生物多样性 ›› 2021, Vol. 29 ›› Issue (1): 118-122.  DOI: 10.17520/biods.2020235  cstr: 32101.14.biods.2020235

• 技术与方法 • 上一篇    下一篇

获取生物物种名录信息的R程序包SP2000

丁刘勇1,2(), 李昊3, 陶捐1,2, 张金龙4(), 黄敏睿1,2, 杨科1,2, 王军1,2(), 丁城志1,2,*()(), 何大明1,2,*()   

  1. 1.云南大学国际河流与生态安全研究院, 昆明 650504
    2.云南大学云南省国际河流与跨境生态安全重点实验室, 昆明 650504
    3.云南大学国家示范性软件学院, 昆明 650504
    4.香港嘉道理农场暨植物园植物保育部, 香港 999077
  • 收稿日期:2020-06-11 接受日期:2020-08-12 出版日期:2021-01-20 发布日期:2020-10-22
  • 通讯作者: 丁城志,何大明
  • 基金资助:
    生态环境部生物多样性调查评估项目(2019HJ2096001006);国家重点研发计划(2016YFA0601600);云南大学研究生科研创新基金(2019227)

SP2000: An open-sourced R package for querying the Catalogue of Life

Liuyong Ding1,2(), Hao Li3, Juan Tao1,2, Jinlong Zhang4(), Minrui Huang1,2, Ke Yang1,2, Jun Wang1,2(), Chengzhi Ding1,2,*()(), Daming He1,2,*()   

  1. 1 Institute of International Rivers and Eco-security, Yunnan University, Kunming 650504
    2 Yunnan Key Laboratory of International Rivers and Transboundary Eco-security, Yunnan University, Kunming 650504
    3 National Pilot School of Software, Yunnan University, Kunming 650504
    4 Flora Conservation Department, Kadoorie Farm and Botanic Garden, Hong Kong 999077
  • Received:2020-06-11 Accepted:2020-08-12 Online:2021-01-20 Published:2020-10-22
  • Contact: Chengzhi Ding, Daming He

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摘要：

物种名录为衡量区域和全球生物多样性提供了数据基础。随着互联网的兴起与发展, 人们将地球上已知的动物、植物、微生物等类群的物种名录信息存储到公共数据平台中, 并对物种名录进行快速及时地更新, 这极大地促进了分类学、保护生物学和宏观生态学等学科的发展, 成为政府或国际组织开展物种保育现状评估、红色名录编撰和生物多样性保护的重要依据。物种2000中国节点(http://www.sp2000.org.cn)和Catalogue of Life网站(http://www.catalogueoflife.org)分别是中国和全球最大的生物物种名录数据平台, 截至2020年6月4日, 其收录的物种数分别为122,280种和1,829,672种。然而这些数据平台仅提供物种查询、检索、下载等基本功能, 难以满足使用者准确、快速地批量获取所需生物物种名录数据信息的需求, 制约了这些大数据平台在生物多样性研究和保护中的作用。因此, 我们选取R语言开发了程序包SP2000, 旨在帮助用户批量获取中国或全球生物物种名录信息。该程序包具有跨Windows、MacOS、Linux等多个系统运行、操作便捷、代码开源等特点。为了方便用户使用, 本文详细介绍了SP2000的基本原理、特点及使用指南, 包括程序包的下载、安装、运行和参数设置等。

关键词: 物种名录, 红色名录, 中国生物多样性, R语言程序包

Abstract

Aims: The Catalogue of Life provides the basis for understanding both regional and global biodiversity. With the invention and development of the internet, the up-to-date species checklists stored in the public databases has greatly promoted the development of taxonomy, conservation biology, and macroecology. Public species checklists play an indispensable role in biodiversity conservation and aid in the assessment of species’ conversation status. The Species 2000 China Node (http://www.sp2000.org.cn) and the Catalogue of Life (http://www.catalogueoflife.org) are among the leading online databases in cataloguing biodiversity, contain 122,280 and 1,829,672 taxa respectively (including infraspecific taxa). Although searching the content of the websites may be relatively straightforward, downloading the data and transferring it into a statistical environment for further analysis can present challenges.
Method: To address this issue, we developed the package SP2000 using the R programming language.
Application: SP2000 is an open-source, cross-platform, and user-friendly package which aims to help users query and download the checklist of organisms (including animals, plants, fungi, and microbes) from within and outside China. Here we introduce and describe the usage of SP2000 including installation, and configuration of parameters.

Key words: species checklist, redlist, China’s biodiversity, R package

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