Biodiversity Science ›› 2014, Vol. 22 ›› Issue (3): 293-301.doi: 10.3724/SP.J.1003.2014.13269

Special Issue: Community Structure and Patterns of Tropical and Subtropical Forest in China

• Orginal Article • Previous Article     Next Article

Sharing and publishing of biodiversity data: recent trends and future suggestions

Xiaolei Huang*(), Gexia Qiao*()   

  1. Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101
  • Received:2013-12-30 Accepted:2014-05-12 Online:2014-06-04
  • Huang Xiaolei,Qiao Gexia E-mail:huangxl@ioz.ac.cn;qiaogx@ioz.ac.cn

Biodiversity research, conservation practices, natural resource management, and scientific decision-making increasingly depend on the sharing and integration of large amounts of primary data. In recent years, there has been an appeal increased sharing of biodiversity data, however, many scientists actively or passively resist sharing data. Some major cultural and technological obstacles exist among scientists, such as keeping data private to conduct other analyses, conflicts of interests with colleagues, lack of benefits, unfamiliarity with public databases, lack of user-friendly data submission tools, and lack of time and funding. One solution to improve the culture of data sharing is to provide benefits to scientists who share data (e.g. data citations). Recently, some organizations and scientists have advocated data publishing under peer review as a reward mechanism for individuals involved in data creation, management and sharing, and as a way to effectively increase the use and reuse of data. New data journals have been launched to fulfill the function of publishing data. In fact, besides the advocate of scholarly publication of data, an improved joint data archiving policy by databases and scientific journals may be more practically feasible to improve data sharing in a broader sense. In this article we review recent progress in data sharing and publishing and discuss to what extent data papers can boost data sharing and how to define ‘data sharing’ and ‘data publishing’. We also provide suggestions for improving data sharing by individual scientists, data repositories, journals, and funding agencies/institutions.

Key words: data publishing, data paper, data journal, science policy, science reproducibility, ecology, environmental conservation

Fig. 1

A sketch of the data sharing flow, including main participants and determining factors in data sharing. Funding agency spans each stage of the data flow."

Fig. 2

Improved joint data archiving policy for biodiversity databases and scientific journals"

Fig. 3

The conceptual relationship between ‘data sharing’ and ‘data publishing’. Data sharing includes data sharing without publishing (e.g. E-mail, removable disk) and data sharing through publishing (public database, data journal, personal website), i.e., data publishing."

Table 1

Some popular data repositories archiving biodiversity data. More repositories refer to Databib (http://databib.org)"

数据保存机构
Data repository
数据类型和说明
Data type and notes
元数据
Metadata
可引用对象
Citable object
开放程度
Access
GenBank
http://www.ncbi.nlm.nih.gov/genbank
DNA序列; 标准格式
DNA sequences; standard format
要求
Required
序列号
Accession number
开放
Open
Barcode of Life Database (BOLD)
http://www.boldsystems.org
DNA条形码及相关数据; 标准格式
DNA barcodes; standard format
要求
Required
序列号
Accession number
开放
Open
Global Biodiversity Information Facility (GBIF) http://www.gbif.org 物种分布数据; 标准格式
Species occurrence data; standard format
要求
Required

No
开放
Open
TreeBASE
http://www.treebase.org
系统发育树及相关数据
Phylogenetic trees and related data
建议
Suggested

No
开放
Open
Dryad
http://datadryad.org
生态进化出版物相关数据; 无标准格式
Ecology & evolution data associated with publications; no standard format
建议
Suggested
数字对象标识
DOI
开放
Open
figshare
http://figshare.com
任何类型的数据; 无标准格式
Any type of data; no standard format
可选
Optional
数字对象标识
DOI
根据情况
Variable
中国国家标本资源共享平台
China National Specimen Information Infrastructure http://www.nsii.org.cn
标本数据
Specimen data
可选
Optional

No
根据情况
Variable
[1] Alsheikh-Ali AA, Qureshi W, Al-Mallah MH, Loannidis JPA (2011) Public availability of published research data in high-impact journals.PLoS ONE, 6, e24357.
[2] BBSRC (2010) BBSRC Data Sharing Policy.. (accessed 2013-12-20)
[3] Cassey P, Blackburn TM (2006) Reproducibility and repeatability in ecology.BioScience, 56, 958-959.
[4] Chavan V, Penev L (2011) The data paper: a mechanism to incentivize data publishing in biodiversity science.BMC Bioinformatics, 12(Suppl. 15), S2. doi:10.1186/1471-2105- 12-S15-S2
[5] Chavan V, Penev L, Hobern D (2013) Cultural change in data publishing is essential.BioScience, 63, 419-420.
[6] Convention on Biological Diversity (2012) A Review of Barriers to the Sharing of Biodiversity Data and Information, with Recommendations for Eliminating Them.. (accessed 2013-12-20)
[7] Costello MJ, Michener WK, Gahegan M, Zhang ZQ, Bourne PE (2013) Biodiversity data should be published, cited, and peer reviewed.Trends in Ecology and Evolution, 28, 454-461.
[8] Costello MJ, Wieczorek J (2013) Best practice for biodiversity data management and publication.Biological Conservation, doi: 10.1016/j.biocon.2013.10.018.
[9] De Wever A, Schmidt-Kloiber A, Gessner MO, Tockner K (2012) Freshwater journals unite to boost primary biodiversity data publication.BioScience, 62, 529-530.
[10] Giles J (2006) The trouble with replication.Nature, 442, 344-347.
[11] Haddaway N, Pullin A (2013) Evidence-based conservation and evidence-informed policy: a response to Adams & Sandbrook.Oryx, 47, 336-338.
[12] Hampton SE, Strasser CA, Tewksbury JJ, Gram WK, Budden AE, Batcheller AL, Duke CS, Porter JH (2013) Big data and the future of ecology.Frontiers in Ecology and the Environment, 11, 156-162.
[13] Huang XL, Hawkins BA, Lei FM, Miller GL, Favret C, Zhang RL, Qiao GX (2012) Willing or unwilling to share primary biodiversity data: results and implications of an international survey.Conservation Letters, 5, 399-406.
[14] Huang XL, Hawkins BA, Qiao GX (2013) Biodiversity data sharing: will peer-reivewed data papers work?BioScience, 63, 5-6.
[15] Huang XL, Qiao GX (2011) Biodiversity databases should gain support from journals.Trends in Ecology and Evolution, 26, 377-378.
[16] Huang XL, Qiao GX (2012) Biodiversity data sharing is not just about species names: response to Santos and Branco.Trends in Ecology and Evolution, 27, 7-8.
[17] Ma KP (马克平), Lou ZP (娄治平), Su RH (苏荣辉) (2010) Review and outlook of biodiversity research in Chinese Academy of Sciences.Bulletin of Chinese Academy of Sciences(中国科学院院刊), 25, 634-644. (in Chinese with English abstract)
[18] Michener WK, Jones MB (2012) Ecoinformatics: supporting ecology as a data-intensive science.Trends in Ecology and Evolution, 27, 85-93.
[19] National Research Council (2003) Sharing Publication-Related Data and Materials: Responsibilities of Authorship in the Life Sciences. The National Academies Press, Washington, DC.
[20] National Science Foundation (2011) Proposal Award Policies and Procedures Guide. (accessed 2013-12-20)
[21] Penev L, Mietchen D, Chavan V, Hagedorn G, Remsen D, Smith V, Shotton D (2011) Pensoft data publishing policies and guidelines for biodiversity data. (accessed 2013-12-20)
[22] Pullin AS, Salafsky N (2010) Save the whales? Save the rainforest? Save the data!Conservation Biology, 24, 915-917.
[23] Reichman OJ, Jones MB, Schildhauer MP (2011) Challenges and opportunities of open data in ecology.Science, 331, 703-705.
[24] Ryan MJ (2011) Replication in field biology: the case of the frog-eating bat.Science, 334, 1229-1230.
[25] Shapiro JT, Báldi A (2012) Lost locations and the (ir)repeatability of ecological studies.Frontiers in Ecology and the Environment, 10, 235-236.
[26] Stoltzfus A, O'Meara B, Whitacre J, Mounce R, Gillespie EL, Kumar S, Rosauer DF, Vos RA (2012) Sharing and re-use of phylogenetic trees (and associated data) to facilitate synthesis.BMC Research Notes, 5, 574.
[27] Tenopir C, Allard S, Douglass K, Aydinoglu AU, Wu L, Read E, Manoff M, Frame M (2011) Data sharing by scientists: practices and perceptions.PLoS ONE, 6, e21101.
[28] Thessen AE, Patterson DJ (2011) Data issues in the life sciences.Zookeys, 150, 15-51.
[29] Thorpe SE (2013) Scutellista caerulea (Fonscolombe, 1832) (Hymenoptera: Pteromalidae), new to New Zealand for the second time!Biodiversity Data Journal, 1, e959.
[30] van den Eynden V, Corti L, Woollard M, Bishop L, Horton L (2011) Managing and Sharing Data: Best Practice for Researchers. . (accessed 2013-12-20)
[31] Vines TH, Albert AYK, Andrew RL, Débarre F, Bock DG, Franklin MT, Gilbert KJ, Moore JS, Renaut S, Rennison DJ (2014) The availability of research data declines rapidly with article age.Current Biology, 24, 94-97.
[32] Vision TJ (2010) Open data and the social contract of scientific publishing.BioScience, 60, 330-331.
[33] White EP, Baldridge E, Brym ZT, Locey KJ, McGlinn DJ, Supp SR (2013) Nine simple ways to make it easier to (re)use your data.Ideas in Ecology and Evolution, 6(2), 1-10.
[34] Whitlock MC (2011) Data archiving in ecology and evolution: best practices.Trends in Ecology and Evolution, 26, 61-65.
[35] Xu ZP (许哲平), Chen B (陈彬), Wang LS (王利松), Qiao HJ (乔慧捷), Liu FH (刘凤红), Qin HN (覃海宁), Ma KP (马克平) (2014) The development and trends of research on biodiversity informatics. In: The New Biology Yearbook 2013 (新生物学年鉴) (ed. Poo, MM (蒲慕明)), pp. 290-312. Science Press,Beijing. (in Chinese)
[36] Yesson C, Brewer PW, Sutton T, Caithness N, Pahwa JS, Burgess M, Gray WA, White RJ, Jones AC, Bisby FA, Culham A (2007) How global is the global biodiversity information facility?PLoS ONE, 2, e1124.
[37] Zhang J (张健), Chen SB (陈圣宾), Chen B (陈彬), Du YJ (杜彦君), Huang XL (黄晓磊), Pan XB (潘绪斌), Zhang Q (张强) (2013) Citizen science: integrating scientific research, ecological conservation and public participation.Biodiversity Science(生物多样性), 21, 738-749. (in Chinese with English abstract)
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