The transPLANT Variation Data Management System

transPLANT (Trans-national Infrastructure for Plant Genomic Science; http://www.transplantdb.eu) is a European consortium of 11 partners from 6 countries addressing critical issues in the management and analysis of data from plant genomes.  As part of this effort, we have implemented a new, reference-based system for the storage, update and visualisation of genomic variation data. The system will accept submissions (describing single nucleotide polymorphisms and small insertions/deletions) in Variant Call Format (VCF) files; merge multiple submissions on a single reference; and critically, migrate variant calls from one version of a reference sequence to another, using the ATAC tool to locate portions of one version of an assembly in the context of another, ensuring that annotations made on one version of a genome can be propagated through to subsequent versions.  The infrastructure uses a noSQL backend for operational storage, utilises existing infrastructure developed at EBI for long-term data archiving, and can return submitted or modified data to users in VCF files. The goal is to rapidly assign unique, persistent identifiers to variation features and record the instances of their occurrence in an integrated, searchable resource.  The pipeline is now in beta testing and will be progressively exposed to a larger user community during 2013.

Ensembl Plants (http://plants.ensembl.org) is one platform that can be used for visualising and analysing data about polymorphisms. A web portal provides a number of interactive interfaces (e.g. gene-centric, SNP-centric, individual-centric, population-centric) while a query-optimised data mining tool allows users to filter and download specificed subportions of complete data sets.  Variation data for six species is available in Ensembl Plants, and coverage is expected to increase with the implementation of the new data management back end. Ensembl Plants is one of a number of European resources whose development will be aligned, and whose interoperability will be increased, through the activities of transPLANT; while activities between Europe and the United States are coordinated through a close collaboration with Gramene (http://www.gramene.org).