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GCM and gcType in 2024: comprehensive resources for microbial strains and genomic data
Guomei Fan1,2,3,4, Qinglan Sun1,2,3,4, Yan Sun1,2,3,4
1Microbial Resource and Big Data Center, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China.
Nucleic Acids Research
|November 5, 2024
Summary
The World Data Center for Microorganisms developed the Global Catalogue of Microorganisms (GCM) and Global Catalogue of Type Strains (gcType) to improve access to microbial resources and data. These platforms enhance data sharing for microbial research and taxonomic studies.
Area of Science:
- Microbiology
- Bioinformatics
- Data Science
Background:
- Microbial culture collections are vital for preserving and distributing microbial strains and associated data.
- Ensuring data findability, accessibility, interoperability, and reusability (FAIR) is crucial for maximizing the impact of microbial resources.
- Existing data platforms require enhancement to effectively link and mine information from diverse microbial resources.
Purpose of the Study:
- To develop and implement integrated platforms for microbial resources, enhancing data utilization.
- To create comprehensive catalogues of microbial strains and type strains with detailed metadata.
- To facilitate data mining and link microbial information with external scientific and patent literature.
Main Methods:
- Development of the Global Catalogue of Microorganisms (GCM) and Global Catalogue of Type Strains (gcType) by the World Data Center for Microorganisms (WDCM).
- Implementation of interactive interfaces for cataloging culture collection holdings and annotating type strain genomes.
- Integration of curated metadata (ecosystems, growth conditions, locations) and a data mining tool linking to public resources, articles, and patents.
Main Results:
- The GCM and gcType currently host 574,422 strains from 154 collections in 51 countries, including 25,980 type species genomes.
- Over 2.7 million articles and 103,000 patents are integrated, linking microbial resources to scientific literature and intellectual property.
- The platforms provide freely accessible, interactive interfaces for exploring microbial data.
Conclusions:
- The GCM and gcType significantly enhance the FAIRness and scientific impact of microbial resources and culture collections.
- These integrated platforms support microbial taxonomic research and provide evidence for the Nagoya Protocol concerning microbial resources and digital sequence information (DSI).
- The developed system offers a valuable, accessible resource for the global scientific community.
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