Advancing Informatics for Microbiology
Approved by the CODATA 28th General Assembly,Taipei, 2012
Microbes play a key role in the material cycles of Earth. Microbes sustain the homeostasis of the planet and constitute the largest part of its biomass. Microbiologists have studied microbes for hundreds of years, producing new research insights and applications. Many industries—biomedical, agricultural, food, environmental and most recently, energy—have been created based on the different functions of microbes. As a result of this long history of research and industrialization, many microbes have been isolated, characterized and preserved (when possible) in culture collections, although the vast majority of them have yet to be discovered.
Recognizing the value of microbes and the importance of preserving them ex situ for the reproducibility of science and technology, the Organisation for Economic Co-operation and Development (OECD) published a report entitled, "Biological Resource Centres (BRCs) - underpinning the future of life sciences and biotechnology", in 2001. This seminal report pointed out the impacts of biodiversity, genomics and informatics to microbiology and the emerging BRCs and recommended that culture collections evolve toward higher BRC standards.
The developments in the past decade have been even greater than the report foresaw. Since 2001, the observational data of biodiversity have increased very much, sequence data have increased explosively and the capabilities and uses of information technologies have expanded greatly. Therefore, microbiology has also become a data science. BRCs also have to function as data and information repositories to serve CODATA Task Group on Advancing Informatics for Microbiology (TG-AIM) 2 academia, industry and the public. In the age of microbial data diversification and explosion, this proposed CODATA Task Group on Advancing Informatics for Microbiology (TG-AIM) would focus on developing an effective information environment that promotes and sustains microbial research data activities, sharing and use to help advance progress and bridge the gaps within and outside the microbiology communities.
As of early 2011, 586 culture collections in 68 countries have registered in WDCM, submitting 224 online catalogues of cultures including 1.7 million strains. A large amount of microbial resource information, however, remains unregistered and not online. Each culture collection is independently responsible for the maintenance of its own cultured microbes. At present, there is no existing uniform data and information sharing and collecting mechanism, which hinders both the management and statistics of world microbial resources and the potential users’ query and retrieval of information. Therefore, developing a digital, online resource sharing mechanism is an urgent need and a foundational premise for good information management. This should include a mechanism for improving the sharing of microbial strains and pertinent related information, the ability for users to provide feedback after the resource sharing, appropriate intellectual property rights, and other characteristics identified by the Task Group. Moreover, we plan to involve and coordinate experts within the WDCM and outside to formulate data standards. These standards should include the data acquisition process, data quality control, data specification and other requirements for meaningful data sharing. We plan to issue, on behalf of WDCM and CODATA, a global microbiological data and information sharing mechanism and interchange standards.
Recent Activities of the Task Group
(1) Global Catalogue of Microorganisms project:
The increasing demands on culture collections for authenticated, reliable biological material and associated information have paralleled the growth of biotechnology. WFCC Global Catalogue of Microorganisms (GCM) is expected to be a robust, reliable and user-friendly system to help culture collections to manage, disseminate and share the information related to their holdings. It also provides a uniform interface for the scientific and industrial communities to access the comprehensive microbial resource information. http://gcm.wfcc.info/
(2) The symposium of World Data Center for Microorganisms
(3) WDCM Asian Training Course on Management and Application of Microbial Data Resources
Achievements and Impacts of the Task Group Activities