wuellerstorfi from sediment core MD95-2042 on the Iberian margin, North Atlantic. Shackleton NJ, Hall MA, Vincent E, PANGAEA-Data Publisher for Earth & Environmental Science 2001 http://doi.pangaea.de/10.1594/PANGAEA.58229
28. The protein data bank. Berman HM, Westbrook J, Feng Z, Gilliland G, Bhat TN, Weissig H, Shindyalov IN, Bourne PE, Nucleic Acids Res 2000 28 235 242 10.1093/nar/28.1.235 10592235 (Pubitemid 30047768)
29. Data growth and its impact on the SCOP database: new developments. Andreeva A, Howorth D, Chandonia J-M, Brenner SE, Hubbard TJP, Chothia C, Murzin AG, Nucleic Acids Res 2008 36 419 D425 18000004
30. Integration of open access literature into the RCSB Protein Data Bank using BioLit. Prli A, Martinez MA, Dimitropoulos D, Beran B, Yukich BT, Rose PW, Bourne PE, Fink JL, BMC Bioinformatics 2010 11 220 10.1186/1471-2105-11-220 20429930
31. Earth Systems Science Data Journal. http://www.earth-system-science-data. net/home.html
32. Semantic tagging of and semantic enhancements to systematics papers: ZooKeys working examples. Penev L, Agosti D, Georgiev T, Catapano T, Miller J, Blagoderov V, Roberts D, Smith VS, Brake I, Ryrcroft S, Scott B, Johnson NF, Morris RA, Sautter G, Chavan V, Robertson T, Remsen D, Stoev P, Parr C, Knapp S, Kress WJ, Thompson CF, Erwin T, Zookeys 2010 50 1 16 http://www.ncbi.nlm.nih. gov/pubmed/21594113 21594113
33. Adventures in semantic publishing: exemplar semantic enhancements of a research article. Shotton D, Portwin K, Klyne G, Miles A, PLoS Comput Biol 2009 5 1000361 10.1371/journal.pcbi.1000361 19381256
34. Franz ingelfingers legacy shaped biology publishing. Marshall E, Science 1998 282 861 9841429
35. Genomic data from Escherichia coli O104:H4 isolate TY-2482. Li D, Xi F, Zhao M, Chen W, Cao S, Xu R, Wang G, Wang J, Zhang Z, Li Y, Cui C, Chang C, Cui C, Luo Y, Qin J, Li S, Li J, Peng Y, Pu F, Sun Y, Chen Y, Zong Y, Ma X, Yang X, Cen Z, Song Y, Zhao X, Chen F, Yin X, Rohde H, Liang Y, Li Y, the Escherichia coli O104:H4 TY-2482 isolate genome sequencing consortium, BGI Shenzhen 2011 http://dx.doi.org/10.5524/100001
36. Open-Source Genomic Analysis of Shiga-Toxin-ProducingE. coliO104:H4. Rohde H, Qin J, Cui Y, Li D, Loman NJ, Hentschke M, Chen W, Pu F, Peng Y, Li J, Xi F, Li S, Li Y, Zhang Z, Yang X, Zhao M, Wang P, Guan Y, Cen Z, Zhao X, Christner M, Kobbe R, Loos S, Oh J, Yang L, Danchin A, Gao GF, Song Y, Li Y, Yang H, Wang J, Xu J, Pallen MJ, Wang J, Aepfelbacher M, Yang R, N Engl J Med 2011 365 718 724 http://www.ncbi.nlm.nih.gov/pubmed/21793736 10.1056/NEJMoa1107643 21793736
37. CC0. http://creativecommons.org/choose/zero/
38. Genome Sequence of E. coli O104:H4 Leads to Rapid Development of a Targeted Antimicrobial Agent against This Emerging Pathogen. Scholl D, Gebhart D, Williams SR, Bates A, Mandrell R, PLoS ONE 2012 7 33637 10.1371/journal.pone. 0033637 22432037
39. Genomic data from the Chinese Rhesus Macaque (Macaca mulatta lasiota). Yan G, Zhang G, Fang X, Zhang Y, Li C, Ling F, Cooper DN, Li O, Li Y, van Gool AJ, Du H, Chen J, Chen R, Zhang P, Huang Z, Thompson JR, Meng Y, Bai Y, Wang J, Zhuo M, Wang T, Huang Y, Wei L, Li J, Wang Z, Hu H, Le L, Stenson PD, Li B, Liu X, Ball EV, An N, Huang Q, Zhang Y, Fan W, Zhang X, Li Y, Wang W, Katze MG, Su B, Nielsen R, Yang H, Wang J, Wang X, Wang J, GigaScience 2011 http://dx.doi.org/10.5524/100002
40. Genomic data from the Crab Eating Macaque/Cynomolgus Monkey (Macaca fascicularis). Yan G, Zhang G, Fang X, Zhang Y, Li C, Ling F, Cooper DN, Li O, Li Y, van Gool AJ, Du H, Chen J, Chen R, Zhang P, Huang Z, Thompson JR, Meng Y, Bai Y, Wang J, Zhuo M, Wang T, Huang Y, Wei L, Li J, Wang Z, Hu H, Le L, Stenson PD, Li B, Liu X, Ball EV, An N, Huang Q, Zhang Y, Fan W, Zhang X, Li Y, Wang W, Katze MG, Su B, Nielsen R, Yang H, Wang J, Wang X, Wang J, GigaScience 2011 http://dx.doi.org/10.5524/100003
41. Genome sequencing and comparison of two nonhuman primate animal models, the cynomolgus and Chinese rhesus macaques. Yan G, Zhang G, Fang X, Zhang Y, Li C, Ling F, Cooper DN, Li Q, Li Y, van Gool AJ, Du H, Chen J, Chen R, Zhang P, Huang Z, Thompson JR, Meng Y, Bai Y, Wang J, Zhuo M, Wang T, Huang Y, Wei L, Li J, Wang Z, Hu H, Yang P, Le L, Stenson PD, Li B, Liu X, Ball EV, An N, Huang Q, Zhang Y, Fan W, Zhang X, Li Y, Wang W, Katze MG, Su B, Nielsen R, Yang H, Wang J, Wang X, Wang J, Nat Biotech 2011 29 1019 1023 10.1038/nbt.1992
42. Ball A, Duke M, How to Cite Datasets and Link to Publications. DCC How-to Guides Digital Curation Centre, Edinburgh 2011 http://www.dcc.ac.uk/resources/ how-guides Available online
43. Lepidostroma vilgalysii, a new basidiolichen from the New World. Hodkinson BP, Uehling JK, Smith ME, Mycological Progress 2012 Advance Online Publication
44. Comprehensive analysis of RNA-Seq data reveals extensive RNA editing in a human transcriptome. Peng Z, Cheng Y, Tan BC-M, Kang L, Tian Z, Zhu Y, Zhang W, Liang Y, Hu X, Tan X, Guo J, Dong Z, Liang Y, Bao L, Wang J, Nat Biotech 2012 30 253 260 10.1038/nbt.2122