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Nucleic Acids Res. 2019 Jan 8;47(D1):D637-D648. doi: 10.1093/nar/gky1008.

gcMeta: a Global Catalogue of Metagenomics platform to support the archiving, standardization and analysis of microbiome data.

Shi W1, Qi H1, Sun Q1, Fan G1, Liu S1,2, Wang J3, Zhu B3,4,5,6, Liu H7, Zhao F8, Wang X1, Hu X1, Li W1, Liu J9, Tian Y9, Wu L1,2, Ma J1,2.

Author information

1
Microbial Resource and Big Data Center, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China.
2
State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China.
3
CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Science, Beijing 100101, China.
4
University of Chinese Academy of Sciences, Beijing 100049, China.
5
Collaborative Innovation Centre for Diagnosis and Treatment of Infectious Diseases First Attainted Hospital, College of Medicine, Zhejiang University, Hangzhou 310058, China.
6
Beijing Key Laboratory of Antimicrobial Resistance and Pathogen Genomics, Beijing 100101, China.
7
State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Science, Beijing 100101, China.
8
Computational Genomics Lab, Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing 100101, China.
9
Internet of Things Information Technology and Application Laboratory, Computer Network Information Center, Chinese Academy of Sciences. Beijing 100101, China.

Abstract

Meta-omics approaches have been increasingly used to study the structure and function of the microbial communities. A variety of large-scale collaborative projects are being conducted to encompass samples from diverse environments and habitats. This change has resulted in enormous demands for long-term data maintenance and capacity for data analysis. The Global Catalogue of Metagenomics (gcMeta) is a part of the 'Chinese Academy of Sciences Initiative of Microbiome (CAS-CMI)', which focuses on studying the human and environmental microbiome, establishing depositories of samples, strains and data, as well as promoting international collaboration. To accommodate and rationally organize massive datasets derived from several thousands of human and environmental microbiome samples, gcMeta features a database management system for archiving and publishing data in a standardized way. Another main feature is the integration of more than ninety web-based data analysis tools and workflows through a Docker platform which enables data analysis by using various operating systems. This platform has been rapidly expanding, and now hosts data from the CAS-CMI and a number of other ongoing research projects. In conclusion, this platform presents a powerful and user-friendly service to support worldwide collaborative efforts in the field of meta-omics research. This platform is freely accessible at https://gcmeta.wdcm.org/.

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