IMG/VR Database

Arash Lari

Antonio Porras

General Information

1. Name: [IMG/VR]
2. Type of database: Integrated & Primary Database
3. 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
4. Type of data source: Both primary and secondary data from other curated databases (e.g. [Untiprot]).
5. Organization: [U.S. Department of Energy Joint Genome Institute] is a government (DOE) funded organization that provides publicly available information.
6. Funding sources: Primarily by the DOE Office of Biological and Environmental Research

JGI's expenses breakdown

Scientific Quality

How data is typically represented on a page

1. Does it appear to completely cover its content domain? It does appear to be comprehensive as they claim it to be 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).
2. What species are covered in the database? Viruses are categorized further into their host-associated organisms.
3. Is the database content useful? In the correct hands, e.g. professional researchers, it can be useful as it provides in depth information and data from their own institute and other comprehensive databases. It can be used to answer questions regarding viral genomic information.
4. Is the database content timely? The content itself appears to be updated regularly. However, the data management and analysis system Integrated Microbial Genomes (IMG) was released in 2008. There is a current need for this database in the scientific community as it importantly provides connections to putative hosts and habitat types. It also allows for visualization of meta and primary data on viruses.

References

1. 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].
2. 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].
3. LMU BioDB 2017. (2017). Week 5. Retrieved October 01, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Week_5
4. 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.