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United States Department of Agriculture

Agricultural Research Service

Title: Cotton Databases and Web Resources

item Kohel, Russell
item Yu, John
item Gupta, Piyush - USDA, ARS, SOUTHERN PLAIN
item Agrawal, Rajeev - USDA, ARS, SOUTHERN PLAIN

Submitted to: International Cotton Genome Initiative Workshop
Publication Type: Proceedings
Publication Acceptance Date: January 9, 2002
Publication Date: June 3, 2002

Technical Abstract: There are several web sites for which information is available to the cotton research community. Most of these sites relate to resources developed or available to the research community. Few provide bioinformatic tools, which usually relate to the specific data sets and materials presented in the database. Just as the bioinformatics area is evolving, the available resources reflect this evolution. There are many resources available, some are proprietary, and others are in the public domain. Cotton genomics is developing to the point where the ready availability of bioinformatic tools is in an increasing need for the cotton research community. At this time when the need is more obvious, resources seem to be least available. I would like to review the current situation with cotton database resources by focusing on CottonDB. In the US, The National Plant Genomics System (NPGS), which was to provide the coordination and support for plant genomic databases, apparently no longer exists. The central site that moved from the National Agricultural Library to Cornell University has shut down. This action has required that we have moved CottonDB to our hardware site. What is CottonDB? It was established as an AceDB database, which was the standard established by NPGS. It is desirable as a public domain database for which a dedicated team provides continued development and upgrades. This makes it readily available to the research community, and there is on going support. Currently the platforms on which it operates are being expanded, so that its use is less restricted by hardware requirements. Since we had to move the location of CottonDB, we have the opportunity and responsibility to provide greater support for it. The AceDB format has its unique characteristics that can be intimidating to a new or infrequent user. We have attempted to format CottonDB so that its use is more intuitive to the new or infrequent user. In this process there are some restrictions that limit what we are doing. The first is to operate within the limits of the AceDB format, and equally important are to make it accessible to all browsers. What does CottonDB contain? With the initial development of CottonDB, we tried to include a broad spectrum of information that would consolidate in one place information that cotton researchers would need for their reference. At the time of its development, information for the germplasm collection and National Variety Tests were not available as web sites. So, we included that information. As such information became available on the web, we have provided links for data not in CottonDB. As more genomics data became available it was added with specific attribution to its origin. In this capacity CottonDB is a data archival site. We recognize that more information dynamics is needed. This was the support that was to have been provided by NPGS. So, we need to provide more than just links to other sites. There has to be greater accessibility and exchange of cotton data and information. There need to be available tools with which to work with the data, either by linkages or incorporated into the site. This tool incorporation is of a high priority, and will require greater support to implement.

Last Modified: 4/21/2015
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