Scratchpads 2.0: a virtual research environment for biodiversity sciences in the Internet era

doi:10.3724/SP.J.1003.2014.14012

Abstract

Abstract:

We describe key features of the Scratchpads 2.0 Virtual Research Environment (VRE), which supports the creation, management and reuse of biodiversity data. This paper provides an introduction to recent developments and status of the Scratchpads 2.0 system, including its technical architecture. Key features include mechanisms to integrate individual research data and online resources, creation and management of multilingual content, license and authorization of system and data content, dynamic tracing of data editing history, research team cooperation, and methods of data paper publication. Important technical features include effective maintenance and installation of the system, ability to build distributed architecture, modularized function and development, and implementation of related information standards. These are put into a context with related biodiversity informatics tools. Scratchpads was designed with accurate role orientation, a deep understanding of taxonomic research requirements, and excellent technical solutions. All of these attributes contribute to Scratchpads’ importance to e-infrastrature in the Internet era for taxonomy, thereby providing us with a promising tool to complete ambitious projects like World Online Flora.

Key words: biodiversity informatics, data-publishing, online flora, virtual research environment

Lisong Wang, Vincent S Smith, Hongrui Zhang, Xianchun Zhang. Scratchpads 2.0: a virtual research environment for biodiversity sciences in the Internet era[J]. Biodiv Sci, 2014, 22(3): 264-276.

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URL: https://www.biodiversity-science.net/EN/10.3724/SP.J.1003.2014.14012

https://www.biodiversity-science.net/EN/Y2014/V22/I3/264

Figures/Tables 8

References 55

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内容分类 Category	站点名称 Name of sites	使用的S2关键功能 Key Scratchpads features used
农业和园艺 Agriculture and horticulture	世界茄科在线 Solanaceae Source (http://solanaceae.myspecies.info/)	植物分类 Botanical taxonomy 野外调查页面 Field work pages BRAHMS 数据导入 BRAHMS data import 物种多媒体 Taxonomic media 协同管理 Collaborator management
动物多样性 Animal biodiversity	非洲鱼类学门户 African Ichthyology Portal (http://africhthy.org/)	多语言支持(英语/法语) Multi-lingual support (English/French) 社区论坛 Community forums 动物分类 Zoological taxonomy 学术文献 Scientific literature 物种多媒体 Taxonomic media
公众科学 Citizen science	硅藻在线 Diatoms Online (http://diatoms.myspecies.info/)	达尔文核心标准 Darwin-core specimen records 动物分类 Zoological taxonomy 多用户博客 Multi-user blogs
保护 Conservation	植物红皮书索引 IUCN Sampled Red List Index for Plants (http://threatenedplants.myspecies.info/)	保护评估 Conservation assessments IUCN数据整合 IUCN data integration 多元植物分类 Multiple botanical classifications 科学文献 Scientific literature
入侵种 Invasive species	认识蚂蚁 Antkey (http://antkey.org/)	多语言支持(英语/中文/印度尼西亚语) Multi-lingual support (English/Chinese/ Indonesian) 解剖学词汇 Anatomical glossary 物种分布图 Species occurence maps
植物多样性 Plant Biodiversity	加拿大和阿拉斯加极地植物区系 Arctic Flora of Canada and Alaska (http://arcticplants.myspecies.info/)	植物分类 Botanical taxonomy 自定义页面 Custom pages 自定义数据内容 Embedded custom content Google地图 Google Maps
专业组织 Society	国际蝽类昆虫学会 The International Heteropterists’ Society (http://ihs.myspecies.info/)	个人群组 Private organisational groups 群组交流工具 Group communication tools 科学文献 Scientific literature 动物分类 Zoological taxonomy 物种多媒体 Taxonomic media
系统学 Systematics	蚊子的分类和编目 Mosquito Taxonomic Inventory (http://mosquito-taxonomic-inventory.info/)	解剖学词汇 Anatomical glossary 动物分类 Zoological taxonomy 物种多媒体 Taxonomic media 图库 Galleries 科学文献 Scientific literature

内容分类 Category	站点名称 Name of sites	使用的S2关键功能 Key Scratchpads features used
农业和园艺 Agriculture and horticulture	世界茄科在线 Solanaceae Source (http://solanaceae.myspecies.info/)	植物分类 Botanical taxonomy 野外调查页面 Field work pages BRAHMS 数据导入 BRAHMS data import 物种多媒体 Taxonomic media 协同管理 Collaborator management
动物多样性 Animal biodiversity	非洲鱼类学门户 African Ichthyology Portal (http://africhthy.org/)	多语言支持(英语/法语) Multi-lingual support (English/French) 社区论坛 Community forums 动物分类 Zoological taxonomy 学术文献 Scientific literature 物种多媒体 Taxonomic media
公众科学 Citizen science	硅藻在线 Diatoms Online (http://diatoms.myspecies.info/)	达尔文核心标准 Darwin-core specimen records 动物分类 Zoological taxonomy 多用户博客 Multi-user blogs
保护 Conservation	植物红皮书索引 IUCN Sampled Red List Index for Plants (http://threatenedplants.myspecies.info/)	保护评估 Conservation assessments IUCN数据整合 IUCN data integration 多元植物分类 Multiple botanical classifications 科学文献 Scientific literature
入侵种 Invasive species	认识蚂蚁 Antkey (http://antkey.org/)	多语言支持(英语/中文/印度尼西亚语) Multi-lingual support (English/Chinese/ Indonesian) 解剖学词汇 Anatomical glossary 物种分布图 Species occurence maps
植物多样性 Plant Biodiversity	加拿大和阿拉斯加极地植物区系 Arctic Flora of Canada and Alaska (http://arcticplants.myspecies.info/)	植物分类 Botanical taxonomy 自定义页面 Custom pages 自定义数据内容 Embedded custom content Google地图 Google Maps
专业组织 Society	国际蝽类昆虫学会 The International Heteropterists’ Society (http://ihs.myspecies.info/)	个人群组 Private organisational groups 群组交流工具 Group communication tools 科学文献 Scientific literature 动物分类 Zoological taxonomy 物种多媒体 Taxonomic media
系统学 Systematics	蚊子的分类和编目 Mosquito Taxonomic Inventory (http://mosquito-taxonomic-inventory.info/)	解剖学词汇 Anatomical glossary 动物分类 Zoological taxonomy 物种多媒体 Taxonomic media 图库 Galleries 科学文献 Scientific literature

数据和元数据标准 Data and metadata standards	说明 Notes
BibTeX, RIS, XML bibliographic citations (export can also be in XML, RTF or Tagged Field)	与各种桌面和在线文献管理工具, 如Endnote, ReferenceManager, BitText和Google Scholar等进行双向数据交换
CSV / XLSX (spreadsheet content)	与电子表格数据如Excel、Access等进行数据交换(需要使用指定的数据模板格式)
Darwin Core Archive and selected extensions	达尔文数据标准, 标本数据交换标准
EXIF, XMP image metadata	图像元数据交换标准
ITIS taxon metadata standard (for taxon names and hierarchies)	ITIS分类群元数据标准(适用于类群学名和分类树)
LUCID (for taxonomic keys)	与鉴定工具LUCID系统的数据交换
Nexus (character data, export only)	与系统发育分析系统或性状矩阵软件的数据交换格式Nexus
Species Profile Model (for taxon descriptions)	TDWG推荐的结构化的物种描述模型标准
XML (export only, selected content in the TaxPub schema, http://www.ncbi.nlm.nih.gov/books/NBK47081/)	NCBI所推荐的与NCBI相关期刊中物种描述的信息标准

数据和元数据标准 Data and metadata standards	说明 Notes
BibTeX, RIS, XML bibliographic citations (export can also be in XML, RTF or Tagged Field)	与各种桌面和在线文献管理工具, 如Endnote, ReferenceManager, BitText和Google Scholar等进行双向数据交换
CSV / XLSX (spreadsheet content)	与电子表格数据如Excel、Access等进行数据交换(需要使用指定的数据模板格式)
Darwin Core Archive and selected extensions	达尔文数据标准, 标本数据交换标准
EXIF, XMP image metadata	图像元数据交换标准
ITIS taxon metadata standard (for taxon names and hierarchies)	ITIS分类群元数据标准(适用于类群学名和分类树)
LUCID (for taxonomic keys)	与鉴定工具LUCID系统的数据交换
Nexus (character data, export only)	与系统发育分析系统或性状矩阵软件的数据交换格式Nexus
Species Profile Model (for taxon descriptions)	TDWG推荐的结构化的物种描述模型标准
XML (export only, selected content in the TaxPub schema, http://www.ncbi.nlm.nih.gov/books/NBK47081/)	NCBI所推荐的与NCBI相关期刊中物种描述的信息标准

序号 No.	主题术语 Items	解释和说明 Description
1	关系 Associations	描述捕食者-被捕食者; 寄主-寄生虫; 传粉, 共生, 互惠, 共栖, 杂交等生物相互关系的信息 Predator-prey; host-parasite, pollinators, symbiosis, mutualism, commensalism, hybridization…
2	行为 Behaviour	描述生物有机体对生物或非生物环境的反应 Cover actions and reactions of organism in relation to its biotic and abiotic environment
3	保护状况 Conservation status	描述物种目前或将来面临绝灭的可能性 A description of the likelihood of the species becoming extinct in the present day or in the near future
4	周期性 Cyclicity	描述物种周期性的特征, 比如物候 A state or condition characterised by regular repetition in time
5	细胞学 Cytology	描述物种的细胞生物学, 例如结构、功能等 Cell biology formation, structure and function of cells
6	特征摘要 Diagnostic description	描述物种与其相似物种的区别性特征 Distinguishing feature of this taxon from its closest relatives
7	疾病 Diseases	描述物种的疾病危害 Diseases of organisms
8	散布 Dispersal	描述物种的散布策略和机制 Dispersal strategies and mechanisms
9	分布 Distribution	描述物种按行政区域或生物地理区域界定的地理分布范围, 可以是全球性分布, 也可以是局部尺度上的分布情况。Cover ranges, e.g., a global range, or a narrower one; may be biogeographical, political or other (e.g., managed areas like conservencies); endemism; native or exotic; ref Darwin Core Geospatial extension.
10	演化 Evolution	描述物种的系统演化信息 Phylogenetic information relating to the taxon
11	一般描述 General description	广泛描述物种的综合信息 A comprehensive description of the characteristics of the taxon
12	遗传学 Genetics	有关物种的遗传信息, 包括染色体信息 Including karyotypes
13	生长 Growth	描述物种的生长速率、参数等 Rate; parameters; allometries.
14	生境 Habitat	描述物种的栖息环境, 包括地表分类(陆地、海洋)以及气候条件、忍耐幅、水平和垂直梯度上的特征 Include realm (e.g. Terrestrial etc) and climatic information (e.g. Boreal); also include requirements and tolerances; horizontal and vertical distribution.
15	立法 Legislation	描述有关该物种的立法情况 Legal regulations or statutes relating to the taxon
16	生活周期 Life cycle	专性发育转换 Obligatory developmental transformations
17	寿命 Life expectancy	描述物种的平均寿命 The average period an organism can be expected to survive
18	相似物种 Look alikes	描述与该物种相似的其他物种, 例如在入侵种群落中 Other taxa that this taxon may be confused with. Common in invasive species communities.
19	管理 Management	描述与物种的立法相关的管理情况, 比如CITES名录 A statement about the level of need to manage a taxon which can be related to a piece of legislation, e.g., a CITES list.
20	迁移 Migration	描述物种定期从一个地点移动到另外一个地点的情况, 例如动物繁殖期间的移动 Periodic movement of organisms from one locality to another (e.g., for breeding).
21	分子生物学 Molecular biology	描述物种的基因、蛋白质、生物化学(例如毒理) Include genomic, proteomic and biochemistry (e.g. toxicity)
22	形态学 Morphology	描述物种的形态特征(也包括解剖特征) The appearance of the taxon; e.g. habit; anatomy (the branch of morphology that deals with structure of animals)
23	生理学 Physiology	描述物种的生理学过程 An account of the physiological processes
24	居群生物学 Population biology	描述物种的丰度信息 Include abundance information
25	管理步骤 Procedures	如何处理某一类群, 已知的威胁是什么? Deal with how you go about managing this taxon; what are the known threats to this taxon?
26	生殖 Reproduction	描述物种的生殖策略、信号和限制条件 Reproduction cues, strategies, restraints.
27	风险评估 Risk statement	描述物种的入侵风险和影响 Include invasiveness, impact
28	体积 Size	描述物种的体积, 例如周长、长、体积、重量 Average size, max, range; type of size (perimeter, length, volume, weight ...)
29	分类群生物学 Taxon biology	描述分类群的生物学特征 An account of the biology of the taxon
30	威胁 Threats	描述物种面临的威胁 The threats to which this taxon is subject
31	趋势 Trends	描述物种的居群是否稳定?是在增长还是下降等信息 An indication of whether a population is stable, or increasing or decreasing.
32	营养策略 Trophic strategy	描述物种在食物网中的位置和食物偏好 Include nutritional aspects, diet, position in food network.
33	用途 Uses	描述物种与人类利用的关系: 参考“经济植物” Relationships to humans; ref Cook “Economic Botany”