Wheat3BMine, a Data Warehouse Dedicated to Wheat Chromosome 3B

URGI (INRA research unit in genomics and bioinformatics dedicated to plants and crop parasites) develops a multi-species integrative information system: GnpIS (https://urgi.versailles.inra.fr/gnpis/, Steinbach et al. 2013 doi: 10.1093/database/bat058) which manages plants data from genomics to genetics and phenomics.

To bridge these data, we developed Wheat3BMine in the frame of the transPLANT (trans-National Infrastructure for Plant Genomic Science; FP7) and 3BSEQ (aiming at sequencing wheat chromosome 3B) projects.

Wheat3BMine is a data warehouse dedicated to wheat 3B chromosome. It is developed using InterMine technology, providing a fast, flexible and user friendly access to integrated data by multiple ways: a browser, a query builder and a region search tool. Wheat3BMine users can filter their favorite features, save their own queries, and export results under many formats (GFF3, BED or XML). An online documentation and pre-computed queries are also available.

Our data warehouse contains heterogeneous data and is gene-centered. In fact, our typical gene card centralizes relevant information like function, ontology terms and overlapping features. Wheat3BMine provides access to genomic annotation data (genes, mRNA, polypeptides, transposable elements), polymorphisms data (markers), genetic mapping data (QTL, metaQTL) and phenotyping data. Indeed, useful links are available from a card toward wheat 3B genome browser (https://urgi.versailles.inra.fr/gb2/gbrowse/wheat_annot_3B/, Choulet et al. 2014 doi: 10.1126/science.1249721) or toward additional details in GnpIS.

Wheat3BMine is available at: http://urgi.versailles.inra.fr/Wheat3BMine/.