Integrating Genetic with Genomic Data in Legume InterMines

The Java data warehouse InterMine, originally developed by the FlyBase group and now co-developed with groups around the world, has focused strictly on genomic data. However, the Legume Information System (USDA) and Legume Federation (NSF) curate genetic data as well. We have built mines for common bean (BeanMine), soybean (SoyMine), peanut (PeanutMine) and multiple species (LegumeMine). We have extended the core InterMine data model to include genetic maps, genetic markers and QTLs, along with a processor that associates QTLs with genes via the genomic positions of flanking markers. We have added diagrams displaying the genetic position of markers and QTLs on linkage groups, with links out to their individual report pages. One can now perform tasks such as selecting genes spanned by the markers of a given QTL and then analyzing them for GO enrichment or co-expression. We will have a computer available at the poster for visitors to explore the Legume Federation mines, which are all linked at mines.legumeinfo.org.