在线植物志: 网络时代分类学的方法和实践

doi:10.3724/SP.J.1259.2013.00174

摘要/Abstract

摘要： 全球气候变化、环境污染、资源被过度利用、外来物种入侵和生境丧失威胁着地球上物种的生存。分类学研究的主要任务就是在这些物种即将消失之前去发现、记录和认知它们。社会公众、政府决策部门和科学发展本身都对分类学提出了诸多需求。然而, 当前分类学所面临的困境包括认识上的误区、不科学的评价机制、研究队伍的萎缩以及陈旧的知识管理和发布模式等, 这些因素不仅阻碍了分类学的学科发展, 而且也制约了分类学家履行社会责任。利用现代的网络信息技术, 构建一个覆盖分类学研究工作流程、整合已有在线数据资源、满足分类学研究群体、项目和研究机构共同需求的分类学社区网络, 并最终实现分类学的终极目标——在线植物志, 将会极大地改善分类学的知识产出和应用环境, 提升它在当今科学技术发展条件下的竞争力, 使其真正成为一门21世纪的科学。

Abstract: Global change, environmental pollution, over-exploitation, biological invasion, and habitat loss threaten living species of the world. The primary concern of taxonomy is to discover, document, and recognize species before they disappear on the earth. The public, government, and scientific community all have strong knowledge requirements of taxonomy. However, taxonomy is not adequate to fulfill these needs, because of misunderstandings by the scientific community and public, unscientific methods in evaluating scholar contributions by taxonomists, decline in number of professional taxonomists, and outdated ways of knowledge management and publication. In this paper, we consider the implementation of a web-based taxonomy community network, featured by maximum coverage of taxonomic work flow, integration of existing online resources, keeping coordinate among individual researcher, organizations and projects, and finally realize of Online Flora, will partially solve the dilemmas faced by current taxonomic research, improve its environment of knowledge production and reuse, enhance its competition in a changing science and technology landscape, make it becoming a 21 century science.

王利松, 杨永, 张宪春. 在线植物志: 网络时代分类学的方法和实践. 植物学报, 2013, 48(2): 174-183.

Lisong Wang, Yong Yang, Xianchun Zhang. Online Flora: Method and Practice of E-taxonomy. Chinese Bulletin of Botany, 2013, 48(2): 174-183.

导出引用管理器 EndNote|Ris|BibTeX

链接本文: https://www.chinbullbotany.com/CN/10.3724/SP.J.1259.2013.00174

https://www.chinbullbotany.com/CN/Y2013/V48/I2/174

参考文献

Agnarsson I, Kuntner M. (2007). Taxonomy in a Changing World: Seeking Solutions for a Science in Crisis. Systematic Biology, 56: 531-539.
Agosti D. (2006). Biodiversity data are out of local taxonomists' reach. Nature, 439: 392-392.
Agosti D, Johnson NF. (2002). Taxonomists need better access to published data. Nature, 417: 222-222.
Alves RJ, lka, Vianna Filho MDM. (2007). Is classical taxonomy obsolete? Taxon, 56: 287-288.
Berendsohn W, Güntsch A, Hoffmann N, Kohlbecker A, Luther K, Müller A. (2011). Biodiversity information platforms: From standards to interoperability. ZooKeys, 150: 71-87.
Berendsohn WG, Geoffroy M. (2007). Networking taxonomic concepts – uniting without “unitary-ism”. In: Curry G, Humphries C eds. Biodiversity Databases: From Cottage Industry to Industrial Networks. Systematics Association Special. Taylor & Francis, Boca Raton, FL.
Bisby FA, Shimura J, Ruggiero M, Edwards J, Haeuser C. (2002). Taxonomy, at the click of a mouse. Nature, 418: 367.
Blackmore S. (2002). Enviroment: Biodiversity Update- Progress in Taxonomy. Science, 298: 365.
Bowker GC. (2000). Biodiversity Datadiversity. Social Studies of Science, 30: 643-683.
Cigliano MM, Eades D. (2010). New Technologies Challenge the Future of Taxonomy in Orthoptera*. Journal of Orthoptera Research, 19: 15-18.
Clark BR, Godfray HCJ, Kitching IJ, Mayo SJ, Scoble MJ. (2009). Taxonomy as an eScience. Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences, 367: 953-966.
Constance L. (1964). Systematic Botany-An unending synthesis. Taxon, 13: 257.
Davis PH, Heywood VH. (1963). Principles of angiosperm taxonomy, Edinburgh,, Oliver and Boyd.
Drew LW. (2011). Are We Losing the Science of Taxonomy? BioScience, 61: 942-946.
Ebach MC, Holdrege C. (2005). DNA barcoding is no substitute for taxonomy. Nature, 434: 697-697.
Ereshefsky M. (2000). The Poverty of the Linnaean Hierarchy: A Philosophical Study of Biological Taxonomy, Cambridge, Cambridge University Press.
Erwin T, Stoev P, Georgiev T, Penev L. (2011). ZooKeys 150: Three and a half years of innovative publishing and growth. ZooKeys, 150: 5-14.
Franz NM, Peet RK, Weakley AS. (2008). On the use of taxonomic concepts in support of biodiversity research and taxonomy. In: Wheeler QD ed. The New Taxonomy. Systematics Association Special Taylor & Francis, Boca Raton, FL.
Gaston KJ, May RM. (1992). Taxonomy of taxonomists. Nature, 356: 281-282.
Godfray HCJ. (2002). Challenges for taxonomy. Nature, 417: 17-19.
Godfray HCJ. (2005). Taxonomy as Information Science. Proceedings of the Californian Academy of Science, 56 Suppl. I (16): 170-181.
Godfray HCJ. (2007). Linnaeus in the information age Nature 446: 259.
Godfray HCJ, Clark BR, Kitching IJ, Mayo SJ, Scoble MJ. (2007). The Web and the Structure of Taxonomy. Systematic Biology, 56: 943-955.
Godfray HCJ, Knapp S. (2004). Introduction to Theme Issue, "Taxonomy for the 21st Century". Philosophical Transactions of the Royal Society of London. Series B: Biological Sciences, 359: 559-569.
Haigh A, Mayo SJ, Croat T, Reynolds L, Pinto MM, Boyce PC, Lay L, Bogner J, Clark B, Kostelac C, Hay A. (2009). Interactive web-taxonomy for the Araceae: www.cate-araceae.org. Blumea - Biodiversity, Evolution and Biogeography of Plants, 54: 13-15.
Johnson NF. (2007). Biodiversity Informatics. Annual Review of Entomology, 52: 421-438.
Johnson NF. (2012). A collaborative, integrated and electronic future for taxonomy. Invertebrate Systematics, 25: 471-475.
King D, Morse D, Willis A, Dil A. (2011). Towards the bibliography of life. ZooKeys, 150: 151-166.
Knapp S, McNeill J, Turland NJ. (2011). Changes to publication requirements made at the XVIII International Botanical Congress in Melbourne - what does e-publication mean for you? PhytoKeys, 6: 5-11.
Li DZ. (2008). Floristics and Plant Biogeography in China. Journal of Integrative Plant Biology, 50: 771-777.
Li J. (2009). China Searches for an 11th-Hour Lifesaver for a Dying Discipline. Science, 325: 31-31.
Ma J, Clemants S. (2006). A history and overview of the Flora Reipublicae Popularis Sinicae (FRPS, Flora of China, Chinese edition, 1959-2004). Taxon, 55: 451-460.
Martin, T. J, Wheeler QD, Raven PH, Wilson EO. (2004). Taxonomists and Conservation. Science, 305: 1104c-1105.
Mayo SJ. (2008). Alpha e-taxonomy: responses from the systematics community to the biodiversity crisis. Kew Bulletin, 63: 1-16.
MerxmüLler H. (1972). Systematic botany–an unachieved synthesis. Biological Journal of the Linnean Society, 4: 311-321.
Miller G. (2005a). TAXONOMY: Linnaeus's Legacy Carries On. Science, 307: 1038a-1039.
Miller G. (2005b). TAXONOMY: Taxonomy's Elusive Grail. Science, 307: 1038b.
Miller JR. (2005c). Biodiversity conservation and the extinction of experience. Trends in Ecology & Evolution, 20: 430-434.
Mora C, Tittensor DP, Adl S, Simpson AGB, Worm B. (2011). How Many Species Are There on Earth and in the Ocean? PLoS Biol, 9: e1001127.
Page R. (2011). Extracting scientific articles from a large digital archive: BioStor and the Biodiversity Heritage Library. BMC Bioinformatics, 12: 187.
Patterson DJ, Remsen D, Marino WA, Norton C. (2006). Taxonomic Indexing: Extending the Role of Taxonomy. Systematic Biology, 55: 367-373.
Pearson DL, Hamilton AL, Erwin TL. (2011). Recovery Plan for the Endangered Taxonomy Profession. BioScience, 61: 58-63.
Penev L, Kress WJ, Knapp S, Li D-Z, Renner S. (2010). Fast, linked, and open – the future of taxonomic publishing for plants: launching the journal PhytoKeys. PhytoKeys, 1: 1-14.
Raven P. (2004). Taxonomy: where are we now? Philosophical Transactions of the Royal Society B: Biological Sciences, 359: 729-730.
Savolainen V, Cowan RS, Vogler AP, Roderick GK, Lane R. (2005). Towards writing the encyclopaedia of life: an introduction to DNA barcoding. Philosophical Transactions of the Royal Society B: Biological Sciences, 360: 1805-1811.
Scoble M. (2004). Unitary or unified taxonomy? Philosophical Transactions of the Royal Society B: Biological Sciences, 359: 699-710.
Simonetti JA. (1997). Biodiversity and a taxonomy of Chilean taxonomists. Biodiversity and Conservation, 6: 633-637.
Smith G, Figueiredo E. (2010). E-taxonomy: an affordable tool to fill the biodiversity knowledge gap. Biodiversity and Conservation, 19: 829-836.
Smith V, Penev L. (2011). Collaborative electronic infrastructures to accelerate taxonomic research. ZooKeys, 150: 1-3.
Smith V, Rycroft S, Brake I, Scott B, Baker E, Livermore L, Blagoderov V, Roberts D. (2011). Scratchpads 2.0: a Virtual Research Environment supporting scholarly collaboration, communication and data publication in biodiversity science. ZooKeys, 150: 53-70.
Smith V, Rycroft S, Harman K, Scott B, Roberts D. (2009). Scratchpads: a data-publishing framework to build, share and manage information on the diversity of life. BMC Bioinformatics, 10: S6.
Stuessy TF. (1990). Plant taxonomy : the systematic evaluation of comparative data, New York, Columbia University Press.
Stuessy TF. (2009). Plant Taxonomy: The Systematic Evaluation of Comparative Data, 2nd edition., Columbia University Press.
Tillier S, Roberts D. (2006). Taxonomy on the fly in a European web project. Nature, 440: 24-24.
Ung V, Dubus G, Zaragüeta-Bagils R, Vignes-Lebbe R. (2010). Xper2: introducing e-taxonomy. Bioinformatics, 26: 703-704.
Walter DE, Winterton S. (2007). Keys and the Crisis in Taxonomy: Extinction or Reinvention? Annual Review of Entomology, 52: 193-208.
Wang LS, Zhang YC, Xue NX, Qin HN. (2011). Floristics of Higher Plants in China-Report from Catalogue of Life: Higher Plants in China Database. Plant Diversity and Resources, 33: 69-74.
Wheeler QD. (2004). Taxonomic triage and the poverty of phylogeny. Philosophical Transactions of the Royal Society of London. Series B: Biological Sciences, 359: 571-583.
Wheeler QD, Raven PH, Wilson EO. (2004). Taxonomy: Impediment or Expedient? Science, 303: 285.
Wilson EO. (2003). The encyclopedia of life. Trends in Ecology & Evolution, 18: 77-80.
Wilson EO. (2004). Taxonomy as a fundamental discipline. Philosophical Transactions of the Royal Society B: Biological Sciences, 359: 739-739.
Yang QE, Zhu GH, Hong DY, Wu ZY, Raven PH. (2005). World's Largest Flora Completed. Science, 309: 2163b.
Zauner H. (2009). Evolving e-taxonomy. BMC Evolutionary Biology, 9: 141.
中国科学院生物多样性委员会. (2011). 中国高等植物名录. 见.中国生物物种名录-2011版 CD-ROM, 北京, 中国科学院生物多样性委员会,科学出版社.
王文采. (2005). 关于我国植物系统学研究的一些感想和建议. 植物分类学报, 43: 398-402.
王利松, 陈彬, 纪力强, 马克平. (2010). 生物多样性信息学研究进展. 生物多样性, 18: 429-443.
刘全儒, 于明, 马金双. (2007). 中国地方植物志评述. 广西植物, 27: 844-849.
杨亲二. (2001). 过分依赖SCI正在损害我国的传统分类学研究——从《 Nature 》上的两封信说开去. 植物分类学报, 39: 283-288.
马金双. (2011). 东亚高等植物分类学文献概览, 北京, 高等教育出版社.