Video Tip of the Week: Big Changes to NCBI’s Genome Resources


NCBI was created in 1988 and has maintained the GenBank database for years. They also provide many computational resources and data retrieval systems for many types of biological data. As such they know all too well how quickly the data that biologists collect has changed and expanded. As uses for various data types have been developed, it has become obvious that new types of information (such as expanded metadata) need to be collected, and new ways of handling data are required.

NCBI has been adapting to such needs throughout the years and recently has been adapting its genome resources. Today’s tip will be based on some of those changes. My video will focus on the “completely redesigned Genome site”, which was recently rolled out and announced in the most recent NCBI newsletter. I haven’t found a publication describing the changes, but the newsletter goes into some detail and the announcement found at the top of the Genome site (& that I point out in the video) has very helpful details about the changes.

As you will see in the announcement, the Genome resource is not the only related resource to have undergone changes recently, including the redesign of the Genome Project resource into the BioProject resource and the creation of the BioSample resource. I won’t have time to go into detail about those two resources but at the end of my post I will link to two recent NCBI publications that came out in Nucleic Acids Research this month – these are good resources to read for more information on BioProject, BioSample, and on the NCBI as a whole. For a historical perspective I also link to the original Genome reference, which is in Bioinformatics and currently free to access.

Some of the changes are very interesting, including that “Single genome records now represent an organism and not a genome for one isolate.” The NCBI newsletter states that “Major improvements include a more natural organization at the level of the organism for prokaryotic, eukaryotic, and viral genomes. Reports include information about the availability of nuclear or prokaryotic primary genomes as well as organelles and plasmids. ” There’s also a note that “Because of the reorganization to a natural classification system, older genome identifiers are no longer valid. Typically these genome identifiers were not exposed in the previous system and were used mainly for programmatic access. ” That makes me wonder what changes this will mandate to other NCBI’s resources, as well as external resources. I haven’t seen any announcements on that yet, so I’ll just have to stay tuned & check around often.

Enjoy the tip & let us, or NCBI, know what you think of their changes! :)

Quick Links:

NCBI Homepage: http://www.ncbi.nlm.nih.gov/

Entrez Genome Resource Homepage: http://www.ncbi.nlm.nih.gov/genome

BioProject Resource Homepage: http://www.ncbi.nlm.nih.gov/bioproject/

References:

Historic Entrez Genome reference: Tatusova, T., Karsch-Mizrachi, I., & Ostell, J. (1999). Complete genomes in WWW Entrez: data representation and analysis Bioinformatics, 15 (7), 536-543 DOI: 10.1093/bioinformatics/15.7.536

Barrett, T., Clark, K., Gevorgyan, R., Gorelenkov, V., Gribov, E., Karsch-Mizrachi, I., Kimelman, M., Pruitt, K., Resenchuk, S., Tatusova, T., Yaschenko, E., & Ostell, J. (2011). BioProject and BioSample databases at NCBI: facilitating capture and organization of metadata Nucleic Acids Research DOI: 10.1093/nar/gkr1163

Sayers, E., Barrett, T., Benson, D., Bolton, E., Bryant, S., Canese, K., Chetvernin, V., Church, D., DiCuccio, M., Federhen, S., Feolo, M., Fingerman, I., Geer, L., Helmberg, W., Kapustin, Y., Krasnov, S., Landsman, D., Lipman, D., Lu, Z., Madden, T., Madej, T., Maglott, D., Marchler-Bauer, A., Miller, V., Karsch-Mizrachi, I., Ostell, J., Panchenko, A., Phan, L., Pruitt, K., Schuler, G., Sequeira, E., Sherry, S., Shumway, M., Sirotkin, K., Slotta, D., Souvorov, A., Starchenko, G., Tatusova, T., Wagner, L., Wang, Y., Wilbur, W., Yaschenko, E., & Ye, J. (2011). Database resources of the National Center for Biotechnology Information Nucleic Acids Research DOI: 10.1093/nar/gkr1184