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

作者：Linhuan Wu, Qinglan Sun, Hideaki Sugawara, Song Yang, Yu‐Guang Zhou, Kevin McCluskey, Alexander Vasilenko, Ken‐ichiro Suzuki, Moriya Ohkuma, Yeonhee Lee, Vincent Robert, Supawadee Ingsriswang, François Guissart, Philippe Desmeth, Juncai Ma · 发表于：BMC Genomics · 年份：2013 · DOI：10.1186/1471-2164-14-933 · 被引用次数：55 · 研究领域：Genomics and Phylogenetic Studies、Microbial Community Ecology and Physiology、Bacterial Identification and Susceptibility Testing

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 43,436 bacterial, fungal and archaea species from 52 collections in 25 c...