GDR, the Genome Database for Rosaceae, in Chado and Tripal

The Genome Database for Rosaceae (GDR, http:/ ww.rosaceae.org) is the long-standing central repository and data-mining resource for genomics, genetics, and breeding data of Rosaceae, an economically important crop family that includes almond, apple, blackberry, cherry, peach, pear, plum, raspberry, rose, and strawberry. GDR contains whole genome sequences and annotation, unigenes for the family and the genera, gene sequences from NCBI, genetic maps, trait loci, germplasm, marker diversity, breeding and publication data. The predicted genes of the whole genome sequence, unigenes and NCBI genes have been further annotated by homology to genes in other species, InterPro protein domains, GO terms and KEGG pathway terms. Whole genome sequences and annotation including genes, mRNAs, markers, re-sequencing data, NCBI sequences and homologous genes from other species, can be viewed through GBrowse. Pathway data can also be accessed through the GDR Cyc Pathways databases and synteny among the three sequenced genomes can be viewed through GBrowse_Syn. Major effort on curating genetic maps and trait loci has been underway and GDR now contains extensive qualitative and quantitative trait loci and genetic map data. Recently, all data have been moved to Chado, an open-source, ontology-driven and modular schema for biological data. More interfaces has also been developed using Tripal, an efficient and flexible, toolkit for building online biological databases and managing content.  New interface developed in Tripal include updated search and browse pages for gene, sequence, marker, trait loci, diversity and publication. We also developed a new tool for sequence retrieval. For features aligned to a whole genome, users can include a specified number of upstream and downstream bases in the retrieved sequence.