Building and Materializing of China Soil Microbiome Data Platform

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The Strategic Priority Research Program(Category B)of the Chinese Academy of Sciences, China Soil Microbiome Initiative(XDB15040300) , the Informatization Special Project of CAS(XXH13506-102).

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    【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.

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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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  • Received:December 24,2018
  • Revised:April 12,2019
  • Adopted:May 14,2019
  • Online: July 03,2019
  • Published: