Brassica Information Portal and Elixir Excelerate
Carlos Horro, John M. Hancock, Wiktor Jurkowski, Annamarie Eckes · 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. By linking standardised trait data with genotypic and phenotypic information, it will in the near future offer tools to perform on-the-fly phenotype-genotype association analysis. In collaboration with the UK Brassica research community, we have built a tool that aims to assist global research on Brassica crops: Users can store and publish their own study results in the Portal thanks to advanced data submission capabilities. Similarly, user-friendly interfaces and programmatic download mechanisms further facilitate work with the data. This makes the database content readily comparable and cross-linkable to that of other tools and resources for further downstream analysis. In the WP7 package, the Earlham Institute with the BIP represents UK and along with six more ELIXIR nodes (EMBL-EBI, Belgium, France, Finland, Netherlands, Portugal and Switzerland). 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, a new minimum controlled vocabulary for plant phenotyping based on MIAPPE v1 has been constructed and agreed on among all participants. As a WP7 collaborator, we provide Brassica trial example data in this new format. Ultimately, this exercise will create an updated version of MIAPPE, with many real world example datasets from different crop species such as maize, pine and potato, and will allow dataset compatibility across all ELIXIR nodes. 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, which is currently used by more than 20 key bioinformatics institutions around the world. ( http://brapi.org/members.html ). Implementation of this infrastructure by all nodes, including distributed computational resources at node level, a centralised API entry point, automatic data validation and a unified search interface is currently under development.