中国生物多样性e-Science平台建设构想

doi:10.3724/SP.J.1003.2010.480

摘要/Abstract

摘要：

本文结合国际生物多样性信息学发展趋势和生物多样性e-Science相关平台, 在分析我国前期工作成果和相关问题的基础上, 提出了基于服务架构(Service-Oriented Architecture, 简称SOA)和国际空间标准服务ISO 19119的中国生物多样性e-Science平台的三层结构(资源层、服务层和应用层), 并对e-Science平台建设的几个重要方向进行阐述: 组建强有力的协调组织、数据规范化和扩展、海量数据存储和计算、本体构建和语义分析、专题分析和领域建模、服务标准和服务内容以及科学社区的建设, 为我国进行生物多样性e-Science平台建设提供理论依据。

关键词: 生物多样性, 生物多样性信息学, e-Science, ISO 19119, 面向服务架构(SOA)

Abstract

Considering analyses of the development of biodiversity informatics techniques, the introduction of related international biodiversity e-Science infrastructure and previous similar achievements, we suggest and describe a biodiversity e-Science infrastructure of China based on SOA and ISO 19119 Standards. Moreover, the major steps in construction of the biodiversity e-Science infrastructure are also introduced, including strong coordination and organization, data standardization and extension, data storage and computation, ontology and semantic web development, thematic analysis and modeling, and service standardization. This architecture can provide references for future construction of biodiversity e-Science infrastructure in China.

Key words: biodiversity, biodiversity informatics, e-Science, ISO 19119, Service-Oriented Architecture

许哲平, 崔金钟, 覃海宁, 马克平 (2010) 中国生物多样性e-Science平台建设构想. 生物多样性, 18, 480-488. DOI: 10.3724/SP.J.1003.2010.480.

Zheping Xu, Jinzhong Cui, Haining Qin, Keping Ma (2010) On the architecture of biodiversity e-Science infrastructure in China. Biodiversity Science, 18, 480-488. DOI: 10.3724/SP.J.1003.2010.480.

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链接本文: https://www.biodiversity-science.net/CN/10.3724/SP.J.1003.2010.480

https://www.biodiversity-science.net/CN/Y2010/V18/I5/480

图/表 2

参考文献 27

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类型 Type	网站名称 Website	主要负责单位 Custodian	网站主要内容 Main content of the website
I. 陆地数据 Terrestrial Data
物种名录 Catalogue	物种2000中国节点 Species 2000 China Node http://www.sp2000.cn/	中科院生物多样性委员会 Biodiversity Committee, Chinese Academy of Sciences (CAS)	2009年版本包括植物34,665种, 动物9,520种 34,665 plant species and 9,520 animal species in 2009 released CD
	中国高等植物名录 Catalogue of Life: Higher Plants in China http://www.cnpc.ac.cn/	中国科学院植物研究所 Institute of Botany, CAS	12万余条植物名录 120 thousand plant species names
	中国动物信息网 Animal Information Network of China http://www.animal.net.cn/	中国科学院动物研究所 Institute of Zoology, CAS	约34,300条物种和5,291条标本记录 about 34,300 animal species names and 5,291 animal specimens
	基础科学生物数据中心 Biological Data Center for Basic Science http://www.bioinfo.cn/	中国科学院微生物研究所 Institute of Microbiology, CAS	包括植物(34,000余种)、动物(30,502种)、微生物(9,169种)编目数据库等 Include 34,000 plant species, 30,502 animal species and 9,169 microbiology species in China
标本 Specimen	中国数字植物标本馆(CVH) Chinese Virtual Herbarium http://www.cvh.org.cn	中国科学院植物研究所 Institute of Botany, CAS	15家植物标本馆的331万份标本, 其中167万份带照片, 180万份含空间信息 15 herbaria, 3.31 million plant specimens (1.67 million specimen photos and 1.8 million records containing geospatial data)
	自然保护区标本平台 Specimen from Nature Reserve http://www.papc.cn/	中国林业科学研究院 The Chinese Academy of Forestry	自然保护区标本55.56万号(动物标本21.1万, 植物标本34.46万) 555.6 thousand specimens from nature reserve(211 thousand animal specimens and 344.6 thousand plant specimens)
	国家岩矿化石标本资源网 National Mineral & Fossil Resource http://www.nimrf.net.cn/	中国地质大学(北京) China University of Geosciences, Beijing	6万件岩矿化石标本信息 60 thousand mineral and fossil specimens
	国家动物数字博物馆 National Digital Animal Museum http://museum.ioz.ac.cn/	中国科学院动物研究所 Institute of Zoology, CAS	150万号生物标本信息, 1万张活体生物图片, 1,200张生物精细解剖图片 1.5 million animal specimen, 10 thousand living photos and 1,200 anatomy pictures
	教学标本资源共享平台 Educational Specimen Resource Center http://mnh.scu.edu.cn/	四川大学 Sichuan University	30多家高校, 共计252.万份动植物标本, 计2.1万张动植物彩色照片 More than 30 universities, 2.52 million plant and animal specimens, 21 thousand living photos
	极地标本资源共享平台 Resource-sharing Platform of Polar Samples http://birds.chinare.org.cn/	中国极地研究中心 The Polar Research Institute of China	来自南北极的6,895个标本描述中英文信息和6,953张标本图片 6,895 specimen with English and Chinese description and 6,953 photos
	GBIF上采自中国的标本 Specimen data collected from China now available on GBIF http://data.gbif.org/countries/CN	GBIF (Global Biodiversity Information Facility)	动物标本21.73万, 植物标本19.1万和微生物标本6,000份 217.3 thousand animal specimens, 191 thousand plant specimens and 6,000 microorganism specimens
	国家农作物种质资源平台 National Crop Germplasm Resources Infrastructure in China http://www.cgris.net/	中国农业科学院作物科学研究所 Institute of Crop Science, Chinese Academy of Agricultural Sciences	实现了2,204个属、13,426个种, 共53.5万份种质资源的网络信息化共享 Information available for 535 thousands accessions of crop germplasm, belonging to 13,426 species and 2,204 genera
文献 Literature	BHL 中国节点 Biodiversity Heritage Library (BHL) China Node http://www.bhl-china.org.cn/	中国科学院生物多样性委员会 Biodiversity Committee of Chinese Academy of Sciences	800多本经典分类书籍, 20多万页, 共计100万物种名称—页码记录, 包括植物分类文献, 少量动物和微生物文献 800 books, 200 thousand pages, about 1 million name-page records, mainly plant literature, several animal and microorganism literature
文献 Literature	中国生命科学文献 Chinese Biological Abstracts http://www.cba.ac.cn/	中国科学院上海生命科学研究院 Shanghai Institutes for Biological Sciences, CAS	800余种源期刊1985年以来的约20万条生物类文献数据 800+ journals, 200 thousand records for biological science from 1985
类型 Type	网站名称 Website	主要负责单位 Custodian	网站主要内容 Main content of the website
图像 Images	中国自然标本馆 Chinese Field Herbarium http://www.cfh.ac.cn/	中国科学院植物研究所 Institute of Botany, CAS	110万张野外植物照片, 其中有40万张得到鉴定 1.1 million plant photos (400 thousand identified)
图像 Images	中国植物图像库 Photo Bank for China Plant http://www.plantphoto.cn/	中国科学院植物研究所 Institute of Botany, CAS	45万张植物彩色照片, 涉及309科, 3,235属, 15,350种 450 thousand photos in 15,350 species, 3,235 genera and 309 families
社区 Community	EOL 中国节点 Encyclopedia of Life, China Node http://www.eolchina.org/	中国科学院生物多样性委员会 Biodiversity Committee, CAS	分植物、动物和微生物三个学科 China Node for Encyclopedia of Life project, aiming at integrating the resource in plant, animal and microorganism
	生物秀 Biology Show http://www.bbioo.com/	上海易秀生物科技有限公司 Shanghai Yixiu Biotechnology Limited Company	20余万社区用户, 已经形成论坛、知识、人才等频道的生物类门户雏形 200 thousand registered users, a large community on biology consisting of forum and knowledge columns
	普兰塔(生物多样性论坛) Biodiversity Forum in China http://www.planta.cn/	中科院植物研究所 Institute of Botany, CAS	1.3万名用户, 主要讨论以植物学为主的生物多样性专业社区 13 thousand registered users, mainly focusing on biodiversity research in plant
野外台站 Field Observatory	中国生态系统研究网络 Chinese Ecosystem Research Network(CERN) http://www.cern.ac.cn/	中国科学院地理与资源科学研究所 Institute of Geography and Natural Resource Science, CAS	由36个长期定位研究站、5个学科分中心和1个综合研究中心所组成 Data from 36 long-term research stations, 5 disciplinary centers and 1 synthesis center
II. 海洋数据 Marine Data
	中国海洋信息网 China Oceanic Information Network http://www.coi.gov.cn/	国家海洋信息中心 The National Marine Data and Information Service	水文数据、海洋生物数据、Near-Goos气象数据、海洋环境监测站数据 Hydrological data, marine biology data, Near-Goos climate data and monitoring station data
	南海海洋科学数据服务平台 South China Sea Scientific Data Service Platform http://www.ocdb.csdb.cn/	中国科学院南海海洋研究所 South China Sea Science Database	南海海洋化学、海洋生物、海洋地质、地球物理、海洋文献资料库等相关数据 Database on marine chemistry, marine biology, marine geology, geophysics and literature for South China Sea
III. 综合数据 Aggregate Data
	中国科技资源共享网 National Scientific & Technique Infrastructure http://www.escience.gov.cn/	国家科技基础条件平台中心 Computer Network Information Center, CAS	标本324万, 动物种质资源9.36万份, 微生物种质资源8.1万份, 植物种质资源8.1万份 3.24 million specimen. Germplasm: animal (93.6 thousand), microorganism (81 thousand) and plant (81 thousand)
	中国科普博览 Science & Museums of China http://www.kepu.net.cn/	中科院计算机网络信息中心 Computer Network Information Center, CAS	国家大型科普网站, 含生物类相关科普知识 National popular science website, including popular biological knowledge

类型 Type	网站名称 Website	主要负责单位 Custodian	网站主要内容 Main content of the website
I. 陆地数据 Terrestrial Data
物种名录 Catalogue	物种2000中国节点 Species 2000 China Node http://www.sp2000.cn/	中科院生物多样性委员会 Biodiversity Committee, Chinese Academy of Sciences (CAS)	2009年版本包括植物34,665种, 动物9,520种 34,665 plant species and 9,520 animal species in 2009 released CD
	中国高等植物名录 Catalogue of Life: Higher Plants in China http://www.cnpc.ac.cn/	中国科学院植物研究所 Institute of Botany, CAS	12万余条植物名录 120 thousand plant species names
	中国动物信息网 Animal Information Network of China http://www.animal.net.cn/	中国科学院动物研究所 Institute of Zoology, CAS	约34,300条物种和5,291条标本记录 about 34,300 animal species names and 5,291 animal specimens
	基础科学生物数据中心 Biological Data Center for Basic Science http://www.bioinfo.cn/	中国科学院微生物研究所 Institute of Microbiology, CAS	包括植物(34,000余种)、动物(30,502种)、微生物(9,169种)编目数据库等 Include 34,000 plant species, 30,502 animal species and 9,169 microbiology species in China
标本 Specimen	中国数字植物标本馆(CVH) Chinese Virtual Herbarium http://www.cvh.org.cn	中国科学院植物研究所 Institute of Botany, CAS	15家植物标本馆的331万份标本, 其中167万份带照片, 180万份含空间信息 15 herbaria, 3.31 million plant specimens (1.67 million specimen photos and 1.8 million records containing geospatial data)
	自然保护区标本平台 Specimen from Nature Reserve http://www.papc.cn/	中国林业科学研究院 The Chinese Academy of Forestry	自然保护区标本55.56万号(动物标本21.1万, 植物标本34.46万) 555.6 thousand specimens from nature reserve(211 thousand animal specimens and 344.6 thousand plant specimens)
	国家岩矿化石标本资源网 National Mineral & Fossil Resource http://www.nimrf.net.cn/	中国地质大学(北京) China University of Geosciences, Beijing	6万件岩矿化石标本信息 60 thousand mineral and fossil specimens
	国家动物数字博物馆 National Digital Animal Museum http://museum.ioz.ac.cn/	中国科学院动物研究所 Institute of Zoology, CAS	150万号生物标本信息, 1万张活体生物图片, 1,200张生物精细解剖图片 1.5 million animal specimen, 10 thousand living photos and 1,200 anatomy pictures
	教学标本资源共享平台 Educational Specimen Resource Center http://mnh.scu.edu.cn/	四川大学 Sichuan University	30多家高校, 共计252.万份动植物标本, 计2.1万张动植物彩色照片 More than 30 universities, 2.52 million plant and animal specimens, 21 thousand living photos
	极地标本资源共享平台 Resource-sharing Platform of Polar Samples http://birds.chinare.org.cn/	中国极地研究中心 The Polar Research Institute of China	来自南北极的6,895个标本描述中英文信息和6,953张标本图片 6,895 specimen with English and Chinese description and 6,953 photos
	GBIF上采自中国的标本 Specimen data collected from China now available on GBIF http://data.gbif.org/countries/CN	GBIF (Global Biodiversity Information Facility)	动物标本21.73万, 植物标本19.1万和微生物标本6,000份 217.3 thousand animal specimens, 191 thousand plant specimens and 6,000 microorganism specimens
	国家农作物种质资源平台 National Crop Germplasm Resources Infrastructure in China http://www.cgris.net/	中国农业科学院作物科学研究所 Institute of Crop Science, Chinese Academy of Agricultural Sciences	实现了2,204个属、13,426个种, 共53.5万份种质资源的网络信息化共享 Information available for 535 thousands accessions of crop germplasm, belonging to 13,426 species and 2,204 genera
文献 Literature	BHL 中国节点 Biodiversity Heritage Library (BHL) China Node http://www.bhl-china.org.cn/	中国科学院生物多样性委员会 Biodiversity Committee of Chinese Academy of Sciences	800多本经典分类书籍, 20多万页, 共计100万物种名称—页码记录, 包括植物分类文献, 少量动物和微生物文献 800 books, 200 thousand pages, about 1 million name-page records, mainly plant literature, several animal and microorganism literature
文献 Literature	中国生命科学文献 Chinese Biological Abstracts http://www.cba.ac.cn/	中国科学院上海生命科学研究院 Shanghai Institutes for Biological Sciences, CAS	800余种源期刊1985年以来的约20万条生物类文献数据 800+ journals, 200 thousand records for biological science from 1985
类型 Type	网站名称 Website	主要负责单位 Custodian	网站主要内容 Main content of the website
图像 Images	中国自然标本馆 Chinese Field Herbarium http://www.cfh.ac.cn/	中国科学院植物研究所 Institute of Botany, CAS	110万张野外植物照片, 其中有40万张得到鉴定 1.1 million plant photos (400 thousand identified)
图像 Images	中国植物图像库 Photo Bank for China Plant http://www.plantphoto.cn/	中国科学院植物研究所 Institute of Botany, CAS	45万张植物彩色照片, 涉及309科, 3,235属, 15,350种 450 thousand photos in 15,350 species, 3,235 genera and 309 families
社区 Community	EOL 中国节点 Encyclopedia of Life, China Node http://www.eolchina.org/	中国科学院生物多样性委员会 Biodiversity Committee, CAS	分植物、动物和微生物三个学科 China Node for Encyclopedia of Life project, aiming at integrating the resource in plant, animal and microorganism
	生物秀 Biology Show http://www.bbioo.com/	上海易秀生物科技有限公司 Shanghai Yixiu Biotechnology Limited Company	20余万社区用户, 已经形成论坛、知识、人才等频道的生物类门户雏形 200 thousand registered users, a large community on biology consisting of forum and knowledge columns
	普兰塔(生物多样性论坛) Biodiversity Forum in China http://www.planta.cn/	中科院植物研究所 Institute of Botany, CAS	1.3万名用户, 主要讨论以植物学为主的生物多样性专业社区 13 thousand registered users, mainly focusing on biodiversity research in plant
野外台站 Field Observatory	中国生态系统研究网络 Chinese Ecosystem Research Network(CERN) http://www.cern.ac.cn/	中国科学院地理与资源科学研究所 Institute of Geography and Natural Resource Science, CAS	由36个长期定位研究站、5个学科分中心和1个综合研究中心所组成 Data from 36 long-term research stations, 5 disciplinary centers and 1 synthesis center
II. 海洋数据 Marine Data
	中国海洋信息网 China Oceanic Information Network http://www.coi.gov.cn/	国家海洋信息中心 The National Marine Data and Information Service	水文数据、海洋生物数据、Near-Goos气象数据、海洋环境监测站数据 Hydrological data, marine biology data, Near-Goos climate data and monitoring station data
	南海海洋科学数据服务平台 South China Sea Scientific Data Service Platform http://www.ocdb.csdb.cn/	中国科学院南海海洋研究所 South China Sea Science Database	南海海洋化学、海洋生物、海洋地质、地球物理、海洋文献资料库等相关数据 Database on marine chemistry, marine biology, marine geology, geophysics and literature for South China Sea
III. 综合数据 Aggregate Data
	中国科技资源共享网 National Scientific & Technique Infrastructure http://www.escience.gov.cn/	国家科技基础条件平台中心 Computer Network Information Center, CAS	标本324万, 动物种质资源9.36万份, 微生物种质资源8.1万份, 植物种质资源8.1万份 3.24 million specimen. Germplasm: animal (93.6 thousand), microorganism (81 thousand) and plant (81 thousand)
	中国科普博览 Science & Museums of China http://www.kepu.net.cn/	中科院计算机网络信息中心 Computer Network Information Center, CAS	国家大型科普网站, 含生物类相关科普知识 National popular science website, including popular biological knowledge