Dataset Information

Current and future resources for functional metagenomics.

ABSTRACT: Functional metagenomics is a powerful experimental approach for studying gene function, starting from the extracted DNA of mixed microbial populations. A functional approach relies on the construction and screening of metagenomic libraries-physical libraries that contain DNA cloned from environmental metagenomes. The information obtained from functional metagenomics can help in future annotations of gene function and serve as a complement to sequence-based metagenomics. In this Perspective, we begin by summarizing the technical challenges of constructing metagenomic libraries and emphasize their value as resources. We then discuss libraries constructed using the popular cloning vector, pCC1FOS, and highlight the strengths and shortcomings of this system, alongside possible strategies to maximize existing pCC1FOS-based libraries by screening in diverse hosts. Finally, we discuss the known bias of libraries constructed from human gut and marine water samples, present results that suggest bias may also occur for soil libraries, and consider factors that bias metagenomic libraries in general. We anticipate that discussion of current resources and limitations will advance tools and technologies for functional metagenomics research.

SUBMITTER: Lam KN

PROVIDER: S-EPMC4625089 | biostudies-literature | 2015

REPOSITORIES: biostudies-literature

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Current and future resources for functional metagenomics.

Lam Kathy N KN Cheng Jiujun J Engel Katja K Neufeld Josh D JD Charles Trevor C TC

Frontiers in microbiology 20151029

Functional metagenomics is a powerful experimental approach for studying gene function, starting from the extracted DNA of mixed microbial populations. A functional approach relies on the construction and screening of metagenomic libraries-physical libraries that contain DNA cloned from environmental metagenomes. The information obtained from functional metagenomics can help in future annotations of gene function and serve as a complement to sequence-based metagenomics. In this Perspective, we b ...[more]

PMID: 26579102

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Project description:Effective research, education, and outreach efforts by the Arabidopsis thaliana community, as well as other scientific communities that depend on Arabidopsis resources, depend vitally on easily available and publicly-shared resources. These resources include reference genome sequence data and an ever-increasing number of diverse data sets and data types. TAIR (The Arabidopsis Information Resource) and Araport (originally named the Arabidopsis Information Portal) are community informatics resources that provide tools, data, and applications to the more than 30,000 researchers worldwide that use in their work either Arabidopsis as a primary system of study or data derived from Arabidopsis. Four years after Araport's establishment, the IAIC held another workshop to evaluate the current status of Arabidopsis Informatics and chart a course for future research and development. The workshop focused on several challenges, including the need for reliable and current annotation, community-defined common standards for data and metadata, and accessible and user-friendly repositories/tools/methods for data integration and visualization. Solutions envisioned included (a) a centralized annotation authority to coalesce annotation from new groups, establish a consistent naming scheme, distribute this format regularly and frequently, and encourage and enforce its adoption. (b) Standards for data and metadata formats, which are essential, but challenging when comparing across diverse genotypes and in areas with less-established standards (e.g., phenomics, metabolomics). Community-established guidelines need to be developed. (c) A searchable, central repository for analysis and visualization tools. Improved versioning and user access would make tools more accessible. Workshop participants proposed a "one-stop shop" website, an Arabidopsis "Super-Portal" to link tools, data resources, programmatic standards, and best practice descriptions for each data type. This must have community buy-in and participation in its establishment and development to encourage adoption.

Project description:BackgroundStrengthening the national health information system is one of Ethiopia's priority transformation agendas. A well-trained and competent workforce is the essential ingredient to a strong health information system. However, this workforce has neither been quantified nor characterized well, and there is no roadmap of required human resources to enhance the national health information system.ObjectiveWe aimed to determine the current state of the health information system workforce and to forecast the human resources needed for the health information system by 2030.MethodsWe conducted a survey to estimate the current number of individuals employed in the health information system unit and the turnover rate. Document review and key-informant interviews were used to collect current human resources and available health information system position data from 110 institutions, including the Ministry of Health, federal agencies, regional health bureaus, zonal health departments, district health offices, and health facilities. The Delphi technique was used to forecast human resources required for the health information system in the next ten years: 3 rounds of workshops with experts from the Ministry of Health, universities, agencies, and regional health bureaus were held. In the first expert meeting, we set criteria, which was followed by expert suggestions and feedback.ResultsAs of April 2020, there were 10,344 health information system professionals working in the governmental health system. Nearly 95% (20/21) of district health offices and 86.7% (26/30) of health centers reported that the current number of health information system positions was inadequate. In the period from June 2015 to June 2019, health information technicians had high turnover (48/244, 19.7%) at all levels of the health system. In the next ten years, we estimate that 50,656 health information system professionals will be needed to effectively implement the Ethiopia's national health information system.ConclusionsCurrent health information system-related staffing levels were found to be inadequate. To meet the estimated need of 50,656 multidisciplinary health information system professionals by 2030, the Ministry of Health and regional health bureaus, in collaboration with partners and academic institutions, need to work on retaining existing and training additional health information system professionals.

Dataset Information

Current and future resources for functional metagenomics.

Publications

Current and future resources for functional metagenomics.

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