ARS | Publication request: CROP GENOME DATABASES -- CRITICAL ISSUES

Submitted to: Plant and Animal Genome VX Conference Abstracts
Publication Type: Abstract Only
Publication Acceptance Date: January 11, 2003
Publication Date: January 12, 2003
Citation: POLACCO, M.L., HANCOCK, D., COE JR, E.H., SCHROEDER, S., SANCHEZ-VILLEDA, H., FANG, Z. CROP GENOME DATABASES -- CRITICAL ISSUES. PLANT AND ANIMAL GENOME ABSTRACTS. 2003.

Technical Abstract: Crop genome databases, see www.agron.missouri.edu/bioservers.html of the past decade have had designed and implemented (1) models and schema for the genome and related domains; (2) methodologies for input of data by expert biologists and high-throughput projects; and (3) various text, graphical, and computational interfaces. Key problems that have not been solved are the community curation of data and a high level of database interoperability. Solution of these problems will enormously reduce costs in maintaining information currency and completeness, while making all available public data accessible to discovery tools and harmonious interfaces. Comparative genomics will particularly benefit from interoperability, as will microarray and other functional-genomics areas. Encouraging the community to become engaged in depositing data, when curation tools are available, has yet to be solved. Data interoperability, if defined as a seamless interface and involving complex queries, requires many more tools than are currently available. The current strategies include central warehousing of data from the disparate resources, requiring substantial overhead to maintain currency; a basic level of interoperability, by creating record-to-record links, but with a maze of 'clicking'; and default queries, but with little user definition of queries of interest. Options on the drawing board will be discussed.