引用本文:潘恺,郭志英,刘杰,王昌昆,宋歌,贾仲君,潘贤章.中国土壤微生物组数据平台的构建与实现[J].土壤学报,2019,56(5):1023-1033.
PAN Kai,GUO Zhiying,LIU Jie,WANG Changkun,SONG Ge,JIA Zhongjun,PAN Xianzhang.Building and Materializing of China Soil Microbiome Data Platform[J].Acta Pedologica Sinica,2019,56(5):1023-1033
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中国土壤微生物组数据平台的构建与实现
潘恺, 郭志英, 刘杰, 王昌昆, 宋歌, 贾仲君, 潘贤章
中国科学院南京土壤研究所
摘要:
近年来,高通量测序等新技术的快速发展,为大规模、快速、准确、全面认识土壤微生物多样性提供了技术保障。国际上已经建成了一些具有影响力的土壤微生物组数据管理及分析平台,但大多数已有平台聚焦于提供数据存储、管理、访问、注释等基础性服务,难以满足土壤微生物研究需求。借助空间数据库技术、网络地理信息系统(WebGIS)技术,设计并构建了包含土壤及微生物数据集成、数据可视化、知识发现和区域空间制图等功能的中国土壤微生物组数据平台,该平台将进一步推动我国土壤微生物组数据的标准化整合,并为整合数据的充分挖掘利用提供支撑。
关键词:  土壤微生物组数据  数据可视化  微生物多样性  空间分布制图
DOI:10.11766/trxb201812240642
分类号:
基金项目:中国科学院战略性先导科技专项(B类)(XDB15040300)、中国科学院信息化专项(XXH13506-102)
Building and Materializing of China Soil Microbiome Data Platform
PAN Kai, GUO Zhiying, LIU Jie, WANG Changkun, SONG Ge, JIA Zhongjun, PAN Xianzhang
Institute of Soil Science,Chinese Academy of Sciences
Abstract:
【Objective】 Soil is one of the most diversified habitats on earth. It contains not only some large organisms, such as nematodes, ants or moles, but also a huge number of microbes, such as bacteria and fungi. Traditional methods for studying soil microbial diversity, such as laboratory culture, can be used only to isolate and identify a limited number of soil microbial species. In recent years, the rapid development of new technologies, such as high-throughput sequencing, has provided technical guarantees for large scale, rapid, accurate and comprehensive understanding of soil microbial diversity, and promoted the development of specialized and reference databases in the field of microbiology. A series of soil microbiome platforms for soil microbial data management and analysis have been established throughout the world, such as Greengenes, Unite, Silva, RDP, Ez-Taxon, eggNOG, KEGG, etc., which are commonly used in soil microbiology. However, most of these exiting platforms focus on providing basic services, such as data deposition, management, access, annotation, etc., with little attention to systematic collection and standardized integration of data of the environment, in which soil microorganisms live. So it is still difficult to provide effective models and tools for further exploration of soil microbiology data, such as impacts of environmental factors on soil microbial communities, spatial distribution pattern of soil microbial communities, etc. Beginning in 2014, the Chinese Academy of Sciences implemented the Strategic Priority Research Program(Category B)“China Soil Microbiome Initiative”, of which one of the research objectives is to build a professional data integration and analysis platform for soil microbiome research in China. 【Method】 Based on the integration of soil microbial data and soil environmental factor data at different scales, and with the help of spatial database technology and WebGIS, the China Soil Microbiome Data Platform was designed and constructed to synthesize the services of data integration of soil properties and microbial composition, data visualization, knowledge discovery and regional spatial mapping. 【Result】 In respect of architecture design, the platform adopts B/S-based extensible architecture design, which consists of five layers: infrastructure layer, data resource layer, application support layer, management business layer and user service layer, so as to facilitate the integration of massive data resources yielded by specialized researches, while taking into account sustainable development of the platform in future. In materializing the database, PostgreSQL database is used to replace the traditional "relational database + ArcSDE" model, for it has the advantages of strong scalability, perfect function, good compatibility, high access efficiency, and is more suitable for management of soil microbiome data. In terms of function construction, four functional modules, i.e. data management, data visualization, data analysis and user management, are designed and implemented, which provides the platform with supportive guarantees for continuous data services, and maintenance and updating of data resources. The core functions of the platform, such as data integration, visualization analysis and spatial mapping, are exhibited through demonstration data.【Conclusion】 At present, the platform is open for trial operation. Users can register and log in through a concise page to use the platform data resources and professional model tools. With the data resources continuously enriching and the functions steadily improving, the platform will help further promote standardization and integration of China’s soil microbiome data and support full data mining and application of the integrated data.
Key words:  Soil microbiome data  Data visualization  Microbial diversity  Mapping