Submitted to: Nucleic Acids Research
Publication Type: Peer reviewed journal
Publication Acceptance Date: 10/24/2004
Publication Date: 1/4/2005
Citation: Gonzales, M., Archuleta, E., Farmer, A., Gajendran, K., Grant, D.M., Shoemaker, R.C., Beavis, W., Waugh, M. 2005. The legume information resource (lis): an integrated resource for comparative legume biology. Nucleic Acids Research. 33:D660-D665. Interpretive Summary: The vast amount of data being generated by large research projects makes it difficult to efficiently use that data. It is critical to develop methods to manage and sort data or else the data will become lost or not be utilized to maximum benefit. In this report the authors describe a computerized database specializing in genetic data from legumes such as soybean, Lotus and Medicago (relative of alfalfa). The database was developed in collaboration between the National Center for Genome Research and the USDA-Agriculture Research Service. The database allows genetic data to be compared between and among plant species. This database will facilitate interpretation of large amounts of complex data and will aid in decision making involving future research priorities. This database will be valuable to geneticists and students interested in plant genetics.
Technical Abstract: The National Center for Genome Resources (NCGR) is in the third year of a cooperative research agreement with the USDA Agricultural Research Service (ARS) to develop the Legume Information System (LIS:http://www.comparative-legumes.org). LIS is a comparative legume resource integrating genetic and molecular data from multiple species enabling cross-species comparisons. The LIS virtual plant interface allows simplified and intuitive navigation of transcript data from Medicago truncatula, Lotus japonicus, Glycine max, and Aradibopsis thaliana. Transcript libraries are represented as images of plant organs in different developmental stages, which are selected to query the analyzed and annotated data. Complex queries can be accomplished by adding modifiers, keywords and sequence names. LIS also contains annotated genomic data featuring transcript alignments to validate gene predictions as well as motif and similarity analyses. The genomic browser supports comparative analysis via novel dynamic functional annotation comparisons. CMap, developed as part of the GMOD project (http://www.gmod.org/cmap/index.shtml), has been incorporated to support comparative analyses of community linkage and physical map data. LIS is being expanded to incorporate gene expression and biochemical pathways, which will be seamlessly integrated forming knowledge discovery framework.