Difference between revisions of "IMG/VR Database"
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| − | #Does it appear to completely cover its content domain? | + | #'''Does it appear to completely cover its content domain?''' It does appear to be comprehensive as it is the largest publicly available database of isolate reference DNA viruses along with identified viral contigs. The database contains 3908 viral isolates and 264,413 viral contigs (Paez-Espino, et al., 2016). |
| + | #'''What species are covered in the database?''' Viruses are categorized further into their host-associated organisms. | ||
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==Electric Lab Notebook== | ==Electric Lab Notebook== | ||
Revision as of 21:20, 1 October 2017
Contents
General Information
Name: [IMG/VR]
Type of database: Integrated & Primary Database
Biological information: Domain (Microbiome, Bacteria, Archaea, Eukarya, Plasmids, GFragment, Viruses), Genome, Genome Composition, Habitat Type, DNA Nucleotide Composition, Ecosystem, Protein Coding Genes, Families, Chromosome Map
Type of data source: Both primary and secondary data from other curated databases (e.g. [Untiprot]).
Organization: [U.S. Department of Energy Joint Genome Institute] is a government (DOE) funded organization that provides publicly available information.
Funding sources: Primarily by the DOE Office of Biological and Environmental Research
Scientific Quality
- Does it appear to completely cover its content domain? It does appear to be comprehensive as it is the largest publicly available database of isolate reference DNA viruses along with identified viral contigs. The database contains 3908 viral isolates and 264,413 viral contigs (Paez-Espino, et al., 2016).
- What species are covered in the database? Viruses are categorized further into their host-associated organisms.
Electric Lab Notebook
Acknowledgements
References
- DOE Joint Genome Institute. (2017). DOE Joint Genome Institute: A DOE Office of Science User Facility of Lawrence Berkeley National Laboratory. [online] Available at: https://jgi.doe.gov/ [Accessed 1 Oct. 2017].
- Img.jgi.doe.gov. (2017). JGI IMG Home. [online] Available at: https://img.jgi.doe.gov/cgi-bin/vr/main.cgi [Accessed 1 Oct. 2017].
- LMU BioDB 2017. (2017). Week 5. Retrieved October 01, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Week_5
- Paez-Espino, D., Chen, I., Palaniappan, K., Ratner, A., Chu, K., Szeto, E., Pillay, M., Huang, J., Markowitz, V., Nielsen, T., Huntemann, M., K. Reddy, T., Pavlopoulos, G., Sullivan, M., Campbell, B., Chen, F., McMahon, K., Hallam, S., Denef, V., Cavicchioli, R., Caffrey, S., Streit, W., Webster, J., Handley, K., Salekdeh, G., Tsesmetzis, N., Setubal, J., Pope, P., Liu, W., Rivers, A., Ivanova, N. and Kyrpides, N. (2017). IMG/VR: a database of cultured and uncultured DNA Viruses and retroviruses.
