Ensembl Plants - an Integrative Resource for Plant Genome Data

Ensembl Plants (http://plants.ensembl.org) is an integrating web portal for genome-scale data from plant species.  The portal offers access to data including reference sequence, gene annotations, RNA and protein alignments, comparative analyses and variation data. In addtion to the web portal, access is also provided through progammatic (Perl and REST-ful) interfaces, a publicly accessible SQL database, FTP and via gene- and variant- centred query-optimised data warehouse implemented using the BioMart data warehousing platform.  Users can additionally upload their own data for direct visualisation within the resource. Recently added data includes improved resources for the emerging reference genome for bread wheat and two of its progenitor genomes, as well as the genomes of Medicago truncatula and updates to the genome sequences of rice and maize, and numerous alignment and comparative data sets.  A major new development is the launch of a new data submission interface for variant data, and an associated resource to archive, accession and propagate variant loci to subsequent versions of the underlying reference sequence, allowing for the automatic integration and update of earlier submissions. Ensembl Plants is developed in close collaboration with the Gramene database, and with the transPLANT consortium, and we are jointly working to develop a consistent set of reference data for plants.