基于Scopus的植物表型组学研究进展分析
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摘要
[目的]文献计量方法可以用于反映和预测科学技术发展的历史和趋势。本文基于科学大数据的计量方法探讨植物表型组学的研究现状,为植物表型组学的发展提供参考。[方法]基于Scopus数据库,分析2013年—2018年9月数据库中植物表型组学及其相关学术产出的文献数量、引用次数、合作单位、研究方向、学术机构和科研团队等信息,利用Sci Val和Cite Space 5.0等统计分析工具,运用可视化数据方法,分析植物表型组学研究领域的发展特点和趋势。[结果]基于Scopus共检索到与植物表型组学研究和应用相关的文献共20 953篇,总被引数217 105,TOP1%高被引论文为2.0%。相关学术产出总被引量TOP10的国家是美国、中国、德国、英国、法国、日本、澳大利亚、西班牙、加拿大和荷兰。相关论文被引总量TOP10的机构分别是中国科学院、法国国家农业研究院、美国农业部、法国国家科学研究院、中国农业科学院、美国康奈尔大学、西班牙高等科学研究委员会、美国加州大学戴维斯分校、法国巴黎萨克莱大学、荷兰瓦赫宁根大学。学术产出最多的学者是德国克斯·普朗克分子植物生理研究所的Alisdair Robert Fernie,共发表58篇植物细胞表型论文,被引1 246次。目前植物表型组学研究的植物种类较少,主要包括拟南芥、水稻、小麦、玉米、番茄和大豆。[结论]作为一个新兴的研究方向,植物表型组学体现出作物栽培、育种、生物学与计算机科学等多学科交叉发展的特性。高通量图像及相关数据分析是现阶段植物表型组学的重要研究方向,主题显著度指数达到98.8%,受关注度极高。
[Objectives]Bibliometric analyses are capable of demonstrating the history and the tendency of scientific and technological development.This article aims to use big scientific data to explore the present status of plant phenomics,based on which sound recommendations could be provided for the development of this emerging research domain.[Methods]Based on academic outputs such as research publications,citations,collaborations,research areas,academic organizations,and authors retrieved from the Scopus database between 2013 and September 2018,statistical analysis tools such as SciV al and CiteS pace 5.0 were applied to quantitatively visualize the development and tendency of plant phenotyping,plant phenomics,and related research areas.[Results]This Scopus-based research has retrieved 20 953 articles that are related to plant phenotyping,plant phenomics,and related applications in plant research,with a total citation of 217 105 and 2.0%of them are TOP1%highly cited papers.According to total citations,the TOP10countries are the United States,China,Germany,the United Kingdom,France,Japan,Australia,Spain,Canada,and the Netherlands.The TOP10 research organizations based on total citations are Chinese Academy of Sciences(CAS),Institut National de la Recherche Agronomique(INRA),the US Department of Agriculture,Centre National de la Recherche Scientifique(CNRS),Chinese Academy of Agricultural Sciences,Cornell University,Spanish National Research Council,University of California at Davis,Universite Paris-Sacly,and Wageningen University&Research.The scholar with the most academic outputs is Alisdair Robert Fernie at the Koch Planck Institute of Molecular Plant Physiology,Germany.He has published 58 papers using plant cellular phenotypes and was cited 1 246 times.At present,plant phenomics research has focused on a number of plant species,including Arabidopsis,rice,wheat,corn,tomato and soybean.[Conclusion]As an emerging research domain,plant phenomics requires interdisciplinary efforts to integrate agriculture,cultivation,breeding,and other plant biological research with computing sciences.In particular,high-throughput image analysis and related data analysis has become an important research theme at the present stage,with the topical saliency index reaches 98.8%,a very high relevance score.
[Objectives]Bibliometric analyses are capable of demonstrating the history and the tendency of scientific and technological development.This article aims to use big scientific data to explore the present status of plant phenomics,based on which sound recommendations could be provided for the development of this emerging research domain.[Methods]Based on academic outputs such as research publications,citations,collaborations,research areas,academic organizations,and authors retrieved from the Scopus database between 2013 and September 2018,statistical analysis tools such as SciV al and CiteS pace 5.0 were applied to quantitatively visualize the development and tendency of plant phenotyping,plant phenomics,and related research areas.[Results]This Scopus-based research has retrieved 20 953 articles that are related to plant phenotyping,plant phenomics,and related applications in plant research,with a total citation of 217 105 and 2.0%of them are TOP1%highly cited papers.According to total citations,the TOP10countries are the United States,China,Germany,the United Kingdom,France,Japan,Australia,Spain,Canada,and the Netherlands.The TOP10 research organizations based on total citations are Chinese Academy of Sciences(CAS),Institut National de la Recherche Agronomique(INRA),the US Department of Agriculture,Centre National de la Recherche Scientifique(CNRS),Chinese Academy of Agricultural Sciences,Cornell University,Spanish National Research Council,University of California at Davis,Universite Paris-Sacly,and Wageningen University&Research.The scholar with the most academic outputs is Alisdair Robert Fernie at the Koch Planck Institute of Molecular Plant Physiology,Germany.He has published 58 papers using plant cellular phenotypes and was cited 1 246 times.At present,plant phenomics research has focused on a number of plant species,including Arabidopsis,rice,wheat,corn,tomato and soybean.[Conclusion]As an emerging research domain,plant phenomics requires interdisciplinary efforts to integrate agriculture,cultivation,breeding,and other plant biological research with computing sciences.In particular,high-throughput image analysis and related data analysis has become an important research theme at the present stage,with the topical saliency index reaches 98.8%,a very high relevance score.
引文
[1]周济,Tardieu F,Pridmore T,等.植物表型组学:发展、现状与挑战[J].南京农业大学学报,2018,41(4):580-588.DOI:10.7685/jnau.201805100.Zhou Ji,Tardieu F,Pridmore T,et al.Plant phenomics:history,present status and challenges[J].Journal of Nanjing Agricultural University,2018,41(4):580-588(in Chinese with English abstract).
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[5]李宏,韦晓兰.表型组学:解析基因型-表型关系的科学[J].生物技术通报,2013(7):41-47.Li H,Wei X L.Phenomics:a science of unravelling the genotype-phenotype relationship[J].Biotechnology Bulletin,2013(7):41-47(in Chinese with English abstract).
[6]Pieruschka R,Poorter H.Phenotyping plants:genes,phenes and machines introduction[J].Funct Plant Biol,2012,39:813-820.
[7]Tester M,Langridge P.Breeding technologies to increase crop production in a changing world[J].Science,2010,327(5967):818-822.
[8]Yang W,Duan L,Chen G,et al.Plant phenomics and high-throughput phenotyping:accelerating rice functional genomics using multidisciplinary technologies[J].Curr Opin Plant Biol,2013,16:180-187.
[9]Dhondt S,Wuyts N,Inze D.Cell to whole-plant phenotyping:the best is yet to come[J].Trends Plant Sci,2013,18:433-444.
[10]White J W,Andrade-Sanchez P,Gore M A,et al.Field-based phenomics for plant genetics research[J].Field Crops Res,2012,133:101-112.
[11]潘映红.论植物表型组和植物表型组学的概念和范畴[J].作物学报,2015,41(2):175-186.Pan Y H.Analysis of concepts and categories of plant phenome and phenomics[J].Acta Agronomica Sinica,2015,41(2):175-186(in Chinese with English abstract).
[12]邱均平.信息计量学:第二讲文献信息增长规律与应用[J].情报理论与实践,2000,23(2):153-157.Qiu J P.Informetrics:second talk regularity and application of document information growth[J].Intelligence Theory and Practice,2000,23(2):153-157(in Chinese).
[13]马春晖,张南,周晓丽,等.基于Scopus和Scival的国内外高校食品科学研究现状分析[J].食品科学技术学报,2016,34(4):54-60.Ma C H,Zhang N,Zhou X L,et al.Analysis of research status of food science basing on Scopus and Scival[J].Journal of Food Science and Technology,2016,34(4):54-60(in Chinese with English abstract).
[14]马春晖,戴岳,张南.基于文献计量学的高分子材料领域研究现状及热点分析[J].中国塑料,2017,31(6):8-15.Ma C H,Dai Y,Zhang N.Research status and hot spots of polymer materials based on literature metrology[J].China Plastics,2017,31(6):8-15(in Chinese with English abstract).
[15]孙颉.基于文献计量的国内外柿研究现状分析[J].果树学报,2017,34(6):706-714.Sun J.Current situation of persimmon science and technology in the world based on bibliometrics analysis[J].Journal of Fruit Science,2017,34(6):706-714(in Chinese with English abstract).
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[17]SciVal Official Website[EB/OL].[2018-09-26].http://www.scival.com.
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[21]Klavans R,Boyack K W.Research portfolio analysis and topic prominence[J].Journal of Informetrics,2017,11(4):1158-1174.
[22]段凌凤,杨万能.水稻表型组学研究概况和展望[J].生命科学,2016,28(10):1129-1137.Duan L F,Yang W N.Research advances and future scenarios of rice phenomics[J].Chinese Bulletin of Life Sciences,2016,28(10):1129-1137(in Chinese with English abstract).
[23]钟义信.人工智能的突破与科学方法的创新[J].模式识别与人工智能,2012,25(3):456-461.Zhong Y X.Breakthroughs in artificial intelligence and innovation in methodology[J].Pattern Recognition and Artificial Intelligence,2012,25(3):456-461(in Chinese with English abstract).
[24]Daniel R,Frederic B,Claude W,et al.What is cost-efficient phenotyping?Optimizing costs for different scenarios[J].Plant Science(on line),2018.10.1016/j.plantsci.2018.06.015.
[25]Furbank R T,Tester M.Phenomics-technologies to relieve the phenotyping bottleneck[J].Trends Plant Sci,2011,16(12):635-644.
[26]Fiorani F,Schurr U.Future scenarios for plant phenotyping[J].Annu Rev Plant Biol,2013,64:267-291.
[27]Cendrero-Mateo M P,Muller O,Albrecht H,et al.Terrestrial ecosystem research infrastructures:challenges and opportunities[EB/OL].[2018-10-12].http://www.crcnetbase.com/doi/10.1201/9781315368252-4.
[28]Tardieu F,Cabrera-Bosquet L,Pridmore T,et al.Plant phenomics,from sensors to knowledge[J].Current Biology 2017,27(15):770-783.
[2]Gowen C M,Fong S S.Phenome analysis of microorganisms[J].Bioinformatics,2009,79(10):279-292.
[3]Niculescu A B,Kelsoe J R.Finding genes for bipolar disorder in the functional genomics era:from convergent functional genomics to phenomics and back[J].CNS Spectrums,2002,7(3):215-216.
[4]Finkel E.With“Phenomics”,plant scientists hope to shift breeding into overdrive[J].Science,2009,325(5939):380-381.
[5]李宏,韦晓兰.表型组学:解析基因型-表型关系的科学[J].生物技术通报,2013(7):41-47.Li H,Wei X L.Phenomics:a science of unravelling the genotype-phenotype relationship[J].Biotechnology Bulletin,2013(7):41-47(in Chinese with English abstract).
[6]Pieruschka R,Poorter H.Phenotyping plants:genes,phenes and machines introduction[J].Funct Plant Biol,2012,39:813-820.
[7]Tester M,Langridge P.Breeding technologies to increase crop production in a changing world[J].Science,2010,327(5967):818-822.
[8]Yang W,Duan L,Chen G,et al.Plant phenomics and high-throughput phenotyping:accelerating rice functional genomics using multidisciplinary technologies[J].Curr Opin Plant Biol,2013,16:180-187.
[9]Dhondt S,Wuyts N,Inze D.Cell to whole-plant phenotyping:the best is yet to come[J].Trends Plant Sci,2013,18:433-444.
[10]White J W,Andrade-Sanchez P,Gore M A,et al.Field-based phenomics for plant genetics research[J].Field Crops Res,2012,133:101-112.
[11]潘映红.论植物表型组和植物表型组学的概念和范畴[J].作物学报,2015,41(2):175-186.Pan Y H.Analysis of concepts and categories of plant phenome and phenomics[J].Acta Agronomica Sinica,2015,41(2):175-186(in Chinese with English abstract).
[12]邱均平.信息计量学:第二讲文献信息增长规律与应用[J].情报理论与实践,2000,23(2):153-157.Qiu J P.Informetrics:second talk regularity and application of document information growth[J].Intelligence Theory and Practice,2000,23(2):153-157(in Chinese).
[13]马春晖,张南,周晓丽,等.基于Scopus和Scival的国内外高校食品科学研究现状分析[J].食品科学技术学报,2016,34(4):54-60.Ma C H,Zhang N,Zhou X L,et al.Analysis of research status of food science basing on Scopus and Scival[J].Journal of Food Science and Technology,2016,34(4):54-60(in Chinese with English abstract).
[14]马春晖,戴岳,张南.基于文献计量学的高分子材料领域研究现状及热点分析[J].中国塑料,2017,31(6):8-15.Ma C H,Dai Y,Zhang N.Research status and hot spots of polymer materials based on literature metrology[J].China Plastics,2017,31(6):8-15(in Chinese with English abstract).
[15]孙颉.基于文献计量的国内外柿研究现状分析[J].果树学报,2017,34(6):706-714.Sun J.Current situation of persimmon science and technology in the world based on bibliometrics analysis[J].Journal of Fruit Science,2017,34(6):706-714(in Chinese with English abstract).
[16]Scopus Official Website[EB/OL].[2018-09-26].http://www.scopus.com.
[17]SciVal Official Website[EB/OL].[2018-09-26].http://www.scival.com.
[18]侯剑华,胡志刚.CiteSpace软件应用研究的回顾与展望[J].现代情报,2013,33(4):99-103.Hou J H,Hu Z G.Review on the application of CiteSpace at home and abroad[J].Journal of Modern Information,2013,33(4):99-103(in Chinese with English abstract).
[19]orbit Patent Retrieval Platform[EB/OL].[2018-09-26].https://www.orbit.com.
[20]Small H,Boyack K W,Klavans R.Identifying emerging topics in science and technology[J].Research Policy,2014,43(8):1450-1467.
[21]Klavans R,Boyack K W.Research portfolio analysis and topic prominence[J].Journal of Informetrics,2017,11(4):1158-1174.
[22]段凌凤,杨万能.水稻表型组学研究概况和展望[J].生命科学,2016,28(10):1129-1137.Duan L F,Yang W N.Research advances and future scenarios of rice phenomics[J].Chinese Bulletin of Life Sciences,2016,28(10):1129-1137(in Chinese with English abstract).
[23]钟义信.人工智能的突破与科学方法的创新[J].模式识别与人工智能,2012,25(3):456-461.Zhong Y X.Breakthroughs in artificial intelligence and innovation in methodology[J].Pattern Recognition and Artificial Intelligence,2012,25(3):456-461(in Chinese with English abstract).
[24]Daniel R,Frederic B,Claude W,et al.What is cost-efficient phenotyping?Optimizing costs for different scenarios[J].Plant Science(on line),2018.10.1016/j.plantsci.2018.06.015.
[25]Furbank R T,Tester M.Phenomics-technologies to relieve the phenotyping bottleneck[J].Trends Plant Sci,2011,16(12):635-644.
[26]Fiorani F,Schurr U.Future scenarios for plant phenotyping[J].Annu Rev Plant Biol,2013,64:267-291.
[27]Cendrero-Mateo M P,Muller O,Albrecht H,et al.Terrestrial ecosystem research infrastructures:challenges and opportunities[EB/OL].[2018-10-12].http://www.crcnetbase.com/doi/10.1201/9781315368252-4.
[28]Tardieu F,Cabrera-Bosquet L,Pridmore T,et al.Plant phenomics,from sensors to knowledge[J].Current Biology 2017,27(15):770-783.