Location: Bee Research LaboratoryTitle: The i5k Workspace@NAL – enabling genomic data access, visualization, and curation for the i5k community
|TSAVVATAPALLI, VIJAYA - Non ARS Employee|
|LEE, CHIEN-YUEH - National Taiwan University|
|LIN, HAN - National Taiwan University|
|LIN, JUN-WEI - National Taiwan University|
Submitted to: Nucleic Acids Research
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 11/1/2014
Publication Date: 1/28/2015
Citation: Poelchau, M.F., Childers, C., Moore, G.G., Tsavvatapalli, V., Evans, J.D., Lee, C., Lin, H., Lin, J., Hackett, K.J. 2015. The i5k Workspace@NAL – enabling genomic data access, visualization, and curation for the i5k community . Nucleic Acids Research. 43:D714-719.
Interpretive Summary: Honey bees and other insects are key players in agriculture. Insect genome projects play a role in controlling pest insects and improving the survival and agricultural roles of beneficial insects. This database is the most extensive source to date for tools and information related to insect genomics. By comparing beneficial and pest insects in the same place, it will be possible to generate new tools for improving agricultural and for understanding a diverse and important group of organisms.
Technical Abstract: The 5,000 arthropod genomes initiative (i5k) has tasked itself with coordinating the sequencing of 5,000 insect or related arthropod genomes. The resulting influx of data, mostly from small research groups or communities with little bioinformatics experience, will require visualization, dissemination, and curation, preferably from a centralized platform. The i5k Workspace@NAL (http://i5k.nal.usda.gov/) was implemented to help meet the i5k initiative’s genome hosting needs. Any i5k member is encouraged to contact the i5k Workspace with their genome project details. Once submitted, new content will be accessible via organism pages, genome browsers and BLAST search engines, which are implemented via the open-source Tripal framework, a web interface for the underlying Chado database schema. We also implement the Web Apollo software for groups that choose to curate gene models. New content will add to the existing body of 33 arthropod species, which include species relevant for many aspects of arthropod genomic research, including agriculture, invasion biology, systematics, ecology and evolution, and developmental research.