World data centre for microorganisms: an information infrastructure to explore and utilize preserved microbial strains worldwide

Linhuan Wu; Qinglan Sun; Philippe Desmeth; Hideaki Sugawara; Zhenghong Xu; Kevin McCluskey; David Smith; Vasilenko Alexander; Nelson Lima; Moriya Ohkuma; Vincent Robert; Yuguang Zhou; Jianhui Li; Guomei Fan; Supawadee Ingsriswang; Svetlana Ozerskaya; Juncai Ma

doi:10.1093/nar/gkw903

World data centre for microorganisms: an information infrastructure to explore and utilize preserved microbial strains worldwide

Nucleic Acids Res. 2017 Jan 4;45(D1):D611-D618. doi: 10.1093/nar/gkw903. Epub 2016 Oct 7.

Authors

Linhuan Wu^{1

2}, Qinglan Sun¹, Philippe Desmeth³, Hideaki Sugawara⁴, Zhenghong Xu², Kevin McCluskey⁵, David Smith⁶, Vasilenko Alexander⁷, Nelson Lima⁸, Moriya Ohkuma⁹, Vincent Robert¹⁰, Yuguang Zhou¹¹, Jianhui Li¹², Guomei Fan¹, Supawadee Ingsriswang¹³, Svetlana Ozerskaya⁷, Juncai Ma¹⁴

Affiliations

¹ Network information center, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China.
² Key Laboratory of Industrial Biotechnology of Ministry of Education, School of Pharmaceutical Science, Jiangnan University, Wuxi 214122, Jiangsu, China.
³ Belgian Coordinated Collections of Micro-organisms Programme, Belgian Science Policy Office, Brussels 231 1050, Belgium.
⁴ National Institute of Genetics, Yata, Mishima 411-8540, Japan.
⁵ Fungal Genetics Stock Center, University of Missouri- Kansas City, MO, USA.
⁶ CABI, Bakeham Lane, Egham, Surrey TW20 9TY, UK.
⁷ All-Russian Collection of Microorganisms, G.K. Skryabin Institute of Biochemistry and Physiology of Microorganisms RAS, Pushchino, Moscow region 142290, Russia.
⁸ Micoteca da Universidade do Minho, Universidade do Minho Braga, 4710-057, Portugal.
⁹ Japan Collection of Microorganisms/ Microbe Divion, RIKEN BioResource Center, Koyadai 3-1-1, Tsukuba, Ibaraki 305-0074, Japan.
¹⁰ Fungal Biodiversity Centre, Centraalbureau voor Schimmelcultures, Utrecht, Utrecht 3534CT, Netherlands.
¹¹ China General Microbiological Culture Collection Center, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China.
¹² Scientific Data Center, Computer Network Information Center, Chinese Academy of Sciences, Beijing 100190, China.
¹³ Bioresources Technology Unit, National Center for Genetic Engineering and Biotechnology, Bangkok113, Thailand.
¹⁴ Network information center, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China [email protected].

Abstract

The World Data Centre for Microorganisms (WDCM) was established 50 years ago as the data center of the World Federation for Culture Collections (WFCC)-Microbial Resource Center (MIRCEN). WDCM aims to provide integrated information services using big data technology for microbial resource centers and microbiologists all over the world. Here, we provide an overview of WDCM including all of its integrated services. Culture Collections Information Worldwide (CCINFO) provides metadata information on 708 culture collections from 72 countries and regions. Global Catalogue of Microorganism (GCM) gathers strain catalogue information and provides a data retrieval, analysis, and visualization system of microbial resources. Currently, GCM includes >368 000 strains from 103 culture collections in 43 countries and regions. Analyzer of Bioresource Citation (ABC) is a data mining tool extracting strain related publications, patents, nucleotide sequences and genome information from public data sources to form a knowledge base. Reference Strain Catalogue (RSC) maintains a database of strains listed in International Standards Organization (ISO) and other international or regional standards. RSC allocates a unique identifier to strains recommended for use in diagnosis and quality control, and hence serves as a valuable cross-platform reference. WDCM provides free access to all these services at www.wdcm.org.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Biodiversity
Computational Biology / methods*
Data Mining
Databases, Factual*
Metagenomics / methods
Microbiology*
Microbiota*
Phylogeny
Software*
Web Browser
Workflow