Brassica Information Portal and Elixir: MIAPPE & BrAPI
Carlos Horro, John M. Hancock, Wiktor Jurkowski, Annemarie Hildegard Eckes-Shephard · 2017
Brassica Information Portal (BIP) provides an open access web repository for Brassica phenotyping data (https://bip.earlham.ac.uk). It aims to fill the gap between physical genome information and quantitative phenotypic information. Earlham Institute with the BIP represents UK in Elixir EXCELERATE WP7, working along with six more ELIXIR nodes. Together, we are establishing a common infrastructure and an open model for the publication and sharing of plant genotype-phenotype data, addressed on several fronts. For example, the controlled vocabulary Minimum Information About Plant Phenotyping Experiments (MIAPPE) is updated and agreed among all participants. As a WP7 collaborator, we provide Brassica trial example data in this new format. Ultimately, we will create an updated version of MIAPPE which will allow dataset compatibility across all species and ELIXIR nodes. Further, in order to make data easily accessible and interoperable, all partners are also defining a new common API, initially based on BrAPI (Breeding API) v1. BIP and all other nodes are implementing a subset of BrAPI v1 and working on its next version, enabling its alignment to MIAPPE, which will be fully adopted by all WP7 members. Phenotypic traits measured in Brassica field trials are very heterogeneous in terms of data types, units and detailedness of experimental protocols. The development of a Brassica-specific ontology BRATO was necessary to overcome these issues. Using the Crop Ontology model, we collaborate with INRA and Southern Cross University to describe traits with this standard. Harmonised Brassica trait data will enable comparison valuable for scientists and breeders alike.