Title |
A standardized workflow for submitting data to the Minimum Information about a Biosynthetic Gene cluster (MIBiG) repository: prospects for research-based educational experiences
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Published in |
Environmental Microbiome, July 2018
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DOI | 10.1186/s40793-018-0318-y |
Pubmed ID | |
Authors |
Samuel C. Epstein, Louise K. Charkoudian, Marnix H. Medema |
Abstract |
Microorganisms utilize complex enzymatic pathways to biosynthesize structurally complex and pharmacologically relevant molecules. These pathways are encoded by gene clusters and are found in a diverse set of organisms. The Minimum Information about a Biosynthetic Gene cluster repository facilitates standardized and centralized storage of experimental data on these gene clusters and their molecular products, by utilizing user-submitted data to translate scientific discoveries into a format that can be analyzed computationally. This accelerates the processes of connecting genes to chemical structures, understanding biosynthetic gene clusters in the context of environmental diversity, and performing computer-assisted design of synthetic gene clusters. Here, we present a Standard Operating Procedure, Excel templates, a tutorial video, and a collection of relevant review literature to support scientists in their efforts to submit data into MiBIG. Further, we provide tools to integrate gene cluster annotation projects into the classroom environment, including workflows and assessment materials. |
X Demographics
Geographical breakdown
Country | Count | As % |
---|---|---|
United States | 4 | 27% |
Mexico | 3 | 20% |
United Kingdom | 2 | 13% |
Denmark | 1 | 7% |
France | 1 | 7% |
Netherlands | 1 | 7% |
Unknown | 3 | 20% |
Demographic breakdown
Type | Count | As % |
---|---|---|
Scientists | 9 | 60% |
Members of the public | 6 | 40% |
Mendeley readers
Geographical breakdown
Country | Count | As % |
---|---|---|
Unknown | 77 | 100% |
Demographic breakdown
Readers by professional status | Count | As % |
---|---|---|
Student > Ph. D. Student | 19 | 25% |
Student > Master | 13 | 17% |
Student > Bachelor | 9 | 12% |
Researcher | 5 | 6% |
Student > Doctoral Student | 3 | 4% |
Other | 6 | 8% |
Unknown | 22 | 29% |
Readers by discipline | Count | As % |
---|---|---|
Biochemistry, Genetics and Molecular Biology | 16 | 21% |
Agricultural and Biological Sciences | 15 | 19% |
Chemistry | 6 | 8% |
Pharmacology, Toxicology and Pharmaceutical Science | 3 | 4% |
Arts and Humanities | 3 | 4% |
Other | 7 | 9% |
Unknown | 27 | 35% |