Location: Plant Genetics ResearchTitle: POPcorn: An online resource providing access to distributed and diverse maize project data Author
Submitted to: International Journal of Plant Genomics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 11/29/2011
Publication Date: 12/28/2011
Publication URL: http://handle.nal.usda.gov/10113/53976
Citation: Cannon, E.K., Birkett, S.M., Braun, B.L., Kodavali, S., Jennewein, D.M., Yilmaz, A., Antonescu, V., Antonescu, C., Harper, E.C., Gardiner, J.M., Schaeffer, M.L., Campbell, D.A., Andorf, C.M., Andorf, D., Lisch, D., Koch, K.K., McCarty, D.R., Quackenbush, J., Grotewold, E., Lushbough, C.M., Sen, T.Z., Lawrence, C.J. 2011. POPcorn: An online resource providing access to distributed and diverse maize project data. International Journal of Plant Genomics. 2011:Article 923035. Available http://www.hindawi.com/journals/ijpg/2011/923035. Interpretive Summary: Accessing the appropriate data for a researcher can be a major headache given the miriad of web-sites and databases that are currently available. POPcorn is a project that allows researchers to access any maize data relevant to their research from a single location. Information made accessible in this way includes research project descriptions and contact information as well as data indexed by sequence information. When data are indexed by sequence information, the researcher can use a bit of genome or protein sequence as a query against the database to learn whether, e.g., stocks or publications exist that are relevant to research that involves their sequence of interest. The POPcorn resource enables researchers to spend less time evaluating information at the computer and more time doing the experiments that improve our understanding of how to improve maize.
Technical Abstract: Maize researchers cannot easily leverage all available genetic and genomic data because the online locations of all resources are not easy to find and individual project websites must be searched independently. In addition, project websites degrade over time and sometimes disappear entirely. We created an online resource called POPcorn to overcome these challenges in collaboration with the community of maize researchers. POPcorn makes available (1) a centralized, web-accessible resource to search and browse ongoing maize genomics project descriptions, (2) a single, stand-alone tool that uses web services and minimal data warehousing to allow sequence searches carried out at POPcorn to return matches for many offsite projects’ online resources, and (3) a set of tools that enables researchers to migrate their data to MaizeGDB, the long-term model organism database for maize genetic and genomic information. POPcorn is accessible online at http://popcorn.maizegdb.org.