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Open Access Database

Global catalogue of microorganisms (gcm): a comprehensive database and information retrieval, analysis, and visualization system for microbial resources

Linhuan Wu12, Qinglan Sun12, Hideaki Sugawara4, Song Yang12, Yuguang Zhou1, Kevin McCluskey5, Alexander Vasilenko6, Ken-Ichiro Suzuki7, Moriya Ohkuma8, Yeonhee Lee9, Vincent Robert10, Supawadee Ingsriswang11, François Guissart3, Desmeth Philippe3* and Juncai Ma12*

Author Affiliations

1 Institute of Microbiology, Chinese Academy of Sciences, Beijing, China

2 World Data Centre for Microorganisms(WDCM), Beijing, China

3 Belgian Coordinated Collections of Micro-organisms Programme, Belgian Science Policy Office, avenue Louise, 231 1050 Brussels, Belgium

4 National Institute of Genetics, Yata, Mishima 411-8540 Japan

5 Fungal Genetics Stock Center, University of Missouri, Kansas City, Missouri, USA

6 G.K. Skryabin Institute of Biochemistry and Physiology of Microorganisms RAS, Pushchino, Moscow region, Russia

7 Culture Collection Division Biological Resource Center (NBRC), National Institute of Technology and Evaluation (NITE), 2-5-8 Kazusakamatari, Kisarazu-shi, Chiba 292-0818 Japan

8 Japan Collection of Microorganisms/ Microbe Divion, RIKEN BioResource Center, Koyadai 3-1-1, Tsukuba, Ibaraki 305-0074, Japan

9 Seoul Women’s Unviersity/Korea National Research Resource Center, Seoul, Korea

10 CBS-KNAW, Fungal Biodiversity Centre, Uppsalalaan 8, Utrecht, The Netherlands

11 Bioresources Technology Unit, National Center for Genetic Engineering and Biotechnology, 113 Thailand Science Park, KlongLuang, Prathumthani 12120 Thailand

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BMC Genomics 2013, 14:933  doi:10.1186/1471-2164-14-933

Published: 30 December 2013

Abstract

Background

Throughout the long history of industrial and academic research, many microbes have been isolated, characterized and preserved (whenever possible) in culture collections. With the steady accumulation in observational data of biodiversity as well as microbial sequencing data, bio-resource centers have to function as data and information repositories to serve academia, industry, and regulators on behalf of and for the general public. Hence, the World Data Centre for Microorganisms (WDCM) started to take its responsibility for constructing an effective information environment that would promote and sustain microbial research data activities, and bridge the gaps currently present within and outside the microbiology communities.

Description

Strain catalogue information was collected from collections by online submission. We developed tools for automatic extraction of strain numbers and species names from various sources, including Genbank, Pubmed, and SwissProt. These new tools connect strain catalogue information with the corresponding nucleotide and protein sequences, as well as to genome sequence and references citing a particular strain. All information has been processed and compiled in order to create a comprehensive database of microbial resources, and was named Global Catalogue of Microorganisms (GCM). The current version of GCM contains information of over 273,933 strains, which includes 43,436bacterial, fungal and archaea species from 52 collections in 25 countries and regions.

A number of online analysis and statistical tools have been integrated, together with advanced search functions, which should greatly facilitate the exploration of the content of GCM.

Conclusion

A comprehensive dynamic database of microbial resources has been created, which unveils the resources preserved in culture collections especially for those whose informatics infrastructures are still under development, which should foster cumulative research, facilitating the activities of microbiologists world-wide, who work in both public and industrial research centres. This database is available from http://gcm.wfcc.info webcite.

Keywords:
Microbial resources; Data management; Data sharing